cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.vk7qwd
title: Occurrence Download

description: A dataset containing 2461 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glycaspis brimblecombei",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Specimen, Material sample, Occurrence evidence)"
 ]
}

 The dataset includes 2461 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002337-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dbrv15dxz
title: Determinate growth is predominant and likely ancestral in squamate reptiles

description: Body growth is typically thought to be indeterminate in ectothermic
 vertebrates. Indeed, until recently, this growth pattern was considered to
 be ubiquitous in ectotherms. Our recent observations of a complete growth
 plate cartilage (GPC) resorption, a reliable indicator of arrested
 skeletal growth, in many species of lizards clearly reject the ubiquity of
 indeterminate growth in reptiles and raise the question about the
 ancestral state of the growth pattern. Using X-ray micro-computed
 tomography (µCT), here we examined GPCs of long bones in three basally
 branching clades of squamate reptiles, namely in Gekkota, Scincoidea, and
 Lacertoidea. A complete loss of GPC, indicating skeletal growth arrest,
 was the predominant finding. Using a dataset of 164 species representing
 all major clades of lizards and the tuataras, we traced the evolution of
 determinate growth on the phylogenetic tree of Lepidosauria. The
 reconstruction of character states suggests that determinate growth is
 ancestral for the squamate reptiles (Squamata) and remains common in the
 majority of lizard lineages, while extended (potentially indeterminate)
 adult growth evolved several times within squamates. Although
 traditionally associated with endotherms, determinate growth is coupled
 with ectothermy in this lineage. These findings combined with existing
 literature suggest that determinate growth predominates in both extant and
 extinct amniotes.
description: We analyzed 194 femoral bones from lizards belonging to three
 clades of Squamata (Gekkota, Scincoidea, and Lacertoidea). We analyzed the
 growth plate cartilage (GPC) in the proximal part of the femur. We
 employed X-ray micro-computed tomography (µCT) and micro-radiography
 (µRTG) for vizualization of GPC. We scored the GPC state in a binary
 fashion, as either present (1) or absent (0). Ancestral state
 reconstruction was performed in R using the Hidden State Speciation and
 Extinction (HiSSE) model implemented in the R package hisse. Additionally,
 we performed the ancestral states reconstruction using maximum parsimony,
 as implemented in the R package castor. The reconstructed states were
 plotted using the R package phytools.
DOI: 10.5061/dryad.tmpg4f4w0
title: Code and data of MS "Null models for animal social network analysis and data collected via focal sampling: pre-network or node network permutation?"

description: In social networks analysis, two different approaches have predominated in
 creating null models for hypothesis testing, namely pre-network and node
 network permutation approaches. Although the pre-network permutation
 approach appears more advantageous, its use has mainly been restricted to
 data on associations and sampling methods such as ‘group follows.’ The
 pre-network permutation approach has recently been adapted to data on
 interactions and the focal sampling method, but its performance in
 different scenarios has not been thoroughly explored. Here, we assessed
 the performance of the pre- and node network permutation approach in
 several simulated scenarios based on proneness to false positive or false
 negatives and with or without observation bias. Our results showed that
 the pre-network permutation was sensitive to false positives in scenarios
 with or without observation bias. The node network permutation approach
 produced fewer false positives and negatives than the pre-network
 approach, but only in scenarios without observation bias. In scenarios
 with observation bias, the node network permutation approach was
 outperformed by pre-network permutation.  Caution should be taken
 when using the pre- and node network permutations to create null models
 with data collected via focal sampling. This study provides future
 methodological research perspectives for social network analyses.
description: This is the code used to generate the simulated data, make the
 data analysis, and create the figures of the MS: "Null models for
 animal social network analysis and data collected via focal sampling: pre-
 or network permutation?"
description: All files are written in R statiscial software.
DOI: 10.15468/dl.yg8w2f
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (K-M000202917, K-M000951755)"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002338-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6m905qfx1
title: Circulating myeloid-derived suppressor cells facilitate invasion of thyroid cancer cells by repressing miR-486-3p

description: Background: Myeloid-derived suppressor cells (MDSCs) have become
 increasingly recognized as facilitators of tumor development.
 However, the role of MDSCs in papillary thyroid carcinoma (PTC)
 progression has not been clearly explored. Objective: We aimed to evaluate
 the levels and function of circulating MDSCs in PTC. Methods: The
 proportion of circulating polymorphonuclear (PMN)-MDSCs and
 mononuclearMDSCs from patients with PTC or benign thyroid nodules and
 healthy controls was measured using flow cytometry. For
 immunosuppressive activity analysis, sorted circulating MDSCs
 were cocultured with CD3/CD28-costimulated T lymphocytes and the
 proliferation of T cells was determined. PTC cell lines (TPC-1
 and BC-PAP) were cocultured with PMN-MDSCs, and the effects on
 cell migration, invasion, proliferation, and apoptosis were evaluated. The
 differential expressed microribonucleic acids (RNAs) and
 messenger RNAs and their function were also explored in TPC-1
 cells cocultured with or without PMN-MDSCs. Results: PMN-MDSCs were
 increased in peripheral blood mononuclear cells of patients
 with PTC. Circulating PMN-MDSCs displayed strong T cell
 suppressive activity. PTC cells demonstrated enhanced invasive
 capabilities in vitro and in vivo when cocultured with sorted
 PMN-MDSCs. PMN-MDSCs decreased expression of miR-486-3p and
 activated nuclear factor kappa B2 (NF-κB2), a direct target of miR-486-3p.
 Rescue of miR-486-3p diminished the cell migration and invasion
 induced by PMN-MDSCs. Conclusion: Collectively, our work indicates that
 circulating PMN-MDSCs promote PTC progression. By suppressing
 miR-486-3p, PMN-MDSCs promote the activity of the
 NF-κB2 signaling pathway, resulting in accelerated invasion of
 PTC cells, which may provide new therapeutic strategies for
 treatment of thyroid cancer.
DOI: 10.5061/dryad.vhhmgqnqq
title: Evolution of moult-migration is directly linked to aridity of the breeding grounds in North American passerines

description: To avoid energy allocation conflicts, birds generally separate breeding,
 migration and moult during the annual cycle. North American passerines
 typically moult on the breeding grounds prior to autumn migration.
 However, some have evolved a moult-migration strategy in which they delay
 moult until stopping over during autumn migration. Rohwer et al . (2005)
 proposed the ‘push–pull hypothesis' as an explanation for the
 evolution of this moult strategy, but it has not been empirically tested.
 Poor conditions on the breeding grounds at the end of the summer would
 push birds to depart prior to moult, while productive stopover locations
 would pull them. We tested for a relationship between moult-migration and
 breeding grounds aridity as measured by the normalized difference
 vegetation index. Our results strongly support the ‘push' aspect of
 the push–pull hypothesis and indicate that arid breeding grounds,
 primarily in western North America, would drive species to evolve stopover
 moult-migration, although this relationship may depend upon migration
 distance.
DOI: 10.5061/dryad.mkkwh70wh
title: Data for: Are feeding modes concealing morphofunctional diversity? The case of the New World Parrotfishes

description: In functional ecology, morphology is expected to reflect function,
 however, occasional decoupling of these two can be found. We did not find
 a relationship between feeding functional morphology and feeding modes of
 the American parrotfishes of the
 genera Scarus and Sparisoma. We
 explore some possible morpho-functional reasons for this phenomenon and
 reconsider the functional diversity within the scrapers. A phylogenetic
 tree including 50 species of parrotfishes, based on 12 genes, was
 reconstructed over which all analyses were performed. We found that
 although all Scarus species feed only by scraping, they
 are morpho-functionally more diverse compared
 to Sparisoma species, which have three different feeding
 modes (scraping, browsing and excavating) but appear to be
 morpho-functionally constrained. We quantified and compared the
 morpho-functional diversity within each genus using the disparity of the
 oral jaw feeding mechanics. An ecological convergence on scraping between
 all Scarus species and Sparisoma
 aurofrenatum was found. This result was supported by the
 ancestral feeding mode reconstruction and the absence of morpho-functional
 similarities between Scarus species
 and Sparisoma aurofrenatum. It is possible that different
 selective pressures or ecological conditions have shaped the differences
 both in the feeding ecology and the feeding morphology of these two
 genera. It is probable that key novel structures and
 muscular properties found in the jaw of Scarus species
 played an essential role in the morpho-functional diversification of this
 genus. Finally, there is the possibility that proposed
 feeding modes do not fully capture the complexity of their feeding
 ecology.
description: These files contain morphological quotients (values
 phylogenetical regressed against head length) of parrotfishes feeding
 traits. Raw morphological traits were obtained from photographs of the
 head of 15 species of parrotfishes of the New World. We also attached a
 file with all the corresponding feeding modes, maximum total length, and
 the phylogenetic tree we built to make all the analyses. Additionally, we
 have attached some R scripts we used to calculate the phylogenetical PCA
 and to calculate the morphological disparity.
DOI: 10.15468/dl.yzdvje
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Robsonella campbelli",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002339-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j09885dg
title: Data from: FSHB transcription is regulated by a novel 5’ distal enhancer containing a fertility-associated single nucleotide polymorphism

description: The pituitary gonadotropins, follicle-stimulating hormone (FSH) and
 luteinizing hormone, signal the gonads to regulate male and female
 fertility. FSH is critical for female fertility as it regulates oocyte
 maturation, ovulation, and hormone synthesis. Multiple genome-wide
 association studies (GWAS) link a 130 Kb locus at 11p14.1, which
 encompasses the FSH beta-subunit (FSHB) gene, with fertility-related
 traits including polycystic ovary syndrome, age of natural menopause, and
 dizygotic twinning. The most statistically significant single-nucleotide
 polymorphism from several GWAS studies (rs11031006) resides within a
 highly conserved 450 bp region 26 Kb upstream of the human FSHB gene.
 Given that sequence conservation suggests an important biological
 function, we hypothesized that the region could regulate FSHB
 transcription. In luciferase assays, the conserved region enhanced FSHB
 transcription and gel shifts identified a binding site for Steroidogenic
 factor 1 (SF1) contributing to its function. Analysis of mouse pituitary
 single-cell ATAC-seq demonstrated open chromatin at the conserved region
 exclusive to a gonadotrope cell-type cluster. Additionally,
 enhancer-associated histone markers were identified by immunoprecipitation
 of chromatin from mouse whole pituitary and an immortalized mouse
 gonadotrope-derived LβT2 cell line at the conserved region. Furthermore,
 we found that the rs11031006 minor allele upregulated FSHB transcription
 via increased SF1 binding to the enhancer. All together, these results
 identify a novel upstream regulator of FSHB transcription and indicate
 that rs11031006 can modulate FSH levels.
description: <strong>Supplementary Figure S1:</strong> Chromatin
 accessibility from scATAC-seq with individual pituitary cell populations
 shown separately (grouped as “Other” in Fig. 2).
 <strong>Supplementary Figure S2:</strong> scATAC-seq
 from a second pituitary, replication of Figure 2. scATAC-seq was used on
 adult male pituitary to evaluate chromatin accessibility to transposase
 digestion. (A) t-SNE analysis identified a cluster of gonadotopes (purple)
 marked by (B) chromatin accessibility at <em>Lhb</em>,
 <em>Gnrhr</em>, and (C) <em>Fshb</em>.
 <em>Fshb</em> enhancer chromatin was open in gonadotropes
 (boxed in blue) but not other pituitary cell-types (“other”, depicted in
 gray).
DOI: 10.5061/dryad.z34tmpg9c
title: Data from: Altitude difference might contribute to the genetic divergence of giant panda' staple food Bamboo (Fargesia spathacea complex) based on 14 SSR markers

description: The taxonomy in woody bamboo faces a lot of difficulties due to its long
 blooming intervals and complicated morphological variation. Whether the
 current taxonomy would reflect the genuine species divergence within woody
 bamboo is an intriguing question. Fargesia spathacea complex comprises
 fifteen closely related species with sympatric distribution in China.
 Their classification has long been controversy because of only a handful
 of vegetative traits available, thus providing a good opportunity to
 explore the evolutionary relationship and genetic differentiation in woody
 bamboo. Here we presented a study with 750 individuals from 39
 representative populations in Fargesia spathacea complex using 14 SSR
 markers. We found varying degrees of genetic diversity across populations
 of the Fargesia spathacea complex (He=0.07-0.81) and largely negative F
 values at the population level, implying an excess of heterozygotes in the
 populations. Phylogenetic analyses revealed that all populations were
 divided into two major groups (cluster A and B), with the majority of
 fifteen species representing distinct genetic lineages. Based on the
 population genetic analysis along with morphological evidence, we
 confirmed the identity of three species (F. decurvata, F. spathacea and F.
 murielae) and suggested invalidation of four other species (scabrida, F.
 robusta, F. denudata and F. nitida). The delimitation of the rest eight
 species was yet to be explored. The ecological factor and spatial
 autocorrelation analysis supported that altitude difference might account
 for the distinct genetic divergence between two major groups.
description: SSR genotyping 
description: Population genetic structure of giant panda’ staple food Bamboo
 (Fargesia spathacea complex) and its taxonomic implications 
 You can download to analyze any necessary population genetics
 parameters with these data
DOI: 10.5061/dryad.5mkkwh72q
title: Data associated with 'Metformin rescues Parkinson’s disease phenotypes caused by hyperactive mitochondria'

description: Metabolic dysfunction occurs in many age-related neurodegenerative
 diseases, yet its role in disease etiology remains poorly understood. We
 recently discovered a potential causal link between the branched-chain
 amino acid transferase, BCAT-1, and the
 neurodegenerative movement disorder, Parkinson’s disease (PD).
 RNAi-mediated knockdown of C. elegans
 bcat-1 recapitulates PD-like features, including progressive
 motor deficits and neurodegeneration with age, yet the underlying
 mechanisms have remained unknown. Using transcriptomic, metabolomic, and
 imaging approaches, we show here that bcat-1 knockdown
 increases mitochondrial respiration and induces oxidative damage in
 neurons through mTOR-independent mechanisms. Increased mitochondrial
 respiration, or ‘mitochondrial hyperactivity,’ is required
 for bcat-1(RNAi) neurotoxicity. Moreover, we show that
 post-disease onset administration of the type 2 diabetes medication,
 metformin, reduces mitochondrial respiration to control levels and
 significantly improves both motor function and neuronal viability.
 Together, our findings suggest that mitochondrial hyperactivity may be an
 early event in PD pathogenesis, and strategies aimed at reducing
 mitochondrial respiration may constitute a surprising new avenue for PD
 treatment.
description: High-resolution metabolomics data was generated using samples
 collected per the methods described in the manuscript. Files generated
 from the Thermo orbitrap instrument were extracted using the apLCMS and
 xMSanalyzer R packages. A feature was retained in the feature table if its
 intensity was 1.5 times that of the intensity in the associated bacterial
 blank sample and was present in at least 9 of the samples. Null (intensity
 = 0) values were replaced with the half the value of the minimum intensity
 of that feature.
description: The feature table has been filtered using bacterial blank samples
 and null values of intensity have been imputed.
DOI: 10.5061/dryad.kwh70rz1c
title: Immigration of Sogatella furcifera from the Greater Mekong Subregion into northern China revealed by 2b-RAD sequencing

description: Background The white-backed planthopper (WBPH), Sogatella furcifera
 (Horváth) (Hemiptera, Delphacidae), is a migratory pest of rice in Asia.
 Shandong Province, in northern China, is located on the migration pathway
 of WBPH between southern and northeast China. The potential sources of
 WBPH in northern China are poorly understood. We studied the sources of
 WBPH in Shandong Province by determining the population genetic structure
 of WBPH in 18 sites distributed in Shandong and in six regions of the
 Greater Mekong Subregion (GMS). We used mitochondrial gene and
 single-nucleotide polymorphism (SNP) markers (2b-RAD sequencing) for
 analysis. Results All of the WBPH populations studied in the seven regions
 had low genetic diversity. Pairwise F ST values ranged from -0.061 to
 0.285, while F ST based on SNP data ranged from -0.007 to 0.009. These two
 molecular markers revealed that 4.40% (mtDNA) and 0.19% (SNP) genetic
 variation could be explained by the interpopulation variation, while the
 rest came from intrapopulation variation. The populations in the seven
 geographic regions comprised four hypothetical genetic clusters (K = 4)
 not associated with geographic location. Eighty-four of 129 individuals
 distributed across the given area were designated as recent migrants or of
 admixed ancestry. Although the substantial migration presented, a weak but
 significant correlation between genetic and geographic distances was found
 (r = 0.083, P = 0.004). Conclusion GMS was the main source of WBPH in
 Shandong, while other source populations may also exist. The genetic
 structure of WBPH is shaped by both migration and geographic barriers.
 These results help clarify the migration route and the source of WBPH in
 northern China.
description: Sogatella furcifera individuals were sampled in various
 geographic regions (China and Southeast Asia). These comprised six sites
 in Yunnan Province; four sites in Shandong Province; two sites in Laos,
 Cambodia, and Vietnam, respectively; and one site in Myanmar and Thailand,
 respectively. Samples were put in 95% ethanol and stored at -20°C until
 DNA extraction. Insect DNA was extracted using the TIAMamp Micro DNA Kit
 (Tiangen, Beijing, China) according to the manufacturer protocol. The
 2b-RAD sequencing and genotyping were outsourced to Shanghai OE Biotech
 Ltd. (Shanghai, China). The genotype data contained information for each
 locus and each individual were obtained as vcf file.
DOI: 10.5061/dryad.1ns1rn8qw
title: Environmental correlates of reptile variation on the Houtman Abrolhos archipelago, eastern Indian Ocean

description: Aim: To examine the relationships between island environmental attributes,
 both biotic and abiotic, and three measures of reptilian variation –
 species assemblage, species richness, and body size distributions.
 Location: Houtman Abrolhos archipelago, Western Australia. Taxon:
 Reptiles. Methods: Nineteen islands were sampled from 2002 - 2012 using
 foraging and trapping. Body size (snout-vent length) was measured on first
 capture. Island size varied from 0.3 - 587 ha, encompassing the three
 geomorphic island types, the three bathymetric groups, and a range of
 other environmental attributes. Results: From about 1500 captures, 24
 reptile species were recorded, including three previously undocumented on
 the archipelago, and 55 records of species not previously recorded on
 specific islands. Four significantly different reptile assemblage groups
 were identified. These were highly correlated with geomorphological
 composition - two groups encompassing the three large aeolianite islands;
 another the high rock islands and the largest composite island; and a
 fourth consisting of the remaining composite islands with one very small
 high rock island. Both assemblage and richness on islands were
 significantly correlated with island area, geomorphology and native plant
 species richness. Of the 13 species captured frequently, eleven showed
 statistically significant inter-island variation in body size, and two
 exhibited sexual dimorphism. In three species, size was also correlated
 with environmental attributes, including reptile species richness, native
 plant richness, geomorphology and island area. Six of the eleven species
 captured on the two largest islands (both aeolianite) differed in size on
 these adjacent islands. Main Conclusions: High inter-island variation in
 body size and assemblage composition suggest strong differential selection
 since the most recent isolation event at 6,500 bp. Anthropogenic
 disturbances over the last 150 years have resulted in several island
 extinctions. Species assemblage and richness are strongly associated with
 environmental attributes. Inter-island body size variation in three
 species revealed idiosyncratic responses to environmental pressures.
 Results provide guidance for effective conservation and management
 strategies, and evidence for the extinction debts inherent in more
 recently fragmented mainland habitats.
DOI: 10.5061/dryad.pzgmsbch4
title: Data from: Can multi-species shark longline fisheries be managed sustainably using size limits? Theoretically, yes. Realistically, No.

description: This is the raw data used in : Smart J, White W, Baje
 L, Chin A, D’Alberto B, Grant M, Mukherji S
 and Simpfendorfer C (2020) Can multi-species shark
 longline fisheries be managed sustainably using size limits?
 Theoretically, yes. Realistically, No. Journal of Applied Ecology Included
 are two R scripts which create data inputs and then perform the articles
 analsysis.