cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3bk3j9kpm
title: Data from: Individual life histories: Neither slow nor fast, just diverse

description: The slow-fast continuum is known to structure variation in life-history
 strategies across species. Within populations, it is also assumed to
 structure individual life histories, yet evidence of its existence remains
 unclear. We formally assessed the presence of a slow-fast continuum of
 life histories both within populations and across species using detailed
 individual-based data for 17 bird and mammal species with contrasting life
 histories. We estimated adult lifespan, age at first reproduction,
 breeding frequency and fecundity, and identified the main axes of
 variation using Principal Component Analyses. The slow-fast continuum was
 the main axis of life-history variation across species, but within
 populations individual variation did not follow the slow-fast continuum in
 any species. This suggests that individual life histories are neither slow
 nor fast, but rather follow an idiosyncratic pattern across species
 because of relative differences in the importance of processes such as
 stochasticity, density dependence, and variation in individual
 performance.
description: This dataset was collected through the long-term monitoring of
 individuals from 17 mammal and bird species. It comprises individual
 measurements of life-history traits (age at first reproduction, adult
 lifespan, breeding frequency and fecundity) as well as individual
 generation time.
description: The dataset in a Rdata file, which can be open in R.
DOI: 10.5061/dryad.w3r2280vw
title: Cuisine in transition? Organic residue analysis of domestic containers from 9th-14th century Sicily

description: From the 9th to 14th centuries AD, Sicily experienced a series of rapid
 and quite radical changes in political regime, but the impact of these
 regime changes on the lives of the people that experienced them remains
 largely elusive within the historical narrative. We use a multi-faceted
 lipid residue approach to give direct chemical evidence of the use of 248
 everyday domestic ceramic containers from Islamic and post-Islamic
 contexts in western Sicily to aid our understanding of daily habits
 throughout this period of political change. A range of commodities was
 successfully identified, including animal fats, vegetable products, fruit
 products, (potentially including wine), and plant resins. The study
 highlights the complexity of residues in Early Medieval Mediterranean
 society, as in many cases mixtures of commodities were observed,
 reflecting sequential cooking events and/or the complex mixtures
 reflective of medieval recipes. However, overall there were no clear
 changes in the composition of the residues following the imposition of
 Norman control over the island and through subsequent periods, despite
 some differences between urban centres and rural sites. Thus, lending to
 the idea that post-Islamic populations largely flourished and benefited
 from the agricultural systems, resources, and recipes left by their
 predecessors.
description: This data set is comprised of data files produced by Gas
 Chromatography-Mass Spectrometry (GC-MS) of lipids extracted using acid
 extraction method from pottery sherds from
 9<sup>th</sup>-14<sup>th</sup> century contexts in
 Sicily.  These data are linked to the published journal
 where methods of extraction, the context of pottery and the interpretation
 of data are fully described.  Each file corresponds to
 the sample name as recorded in S1 data and contains a usable cdf. file.
 The acquisition method for all files is given in TEXT format.
DOI: 10.6084/m9.figshare.28688033
title: Schema-driven

description: This dataset contains the raw NCBI/GenBank records retrieved in January 2024 using a lung-associated 16S rRNA marker-gene query strategy for selected bacterial groups relevant to the pulmonary environment. The files are provided as downloaded from the public repository, without modification.<br>
DOI: 10.6084/m9.figshare.28688033.v1
title: Schema-driven

description: This dataset contains the raw NCBI/GenBank records retrieved in January 2024 using a lung-associated 16S rRNA marker-gene query strategy for selected bacterial groups relevant to the pulmonary environment. The files are provided as downloaded from the public repository, without modification.<br>
DOI: 10.5061/dryad.qv9s4mwk6
title: Data for: Speleothem stable isotopes from 670 - 240 ka ago at Cape Limeworks Cave 1, Robertson, South Africa

description: We present stable oxygen and carbon isotope data (δ18O and δ13C ) and U-Th
 chronology data from five speleothems from Cape Limeworks Cave 1 near
 Robertson, Western Cape, South Africa (33.73S°, 19.77E°). The data set
 covers the time interval between 240 and 670 ka BP with hiatuses at
 630-500 ka and 360-310 ka. Stable isotope ratios range between -6.5 and
 -3.7 ‰ for δ18O and -11.0 and -8.5 ‰ for δ13C. Analyses of the dispersion
 of the δ18O and δ13C data sets suggest that the highly diverse western
 part of the Cape Floristic Region experienced climatic stability across
 several glacial-interglacial cycles when compared to less diverse
 Mediterranean Climate Regions and the eastern parts of the Cape Floristic
 Region. This result provides support for the hypothesis that lower
 extinction rates associated with Pleistocene biome stability may explain
 the higher diversity in the CFR relative to other MCEs.
description: Speleothems were extracted from the cave using a hammer and
 chisels and stable isotopes were analyzed at the Geological Survey of
 Israel using methods described in Bar-Matthews et al., (2003, Geochimica
 et Cosmochimica Acta, 67, 3181–3199. https://doi.org/10.1016/S0016-7037(02)01031-1)
 and Bar-Matthews et al., (1997, Quaternary Research, 47, 155–168. https://doi.org/10.1006/qres.1997.1883). U-series dating was done at the Geological Survey of Israel following methods described in Grant et al., (2012, Nature, 491(7426), 744–747. https://doi.org/10.1038/nature11593) and at the University of Minnesota following methods described in Edwards et al., (1987, Earth and Planetary Science Letters, 81, 175–192), Shen et al., (2012, Geochimica et Cosmochimica Acta, 99, 71–86. https://doi.org/10.1016/J.GCA.2012.09.018) and Cheng et al., (2013, Earth and Planetary Science Letters, 371–372, 82–91. https://doi.org/10.1016/j.epsl.2013.04.006)
description: Data is presented in Excel and txt format.
DOI: 10.5061/dryad.gb5mkkwtv
title: Data, code, and output related to water lead levels

description: The purpose of this research was to evaluate the need to repeatedly sample
 water from homes to identify infrequent, but high "spikes" in
 water lead levels due to the sporadic release of lead particulates. The
 Illinois and Pennsylvania data were used in establishing baseline (first
 round of sampling) water lead levels. The simulations were created using
 various assumptions of baseline prevalence and various probabilities of
 spike occurrence on the N+1 round of sampling, given the results on the N
 round. The findings of the research indicate that household tap water
 needs to be sampled at least 5–7 times to achieve a 50% probability of
 identifying hazardous spikes in water lead levels.
description: The Illinois Lead and Copper Rule dataset was downloaded from
 http://163.191.83.31/dww/index.jsp for 2020 and the first half of 2021. It excludes water samples from source water and from water upstream of home/school sampling points. The Pennsylvania Lead and Copper Rule dataset for 2020 and the first half of 2021 were downloaded from http://www.drinkingwater.state.pa.us/. That dataset includes water samples from source water and water upstream of the home/school sampling points. The code was used to simulate water lead levels in 100,000 homes each sampled 15 times, under a variety of assumptions about baseline distribution of water lead levels and transitional probabilities. The tables are the output of that code.
DOI: 10.5061/dryad.2rbnzs7sf
title: Raw data for: Artificial cells eavesdropping on HepG2 cells

description: Cellular communication between artificial and natural cells are explored
 by fabricating hydrogel based artificial cells (ACs) that can eavesdrop on
 liver cells with regards to their cytochrome P450 (CYP450) activity. ACs
 are capable of eavesdropping on HepG2 cells by releasing D-cysteine and
 the D-cysteine release from ACs is quantified by colorimetric and
 luminometric detection. The CYP450 activity of HepG2 cells is evaluated by
 the production of 2-cyano-6-hydroxybenzothiazole (CHB), which react with
 D-cysteine to produce D-luciferin. Thereby, the capability of ACs to
 eavesdrop on HepG2 cells is measured by detecting D-luciferin in the
 presence of luciferase. The eavesdropping experiment is performed in
 different experimental set ups, but is centered around the production of
 D-luciferin due to the production of CHB by HepG2 cells and D-cysteine
 release from ACs. In addition, bright field microscopy and confocal laser
 scanning microscopy was performed to visualize the ACs and aggregates of
 ACs and HepG2 cells.  Our findings thereby present means of
 designing communication between AC and mammalian cells. Further, the ACs
 provides an easily implemented approach to monitor a core hepatic function
 when co-cultured with hepatocytes.
description: The data is arranged according
 to the figures presented in the article.
DOI: 10.15468/dl.mppj4s
title: Occurrence Download

description: A dataset containing 154 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Harleyodendron unifoliolatum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 154 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003470-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aranny
title: Occurrence Download

description: A dataset containing 2479 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rana amurensis"
 ]
}

 The dataset includes 2479 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003469-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m905qfv5j
title: Data from: No evidence for sex differences in the electrophysiological properties and excitatory synaptic input onto nucleus accumbens shell medium spiny neurons

description: Sex differences exist in how the brain regulates motivated behavior and
 reward, both in normal and pathological contexts. Investigations into the
 underlying neural mechanisms have targeted the striatal brain regions,
 including the dorsal striatum and nucleus accumbens core and shell. These
 investigations yield accumulating evidence of sexually different
 electrophysiological properties, excitatory synaptic input, and
 sensitivity to neuromodulator/hormone action in select striatal regions
 both before and after puberty. It is unknown whether the electrical
 properties of neurons in the nucleus accumbens shell differ by sex and
 whether sex differences in excitatory synaptic input are present before
 puberty. To test the hypothesis that these properties differ by sex, we
 performed whole-cell patch-clamp recordings on male and female medium
 spiny neurons (MSNs) in acute brain slices obtained from prepubertal rat
 nucleus accumbens shell. We analyzed passive and active
 electrophysiological properties, and miniature EPSCs (mEPSCs). No sex
 differences were detected; this includes those properties, such as
 intrinsic excitability, action potential after hyperpolarization,
 threshold, and mEPSC frequency, that have been found to differ by sex in
 other striatal regions and/or developmental periods. These findings
 indicate that, unlike other striatal brain regions, the
 electrophysiological properties of nucleus accumbens shell MSNs do not
 differ by sex. Overall, it appears that sex differences in striatal
 function, including motivated behavior and reward, are likely mediated by
 other factors and striatal regions.
description: This dataset was collected using whole-cell patch clamp
 recordings of medium spiny neurons in prepubertal male and female rat
 nucleus accumbens shell. The recordings were analyzed to generate standard
 attributes describing the biophysical properties of these neurons. Please
 see Willett et al., 2016, eNeuro, for further details: https://pubmed.ncbi.nlm.nih.gov/27022621/. 
description: Microsoft Excel and Word. There are many alternatives for
 accessing these files other than using these specific programs. For
 example, the spreadsheet and README can be opened with Google Docs and
 Apache OpenOffice.
DOI: 10.5061/dryad.zpc866tcm
title: Compiled trace element compositions for magmatic zircons from I-type granitoids, S-type granitoids and TTGs, and detrital zircons

description: Here we share the data of compiled global magmatic zircon trace element
 compositions for I-type granitoids, S-type granitoids, and TTGs. We also
 show compiled detrital zircon trace element compositions from the
 Gangdese magmatic belt, southern Tibet, the Western Dharwar
 Craton, southern India, and the Jack Hills, Australia.
description: Methods are described in the following open-access
 manuscript: Zhong S., et al. I-type and S-type granites in
 the Earth’s
 earliest continental
 crust, Nature Comms Earth and Environ., (2023).
description: As a condition of using these data, you kindly ask you use the
 following citation: Zhong S., et al. I-type and S-type granites
 in the Earth’s
 earliest continental
 crust, Nature Comms Earth and Environ., (2023).
DOI: 10.5061/dryad.wh70rxwrw
title: Oxamniquine derivatives overcome praziquantel treatment limitations for schistosomiasis

description: Human schistosomiasis is a neglected tropical disease caused
 by S. mansoni, S. haematobium, and S. japonicum. Praziquantel
 (PZQ) is the method of choice for treatment. Due to constant selection
 pressure, there is an urgent need for new therapies for schistosomiasis.
 Previous treatment of S. mansoni included the use of Oxamniquine (OXA), a
 drug that activated by schistosomes’ sulfotransferase (SULT). Guided by
 data from Xray crystallography and Schistosoma killing assays more than
 350 OXA derivatives were designed, synthesized, and tested. We were able
 to identify CIDD-0150610 and CIDD-0150303 as powerful derivatives in vitro
 that kill (100%) of all three Schistosoma species at a final concentration
 of 143 µM. We evaluated the efficacy of the best OXA derivates in an in
 vivo model after treatment with a single dose of 100 mg/kg by oral gavage.
 The highest rate of worm burden reduction was achieved by CIDD -150303
 (81.8%) against S. mansoni, CIDD-0149830 (80.2%) against S. haematobium
 and CIDD-066790 (86.7%) against S. japonicum. We have also evaluated the
 derivatives ability to kill immature stages since PZQ does not kill
 immature schistosomes. CIDD-0150303 demonstrated (100%) of killing for all
 life stages at a final concentration of 143 µM in vitro and effective
 reduction in worm burden in vivo. To understand how OXA derivatives fit in
 the SULT binding pocket, X-ray crystal structures of CIDD-0150303 and
 CIDD-0150610 demonstrate that the SULT active site will accommodate
 further modifications to our most active compounds as we tune them to
 increase favorable pharmacokinetic properties. Treatment with a single
 dose of 100 mg/kg by oral gavage of each PZQ and CIDD-0150303 reduced the
 worm burden in an animal model by (90.8%). Therefore, we conclude that
 CIDD-0150303, CIDD-0149830 and CIDD-066790 are the novel drugs that
 overcome OXA limitation, and CIDD-0150303 can be used with PZQ in
 combination therapy.
DOI: 10.5061/dryad.kprr4xh8f
title: Data from: Two new species of Eleutherodactylus from Western and Central Mexico (Eleutherodactylus jamesdixoni sp. nov., Eleutherodactylus humboldti sp. nov.)

description: Here, we provide 1) raw and edited recordings of male advertisement calls
 from two new species of Eleutherodactylus (Syrrhophus) and their sister
 species, including R scripts used to analyze the data, and 2) photos of
 preserved specimens from which morphological measurements were collected.
description: Raw call recordings were recorded in waveform audio file format
 (.wav) using a Marantz PMD661 handheld recorder with a Sennheiser shotgun
 microphone at a sampling rate of 44.1 kHz. Background noise was removed
 using Audacity version 3.2.1 (Audacity Team, 2022). Filtered recordings
 were analyzed using Raven Pro 1.6.3 (K. Lisa Yang Center for Conservation
 Bioacoustics at the Cornell Lab of Ornithology) to create selection tables
 of call parameters. Morphometric measurements were collected from digital
 photographs using ImageJ (Rueden et al., 2017). 
 Audacity Team. 2022. Audacity® software is copyright © 1999-2021
 Audacity Team. Website: https://audacityteam.org/. K. Lisa Yang Center for Conservation Bioacoustics at the Cornell Lab of Ornithology. (2023). Raven Pro: Interactive Sound Analysis Software (Version 1.6.4) [Computer software]. Ithaca, NY: The Cornell Lab of Ornithology. Available from https://ravensoundsoftware.com/. Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW. 2017. ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics 18:529. DOI: 10.1186/s12859-017-1934-z.
DOI: 10.5061/dryad.r7sqv9shb
title: Data for: Connectedness and spillover effect between cryptocurrency and financial assets

description: Cryptocurrencies have quickly become one type of important financial
 asset. Accordingly, it is important to understand the interaction between
 cryptocurrency and other financial asset markets. However, previous
 literature paid less attention to the correlation between the price trend
 of cryptocurrencies and other financial assets. Using the vector
 autoregression model, we analyzed price correlation and spillover effect
 between cryptocurrencies and financial assets between November 2017 and
 February 2022. The study concludes that stock price has a spillover effect
 on cryptocurrencies, government bonds, and precious metals. The research
 results are useful while allocating portfolios or hedge strategies that
 include cryptocurrencies and financial assets such as stocks, government
 bonds, and precious metals.
description: The study downloads cryptocurrencies and other financial assets
 data through the price information website investing.com. We wrote a letter to the source website to inquire whether it is possible to use the data for analysis and writing a paper, and received a positive response. We collect price data of the daily transaction. The data period is from November 2017 to February 2022. Cryptocurrencies are traded 24 hours a day. However, stock, bonds, and other financial assets are traded only on business days. We exclude the transaction data of the stock market close day. As a result, we obtain 1087 price data of cryptocurrency and other assets. The return rate is calculated by taking the price to one order difference. Volatility is calculated in the same way as studied by Diebold and Yilmaz (2012), estimated by subtracting the maximum and minimum prices of the day.
DOI: 10.5061/dryad.qv9s4mwk7
title: Altered trait covariances between invasive and native ranges of a global plant invader

description: Increasing evidence suggests that invasive populations adapt to novel
 environments rapidly, and the ability to rapidly adapt depends on
 genetically-based trait variation and covariation. However, few studies
 have investigated the trait covariance in the native and invasive ranges.
 Such investigation will give a more comprehensive picture of how
 historical contingency and adaptation shape invasiveness, contributing to
 the prediction of future invasion dynamics. Here, we collected seven and
 nine populations alongside latitudes from invasive and native ranges of a
 global invasive plant, Spartina alterniflora, and planted them in two
 common gardens at the southernmost and northernmost sites of the invasive
 range. We measured plant traits, including the first flowering time, plant
 height, and seed set, and analyzed how these traits varied with garden
 sites and populations’ origin latitudes and how their covariance changed
 between ranges. We found that plants flowered later, grew taller, and set
 more seeds in the high-latitude garden than in the low-latitude one. The
 growth and expression of genetic variation of traits appeared to be
 limited by high ambient temperature in the low-latitude garden. In the
 high-latitude garden, the flowering time of populations showed clinal
 variation for both invasive and native populations, whereas the plant
 height and seed set showed clinal variation only for native or invasive
 populations. From the native to the invasive range, the flowering time and
 seed set developed negative genetic covariance, and flowering time and
 plant height changed from negative genetically correlated to uncorrelated.
 Our results suggested that S. alterniflora has experienced rapid
 adaptation to clinal and local conditions over the 40-year invasion. Such
 geographic-scale rapid adaptation appeared to have benefited from
 previously identified genetic admixture that has released the trait
 covariance. Our study highlights the importance of integrating full-range
 geographical surveys with introduction history to understand the potential
 and mechanisms of trait evolution during invasion.
DOI: 10.5061/dryad.tx95x6b2v
title: Data from: Obligate endosymbiosis explains genome expansion during eukaryogenesis

description: The endosymbiosis of an alpha-proteobacterium that gave rise to
 mitochondria was one of the key events in eukaryogenesis. One striking
 outcome of eukaryogenesis was a much more complex cell with a large
 genome. Despite the existence of many alternative hypotheses for this and
 other patterns potentially related to endosymbiosis, a constructive
 evolutionary model in which these hypotheses can be studied is still
 lacking. Here, we present a new theoretical approach in which we focus on
 the consequences rather than the causes of the mitochondrial
 endosymbiosis. Using a constructive evolutionary model of cell-cycle
 regulation, we find that genome expansion and genome size asymmetry arise
 from emergent host–symbiont cell-cycle coordination. We also find that
 holobionts with large host and small symbiont genomes perform best on long
 timescales, and mimic the outcome of eukaryogenesis. By designing and
 studying a constructive evolutionary model of obligate
 endosymbiosis, we uncovered some of the forces that may drive the
 patterns observed in nature. Our results provide a theoretical
 foundation for patterns related to the mitochondrial
 endosymbiosis, such as genome size asymmetry, and reveal
 evolutionary outcomes that have not been considered so far, such
 as cell-cycle coordination without direct communication.
description: Genomes are beads-on-a-string virtual genomes evolved using a
 computational model, available on github as Eukaryotes:
 github.com/samvonderdunk/Eukaryotes