cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z8w9ghxj1
title: Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity

description: Hypoplastic left heart syndrome (HLHS) is a severe congenital heart
 disease (CHD) with a likely oligogenic etiology, but our understanding of
 the genetic complexities and pathogenic mechanisms leading to HLHS is
 limited. We therefore performed whole genome sequencing (WGS) on a large
 cohort of HLHS patients and their families to identify candidate genes
 that were then tested in Drosophila heart model for functional and
 structural requirements. Bioinformatic analysis of WGS data from an index
 family comprised of a HLHS proband born to consanguineous parents and
 postulated to have a homozygous recessive disease etiology, prioritized 9
 candidate genes with rare, predicted damaging homozygous variants. Of the
 candidate HLHS gene homologs tested, cardiac-specific knockdown (KD) of
 mitochondrial MICOS complex subunit dCHCHD3/6 resulted in drastically
 compromised heart contractility, diminished levels of sarcomeric actin and
 myosin, reduced cardiac ATP levels, and mitochondrial fission-fusion
 defects. Interestingly, these heart defects were similar to those
 inflicted by cardiac KD of ATP synthase subunits of the electron transport
 chain (ETC), consistent with the MICOS complex’s role in maintaining
 cristae morphology and ETC complex assembly. Analysis of 183 genomes of
 HLHS patient-parent trios revealed five additional HLHS probands with
 rare, predicted damaging variants in CHCHD3 or CHCHD6. Hypothesizing an
 oligogenic basis for HLHS, we tested 60 additional prioritized candidate
 genes in these cases for genetic interactions with CHCHD3/6 in sensitized
 fly hearts. Moderate KD of CHCHD3/6 in combination with Cdk12 (activator
 of RNA polymerase II), RNF149 (E3 ubiquitin ligase), or SPTBN1
 (scaffolding protein) caused synergistic heart defects, suggesting the
 potential involvement of a diverse set of pathways in HLHS. Further
 elucidation of novel candidate genes and genetic interactions of
 potentially-disease-contributing pathways is expected to lead to a better
 understanding of HLHS and other CHDs.
description: Please see the README document ("README_MICOS.txt") and
 the accompanying published article: Katja Birker, Shuchao Ge, Natalie J.
 Kirkland, Jeanne L. Theis, James Marchant, Zachary C. Fogarty, Maria
 Azzurra Missinato, Sreehari Kalvakuri, Paul Grossfeld, Adam J. Engler,
 Karen Ocorr, Timothy J. Nelson, Alexandre R. Colas, Timothy M. Olson,
 Georg Vogler, and Rolf Bodmer. Mitochondrial MICOS complex genes,
 implicated in hypoplastic left heart syndrome, maintain cardiac
 contractility and actomyosin integrity 2022. DOI:
 https://doi.org/10.1101/2022.06.13.22276366
DOI: 10.5061/dryad.05qfttf82
title: Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata

description: Wild wheat relatives have been explored in plant breeding to increase the
 genetic diversity of bread wheat, one of the most important food crops.
 Aegilops umbellulata is a diploid U genome-containing grass species that
 serves as a genetic reservoir for wheat improvement. In this study, we
 report the construction of a chromosome-scale reference assembly of Ae.
 umbellulata accession TA1851 based on corrected PacBio HiFi reads and
 chromosome conformation capture. The total assembly size was 4.25 Gb with
 a contig N50 of 17.7 Mb. In total, 36,268 gene models were predicted. We
 benchmarked the performance of hifiasm and LJA, two of the most widely
 used assemblers using standard and corrected HiFi reads, revealing a
 positive effect of corrected input reads. Comparative genome analysis
 confirmed substantial chromosome rearrangements in Ae. umbellulata
 compared to bread wheat. In summary, the Ae. umbellulata assembly provides
 a resource for comparative genomics in Triticeae and for the discovery of
 agriculturally important genes.
DOI: 10.5061/dryad.rv15dv4d3
title: Data from: Dietary restriction fails to extend life in stressful environments

description: Moderate dietary restriction often prolongs life in laboratory animals,
 and this response has been interpreted as an adaptive strategy that
 promotes survival during famine. However, dietary restriction can also
 increase frailty, and it therefore remains unclear whether restricted
 diets prolong life under stressful conditions like those experienced by
 wild animals.  We manipulated adult dietary protein
 of Drosophila melanogaster across a gradient of ambient
 temperature and examined effects on survival. To test for trade-offs, we
 also quantified the reproduction, and performance of F1, F2 and F3
 descendants. We found that protein restriction increased longevity of one
 or both sexes at benign ambient temperatures (25°C, 27°C) but failed to
 extend longevity of flies maintained in cold (21°C, 23°C) or hot (29°C)
 conditions. Instead, in females, protein restriction resulted in strongly
 elevated mortality at cold temperatures. Protein restriction also
 generally reduced reproductive performance and did not consistently
 enhance performance of F1, F2 or F3 descendants.  Taken together,
 our results challenge the long-held idea that extended longevity of
 diet-restricted laboratory animals represents an adaptive survival
 strategy in natural populations. Our findings suggest instead that this
 response is an artefact of benign laboratory conditions, and that
 DR-induced life extension might not be achieved in the more stressful
 conditions experienced in the wild.
DOI: 10.5061/dryad.vdncjsz0r
title: Data from: Transcriptomic signatures associated with underlying rapid changes in the early phase brain of bi-directional sex change in Trimma okinawae

description: Teleost fish exhibit remarkable sexual plasticity and divergent
 developmental systems, including hermaphroditism. One of the more
 fascinating models of sexual plasticity is socially controlled sex change,
 which is often observed in coral reef fish. The Okinawa rubble goby,
 Trimma okinawae, is a bi-directional sex-changing fish. It can rapidly
 change sex in either direction based on social circumstances. Although
 behavioral and neuroendocrine sex change occurs immediately and is
 believed to trigger gonadal changes, the underlying mechanisms remain
 poorly understood. In this study, we conducted a de novo transcriptome
 analysis of the T. okinawae brain and identified genes that are
 differentially expressed between the sexes and genes that were immediately
 controlled by social stimulation implicating sex change. Several genes
 showed concordant expression shifts regardless of the sex change direction
 and were associated with histone modification in nerve cells. These genes
 are known to function in the neuroendocrine control of reproduction in
 nerve cells. Overall, we identified genes associated with the initiation
 of sex change, which provides insight into the regulation of sex change
 and sexual plasticity.
description: # Transcriptome analysis of the Trimma okinawae brain We conducted a de
 novo transcriptome analysis of the T. okinawae brain to detect the genes
 immediately controlled by social stimulation causing a sex change.
 Subsequently, protein-coding sequences were detected with TransDecoder
 using default parameters and remove the redundancy using CD-hit. We used
 RSEM with bowtie2 as a mapping program to calculate the mRNA abundance of
 the individual samples. Also, those contigs coding proteins were annotated
 by EggNoG2. ## Description of the data and file structure
 Trinity_v265_L20T20S420A20M100.Trinity.fasta: The fasta file resulted from
 de-novo assembly using Trinity.
 Trinity_v265_L20T20S420A20M100_onlyPepetide.fasta: The fasta file of
 putative protein-coding contigs filtered using TransDecoder and CD-hit.
 EggNog_All_Anno.tsv: The annotation file of each protein coded in contigs
 using EggNOG2 mapper. The cells of "-" in this file represent no
 data. RSEM.genes.results_Count_merge: The count table of gene expression
 of each sample calculated by RSEM. RSEM.genes.results_TPM_merge: The TPM
 table of gene expression of each sample calculated by RSEM.
 Expressoin_analysis_summary.R: Summary of R code for expression analysis.
 The version of packages are below: library(tidyverse) # v1.1.1 library(fs)
 # v1.6.2 library(devtools) # v2.4.5 library(ggbiplot) # v0.55
 library(DESeq2) # v1.36.0 library(ggVennDiagram) # v1.2.2
 library(pheatmap) # v1.0.12 library(ggrepel) # v0.9.3 library(pheatmap) #
 1.0.12 library(RColorBrewer) # v1.1-3 library(viridis) # v0.6.3
 library(ggbiplot) # v0.55 library(VennDiagram) # v1.7.3
 library(geneLenDataBase) # v1.32.0 library(goseq) # v1.48.0 library(GO.db)
 # v3.15.0
DOI: 10.5061/dryad.x95x69pqg
title: Data from: Quantifying the gastral mass in Early Cretaceous ornithuromorphs (Aves: Ornithothoraces) from the Jehol avifauna

description: Some birds intentionally ingest stones to facilitate digestion of hard
 foodstuffs, a behavior inherited from non-avian dinosaurs and present in
 some of the earliest birds, as evidenced from clusters of gastroliths
 preserved within the abdominal cavity of a wide range of dinosaurs and
 Cretaceous birds. For the first time, high-resolution computed
 laminographic and computed tomographic scans were used to reconstruct the
 gastral mass in two species of non-neornithine ornithuromorph birds from
 the Lower Cretaceous Jehol Group. Four specimens of each taxon were
 analyzed. Preservation of the gastral mass in most of these specimens is
 in situ and regarded as complete or nearly so. The number of gastroliths,
 their total volume, and their total mass relative to the estimated body
 mass were calculated for each specimen. The resultant gastral mass-to-body
 mass ratios fall within the range observed in extant birds, supporting
 previous inferences that the digestive system in non-neornithine
 ornithuromorphs was comparable to that in extant taxa. Compared to
 available data for non-volant non-avian theropods, the gastral mass is
 proportionately smaller in birds suggesting that the evolution of flight
 constrained gastral mass size in the theropod lineage. Currently,
 available data on gastral mass characteristics suggests that Iteravis ate
 larger food particles compared to Archaeorhynchus but cannot be utilized
 to determine diet more precisely. Better understanding of the relationship
 between gastral mass characteristics and food items across a broader range
 of extant taxa may provide an indirect but important method through which
 to infer diet and digestive function in archosaurs.
description: Eight ornithuromorph
 individuals were scanned by computed tomographic (CT) or computed
 laminographic (CL). After scanning, all data were processed and rendered
 using the software VG Studio 3.4. Lastly, all related parameters were
 extracted in VG Studio 3.4 and processed in Microsoft Excel. R was used to
 demonstrate that all data fell within the confidence
 interval. <br>
DOI: 10.6084/m9.figshare.31164997
title: Provenance

description: metadata
DOI: 10.6084/m9.figshare.31164997.v2
title: Provenance

description: metadata
DOI: 10.5061/dryad.fqz612jxr
title: Data from: Effect of valve opening on starting performance of pump as turbine

description: The study on transient characteristics of pump as turbines during atypical
 startup has not been deeply explored yet. In order to reveal the transient
 characteristics of a small centrifugal pump reversing as turbine during
 startup process in this paper, the transient hydraulic performance
 experiments are conducted for three steady rotational speed cases. Under
 the condition of each case, three, five, and three valve opening scenarios
 are completed to measure the performance. The dimensionless analysis are
 also employed so as to better reveal transient behavior of the pump as
 turbine during atypical startup. The results show that the rise rate of
 each performance parameter is different, wherein the shaft power and
 rotational speed have the fastest rising rate, followed by the flow rate,
 and the head rise is the slowest. It is clearly seen that the shock
 phenomenon in static pressure easily occurs at the outlet of pump as
 turbine. With the increase of valve opening, the dimensionless flow rate,
 head, and power coefficient all show the evolution trend of gradually
 increasing.
description: Experiments
DOI: 10.21223/p3/3vyy8c
title: Replication data for: Genetic Diversity Analysis of a large collection of sweetpotato wild relatives, Ipomoea spp.

description: 694 accessions of sweetpotato wild relatives species (Ipomoea spp.), together with 105 cultivated accessions have been genotyped using DArTseq genotyping technology.
DOI: 10.5061/dryad.4mw6m90g5
title: Landscape heterogeneity provides co-benefits to predator and prey

description: Predator populations are imperiled globally, due in part to changing
 habitat and trophic interactions. Theoretical and laboratory studies
 suggest that heterogeneous landscapes containing prey refuges acting as
 source habitats can benefit both predator and prey populations, although
 the importance of heterogeneity in natural systems is uncertain. Here, we
 tested the hypothesis that landscape heterogeneity mediates predator-prey
 interactions between the California spotted owl (Strix occidentalis
 occidentalis) – a mature forest species – and one of its principal prey,
 the dusky-footed woodrat (Neotoma fuscipes) – a younger forest species –
 to the benefit of both. We did so by combining estimates of woodrat
 density and survival from live-trapping and VHF tracking with direct
 observations of prey deliveries to dependent young by owls in both
 heterogeneous and homogeneous home ranges. Woodrat abundance was
 approximately 2.5x higher in owl home ranges (1,412 hectares) featuring
 greater heterogeneity in vegetation types (1,805.0 ± 50.2 SE) compared to
 those dominated by mature forest (727.3 ± 51.9 SE), in large part because
 of high densities in young forests appearing to act as sources promoting
 woodrat densities in nearby mature forests. Woodrat mortality rates were
 low across vegetation types and did not differ between heterogeneous and
 homogeneous home ranges, yet all observed predation by owls occurred
 within mature forests, suggesting young forests may act as woodrat
 refuges. Owls exhibited a type 1 functional response, consuming
 approximately 2.5x more woodrats in heterogeneous (31.1/month ± 5.2 SE)
 versus homogeneous (12.7/month ± 3.7 SE) home ranges. While consumption of
 smaller-bodied alternative prey partially compensated for lower woodrat
 consumption in homogeneous home ranges, owls nevertheless consumed 30%
 more biomass in heterogeneous home ranges – approximately equivalent to
 the energetic needs of producing one additional offspring. Thus, a mosaic
 of vegetation types including young forest patches increased woodrat
 abundance and availability that, in turn, provided energetic and
 potentially reproductive benefits to mature forest-associated spotted
 owls. More broadly, our findings provide strong empirical evidence that
 heterogeneous landscapes containing prey refuges can benefit both predator
 and prey populations. As anthropogenic activities continue to homogenize
 landscapes globally, promoting heterogeneous systems with prey refuges may
 benefit imperiled predators.
description: These datasets were collected in the central Sierra Nevada,
 California - from captures, VHF collaring, and video camera deployment.
 They have been processed in R and ArcGIS.
description: Microsoft Excel and R are needed to open these data files. For R,
 there are a number of packages utilized in the analysis, but these are all
 publicly available and noted within the R code itself.
DOI: 10.5061/dryad.1jwstqk0v
title: Forest conservation maximises açaí palm pollination services and yield in the Brazilian Amazon

description: Agricultural expansion is one of the main drivers of global pollinator
 loss. Paradoxically, this occurs while agriculture is becoming
 increasingly dependent on biotic pollination, raising concerns about food
 production. Integrated Crop Pollination (ICP), the use of both wild and
 managed pollinators in crop fields, can help conserve pollinator diversity
 while ensuring effective pollination services for growers. However, given
 the context-dependent nature of this approach, there is an urgent need to
 evaluate its application across different landscapes and crops. We apply
 the ICP approach to açaí palm (Euterpe oleracea Mart.) production in the
 eastern Brazilian Amazon to explore effects of a native stingless bee,
 Scaptotrigona aff. postica (Apidae: Meliponini), and landscape-level
 forest conservation on yield and socioeconomic outcomes for açaí fruit
 growers. We assessed flower visitor assemblages and fruit production on 18
 plantations across a landscape forest cover gradient, with bee colonies
 introduced on nine plantations. Field data were combined with information
 from semi-structured interviews of growers to estimate yield and profit
 per hectare under different pollinator management scenarios. Bee colonies
 and forest cover enhanced flower visitor abundance on palm inflorescences,
 but abundance increases attributed to managed bees were associated with
 shifts in flower visitor evenness and diversity (species richness), due to
 reduced visitation of wild bees near managed colonies. Fruit production on
 inflorescences was positively related to bee abundance and bee diversity.
 Consequently, overall pollination performance was lower in plantations
 with bee colonies. This was repeated at the hectare scale, where yield and
 profit were associated with surrounding forest cover and not bee colonies.
 Synthesis and applications. Managed bees can increase pollinator densities
 and fruit production, but the increased environmental and socioeconomic
 risks associated with this activity means açaí growers should prioritise
 forest conservation to safeguard pollination services and improve overall
 sustainability of açaí production in the eastern Brazilian Amazon.
description: Data was collected in 2019 from plantations of açaí palm in the
 Brazilian state of Pará. Field data include observations of flower
 visitors on palm inflorescences (10 min surveys), richness counts from
 active sampling of flower visitors, and palm fruit yield data at two
 distinct time points (initial fruit set and final harvest). All collected
 insects were identified by specialists (see acknowledgements in the main
 manuscript). Data were collated in spreadsheets with
 columns identifying characteristics and measured variables.  
description: Microsoft Excel, R statistical environment ver. 4.1.0, and R
 Studio.
DOI: 10.5061/dryad.5x69p8d8f
title: Beauty or function? The opposing effects of natural and sexual selection on cuticular hydrocarbons in male black field crickets

description: Although many theoretical models of male sexual trait evolution assume
 that sexual selection is countered by natural selection, direct empirical
 tests of this assumption are relatively uncommon. Cuticular hydrocarbons
 (CHCs) are known to play an important role in restricting evaporative
 water loss but also in sexual signalling in most terrestrial arthropods.
 Insects adjusting their CHC layer for optimal desiccation resistance is
 often thought to come at the expense of successful sexual attraction
 suggesting that natural and sexual selection are in opposition for this
 trait. In this study, we sampled the CHCs of male black field crickets
 (Teleogryllus commodus) using solid-phase microextraction and then either
 measured their evaporative water loss or mating success. We then used
 multivariate selection analysis to quantify the strength and form of
 natural and sexual selection targeting male CHCs. Both natural and sexual
 selection imposed significant linear and stabilizing selection on male
 CHCs, although for very different combinations. Natural selection largely
 favoured an increase in the total abundance of CHCs, especially those with
 a longer chain length. In contrast, mating success peaked at a lower total
 abundance of CHCs and declined as CHC abundance increased. However, mating
 success did improve with an increase in a number of specific CHC
 components that also increased evaporative water loss. Importantly, this
 resulted in the combination of male CHCs favoured by natural selection and
 sexual selection being strongly opposing. Our findings suggest that the
 balance between natural and sexual selection is likely to play an
 important role in the evolution of male CHCs in T. commodus and may help
 explain why CHCs are so divergent across populations and species.
description: To estimate sexual selection, we estimated the mating success of
 300 males using no-choice trials. This involved placing a randomly
 selected virgin with each male and recording whether he achieved a mating
 in a 20-minute period. To estimate natural selection, we measured the
 evaporative water loss of 300 males using a custom-built device that
 passed dry purified air over male crickets for a 2-hour period. The
 difference in the weight of the cricket before and after being placed in
 this apparatus was taken as the evaporative water loss. Prior to assessing
 mating success (for sexual selection) and evaporative water loss (for
 natural selection), we sampled the cuticular hydrocarbon (CHC) profile of
 each male using solid phase microextraction (SPME) fibers and ran these
 samples using gas-chromatography mass spectrometry (GCMS) to measure the
 CHCs using established protocols. Sexual and natural selection were
 estimated using the standard procedures of multivariate selection
 analysis.
description: Excel is required to open the data files.
DOI: 10.5061/dryad.bvq83bkfp
title: AutoCore: network-based definition of the core module of human autoimmunity and autoinflammation

description: Although research on rare autoimmune and autoinflammatory diseases has
 enabled definition of non-redundant regulators of homeostasis in human
 immunity, due to the single gene-single disease nature of many of these
 diseases, contributing factors were mostly unveiled in sequential and
 non-coordinated individual studies. Here, we used a network-based approach
 for integrating a set of 186 inborn errors of immunity with predominant
 autoimmunity/autoinflammation into a comprehensive map of human immune
 dysregulation which we termed “AutoCore”. The AutoCore is located
 centrally within the interactome of all protein-protein interactions,
 connecting and pinpointing multi-disease markers for a range of common,
 polygenic autoimmune/autoinflammatory diseases. The AutoCore can be
 subdivided into 19 endotypes that correspond to molecularly and
 phenotypically cohesive disease subgroups, providing a molecular
 mechanism-based disease classification and rationale towards systematic
 targeting for therapeutic purposes. Our study provides a proof-of-concept
 for using network-based methods to systematically investigate the
 molecular relationships between individual rare diseases and address a
 range of conceptual, diagnostic, and therapeutic challenges.