cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2z34tmpq9
title: Target capture methods offer insight into the evolution of rapidly diverged taxa and resolve allopolyploid homeologs in the fern genus Polypodium s.s.

description: Like many fern lineages comprising reticulate species complexes,
 Polypodium s.s. (Polypodiacaeae) has a history shaped by rapid
 diversification, hybridization, and polyploidy that poses substantial
 challenges for phylogenetic inference with plastid and single-locus
 nuclear loci. Using target capture probes for 408 nuclear loci developed
 by the GOFlag project and a custom bioinformatic pipeline, SORTER, we
 constructed multi-locus nuclear datasets for diploid temperate and
 Mesoamerican species of Polypodium and five allotetraploid species
 belonging to the well-studied Polypodium vulgare complex. SORTER employs a
 clustering approach to separate putatively paralogous copies of targeted
 loci into orthologous matrices and haplotype phasing to infer
 allopolyploid haplotypes across loci, resulting in datasets amenable to
 both concatenated maximum likelihood and multi-species coalescent
 phylogenetic analyses. By comparing phylogenies derived from maximum
 likelihood and multi- species coalescent analyses of unphased and phased
 datasets, as well as evaluating discordance among gene trees and species
 trees, we recover support for incomplete lineage sorting within Polypodium
 s.s., novel relationships among diploid taxa of the Polypodium vulgare
 complex and its Mesoamerican sister clade, and the placement of several
 Polypodium species within other genera. Additionally, we were able to
 infer well-supported phylogenies that identified the hypothesized
 progenitors of the allotetraploid species, indicating that SORTER is an
 effective and accurate tool for reconstructing homeolog haplotypes of
 allopolyploids in fern taxa and other non-model organisms from target
 capture data.
description: The resulting alignments and phylogenetic trees (Supplementals C
 and D) were built from target-capture data generated by the Geneology of
 Flagellate Plants Project (GoFlag). All raw data was sourced from various
 researchers that submitted samples to GoFlag with permission from
 respective parties. The resulting trees and alignments were processed by
 the SORTER pipeline (https://github.com/JonasMendez/SORTER). Supplementals C and D also include summary CSV tables for distribution of loci across samples for each dataset. Included are two supplemental texts describing the SORTER pipeline (Supplemental A) as well as effect of clustering on sequence copy number from Stage 1 of the SORTER pipeline (Supplemental B). Supplemental Table S1 summarizes read and sequence statistics for each sample used in the study.
description: Trees can be viewed with free FigTree software, and alignments
 can be observed with text editing software or Mesquite software.
DOI: 10.5061/dryad.qv9s4mwjd
title: Impacts of pastures and forestry plantations on herpetofauna: a global meta-analysis

description: 1.      The establishment of
 pastures and forestry plantations has increased globally to meet growing
 demands for meat and wood products. Pasture and plantation expansion often
 drives deforestation, which causes homogenization of biotic communities
 and is a major driver of the global extinction crisis. A core question is
 how the severity of losses varies between pastures and plantations, and in
 turn, how geographical location and plantation management characteristics
 moderate these impacts.
 2.      Focusing on
 herpetofauna (amphibians and reptiles) as the most endangered vertebrate
 group, we performed a global synthesis using 41 scientific articles that
 reported species richness or abundance in pastures and forestry
 plantations relative to natural forest in 191 case studies among 19
 countries. 3.      We found a
 severe negative effect of pasture and a less negative effect of forestry
 plantations on species richness and abundance of herpetofauna. Within
 plantations, species richness and total abundance were more negatively
 impacted in amphibians than reptiles, in the tropics, when planting exotic
 tree species, monocultures, large or commercial plantations, and when
 clearing understory vegetation. Yet mixed, old, small, or conservation
 plantations and those permitting recovery of understory vegetation had no
 negative impacts relative to the reference natural forest.
 4.      Synthesis and
 applications. The loss of herpetofauna species richness and abundance
 underscores the importance of halting ongoing tropical deforestation for
 pasture and intensive forestry plantations. The potential for
 appropriately managed forestry plantations to support biodiversity in
 regions lacking forest cover, including via replacement of anthropogenic
 pastures, suggests that such plantations have an important role under
 global reforestation agendas.
DOI: 10.5061/dryad.rfj6q57dz
title: Decreased but diverse activity of cortical and thalamic neurons in consciousness-impairing rodent absence seizures

description: Absence seizures are brief episodes of impaired consciousness, behavioral
 arrest, and unresponsiveness, with yet-unknown neuronal mechanisms. Here
 we report that an awake female rat model recapitulates the behavioral,
 electroencephalographic, and cortical functional magnetic resonance
 imaging characteristics of human seizures. Neuronally, seizures feature
 overall decreased but rhythmic firing of neurons in cortex and thalamus.
 Individual cortical and thalamic neurons express one of four distinct
 patterns of seizure-associated activity, one of which causes a transient
 initial peak in overall firing at seizure onset, and another which drives
 sustained decreases in overall firing. 40–60 seconds before seizure onset,
 there begins a decline in low-frequency electroencephalographic activity,
 neuronal firing, and behavior, but an increase in higher-frequency
 electroencephalography and rhythmicity of neuronal firing. Our findings
 demonstrate that prolonged brain state changes precede seizure, and
 consciousness-impairing seizures feature distinct functional groups of
 cortical and thalamic neurons resulting in an overall transient firing
 increase, sustained firing decrease, and increased rhythmicity.
description: Methods are currently available at https://doi.org/10.1038/s41467-022-35535-4
DOI: 10.5061/dryad.vmcvdncwz
title: How much is soil nitrous oxide emission reduced with biochar application? An evaluation of meta‐analyses

description: This data file includes five datasets used to construct the following five
 figures. Fig. 1. Response ratios (RR) of biochar application on soil N2O
 emissions from the meta-analyses and grand mean of RR and its 95%
 confident interval. Number on the right side is the total number of
 experiments used for RR calculation. Fig. 2. Impacts of experimental
 setting including experiment type (a), ecosystem type (b), and
 experimental duration (c) on the response ratios (RR) of biochar
 application on soil N2O emi­­­ssions. Number on the right side is the
 total number of experiments used for RR calculation. Fig. 3. Impacts of
 biochar properties including feedstock (a), pyrolysis temperature (b), pH
 (c), and C:N ratio (d) on the response ratios (RR) of biochar application
 on soil N2O emi­­­ssions.  Number on the right side is the total
 number of experiments used for RR calculation. Fig. 4. Impacts of soil
 properties including soil texture (a), soil organic carbon (SOC, b), C:N
 ratio (c), and soil pH (d) on the response ratios (RR) of biochar
 application on soil N2O emi­­­ssions. Number on the right side is the
 total number of experiments used for RR calculation. Fig. 5. Impacts of
 agricultural practices including biochar application rate (a), type of
 fertilizer (b), and nitrogen (N) application rate (c) on the response
 ratios (RR) of biochar application on soil N2O emi­­­ssion. Number on the
 right side is the total number of experiments used for RR calculation.
description: This data file includes five datasets used to construct the
 following five figures.
DOI: 10.5061/dryad.573n5tbb5
title: Data and code for: Human density modulates spatial associations among tropical forest terrestrial mammal species

description: The spatial aggregation of species pairs often increases with the
 ecological similarity of the species involved. However, the way in which
 environmental conditions and anthropogenic activity affect the
 relationship between spatial aggregation and ecological similarity remains
 unknown despite the potential for spatial associations to affect species
 interactions, ecosystem function, and extinction risk. Given that human
 disturbance has been shown to both increase and decrease spatial
 associations among species pairs, ecological similarity may have a role in
 mediating these patterns. Here, we test the influences of habitat
 diversity, primary productivity, human population density, and species’
 ecological similarity based on functional traits (i.e., functional trait
 similarity) on spatial associations among tropical forest mammals. Large
 mammals are highly sensitive to anthropogenic change and therefore
 susceptible to changes in interspecific spatial associations. Using
 two-species occupancy models and camera trap data, we quantified the
 spatial overlap of 1,216 species pairs from 13 tropical forest-protected
 areas around the world. We found that the association between ecological
 similarity and interspecific species associations depended upon
 surrounding human density. Specifically, aggregation of ecologically
 similar species was more than an order of magnitude stronger in landscapes
 with the highest human density compared to those with the lowest human
 density, even though all populations occurred within protected areas.
 Human-induced changes in interspecific spatial associations have been
 shown to alter top-down control by predators, increase disease
 transmission and increase local extinction rates. Our results indicate
 that anthropogenic effects on the distribution of wildlife within
 protected areas are already occurring and that impacts on species
 interactions, ecosystem functions, and extinction risk warrant further
 investigation.
DOI: 10.5061/dryad.sbcc2fr9m
title: Datasets for: PARNAS: Objectively selecting the most representative taxa on a phylogeny

description: The use of next-generation sequencing technology has enabled phylogenetic
 studies with hundreds of thousands of taxa. Such large-scale phylogenies
 have become a critical component in genomic epidemiology in pathogens such
 as SARS-CoV-2 and influenza A virus. However, detailed phenotypic
 characterization of pathogens or generating a computationally tractable
 dataset for detailed phylogenetic analyses requires objective subsampling
 of taxa. To address this need, we propose PARNAS, an objective and
 flexible algorithm to sample and select taxa that best represent observed
 diversity by solving a generalized k-medoids problem on a phylogenetic
 tree. PARNAS solves this problem efficiently and exactly by novel
 optimizations and adapting algorithms from operations research. For more
 nuanced selections, taxa can be weighted with metadata or genetic sequence
 parameters, and the pool of potential representatives can be
 user-constrained. Motivated by influenza A virus genomic surveillance and
 vaccine design, PARNAS can be applied to identify representative taxa that
 optimally cover the diversity in a phylogeny within a specified distance
 radius. We demonstrated that PARNAS is more efficient and flexible than
 existing approaches. To demonstrate its utility, we applied PARNAS to (i)
 quantify SARS-CoV-2 genetic diversity over time, (ii) select
 representative influenza A virus in swine genes derived from over 5 years
 of genomic surveillance data, and (iii) identify gaps in H3N2 human
 influenza A virus vaccine coverage. We suggest that our method, through
 the objective selection of representatives in a phylogeny, provides
 criteria for quantifying genetic diversity that has application in the the
 rational design of multivalent vaccines and genomic epidemiology. PARNAS
 is available at https://github.com/flu-crew/parnas.
DOI: 10.15468/dl.ah5ney
title: Occurrence Download

description: A dataset containing 882 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Entada abyssinica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 882 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003284-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.05qfttf60
title: Urban population structure and dispersal of an Australian mosquito (Aedes notoscriptus) involved in disease transmission

description: Dispersal is critical for successful pest control measures as it
 determines the rate of movement across target control areas and influences
 the risk of human exposure. We used a fine-scale spatial population
 genomic approach to investigate the dispersal ecology and population
 structure of Aedes notoscriptus, an important
 disease-transmitting mosquito at the Mornington Peninsula, Australia. We
 sampled and reared Ae. notoscriptus eggs at two time
 points from 170 traps up to 5 km apart and generated genomic data from 240
 individuals. We also produced a draft genome assembly from a laboratory
 colony established from mosquitoes sampled near the study area. We found
 low genetic structure (Fst) and high coancestry throughout the study
 region. Using genetic data to identify close kin dyads, we found that
 mosquitoes had moved distances of &gt;1 km within a generation, which
 is further than previously described. A spatial autocorrelation analysis
 of genetic distances indicated genetic similarity at &gt;1 km
 separation, a tenfold higher distance than for a comparable population of
 Ae. aegypti, from Cairns, Australia. These findings point to high
 mobility of Ae. notoscriptus, highlighting challenges of
 localized intervention strategies. Further sampling within the same area 6
 and 12 months after initial sampling showed that egg-counts were
 relatively consistent across time, and that spatial variation in
 egg-counts covaried with spatial variation in Wright’s neighbourhood size
 (NS). As NS increases linearly with population density, egg-counts may be
 useful for estimating relative density
 in Ae. notoscriptus. The results highlight the
 importance of acquiring species-specific data when planning control
 measures.
DOI: 10.5061/dryad.kd51c5b8w
title: Hybrid AgNPs/eggshell calcium carbonate particles and their antimicrobial efficiency

description: In this study, hybrid particles of AgNPs-loaded eggshell calcium carbonate
 (AgNPs/eCaCO3) were prepared in situ by precipitating the eggshell in the
 presence of freshly prepared AgNPs with a particle size of 10-30 nm. The
 hybrid particles were comparatively precipitated in situ at 25 °C and 35
 °C using poly (sodium 4-styrenesulphonate) as a polyelectrolyte. The
 AgNPs/eCaCO3 particles prepared at 25 °C had a spherical morphology with a
 mean diameter of 3.56 mm, and BET surface area of 85.08 m2/g. On the other
 hand, the particles prepared at 35 °C had a broader size distribution with
 a mean diameter of 3.19 mm, and a BET surface area of 79.25 m2/g.
 AgNPs-loaded commercial calcium carbonate particles (AgNPs/e=CaCO3)
 comparatively prepared at 35 °C were perfectly spherical with a mean
 diameter of 5.61 mm. At preparing temperature of 25 °C, the hybrid
 particles contain AgNPs of 0.78 wt% for AgNPs/eCaCO3 and 3.20 wt% for
 AgNPs/CaCO3. The AgNPs/eCaCO3 and AgNPs/CaCO3 particles exhibited the same
 efficiency against bacteria extracted from beef with an average inhibition
 zone diameter of 7–10 mm according to the modified Kirby–Bauer disc
 diffusion assay depending on their concentration and beef source. Freshly
 prepared silver colloids showed comparatively poorer antimicrobial
 efficiency with an inhibition zone diameter around 7 mm. 
description: I. Particle diameter Field Emission Scanning
 Electron Microscopy (FESEM) was carried out on Carl Zeiss,
 Auriga to observe the particle morphology and particle size of AgNPs,
 eCaCO<sub>3</sub>, AgNPs/eCaCO<sub>3</sub>, and
 AgNPs/CaCO<sub>3</sub> using an
 accelerating voltage of 3.0
 kV. Prior to the observation,
 each sample was coated using a gold sputter coater (Neo Coater) for 2 min. The diameter of the particles was
 measured from the SEM micrographs using an analysis software (Image J) and calculated by randomly selecting
 200 particles. MATLAB R2022a
 was used to obtain the mean diameter, size distribution, and respective
 histogram.
 II. Inhibition zone diameters 
 The digital images of the
 Inhibition zone diameters against beef-extracted bacteria obtained from
 AgNPs/eCaCO<sub>3</sub> and AgNPs/CaCO<sub>3</sub>
 were measured three times from a disc using ImageJ and an
 average made from three replica. The antimicrobial test was performed in
 triplicate and the average diameter of the inhibition zone with standard
 deviation was calculated.
description: Excel and image-related program.
DOI: 10.5061/dryad.2jm63xssn
title: KENFIN-EDURA: Explaining non-communicable disease-related behaviour in the context of urbanization, family and wealth

description: Background The prevalence of non-communicable diseases is increasing in
 lower-middle-income countries as these countries transition to unhealthy
 lifestyles. The transition is mostly predominant in urban areas. We
 assessed the association between wealth and obesity in two sub-counties in
 Nairobi City County, Kenya, in the context of family and poverty. Results
 A total of 149 households, response rate of 93%, participated, 72 from
 Embakasi and 77 from Langata. Most of the participants residing in
 Embakasi belonged to the lower income and education groups whereas
 participants residing in Langata belonged to the higher income and
 education groups. About 30% of the pre-adolescent participants in Langata
 were with at least overweight, whereas the respective number in Embakasi
 was only 6% (p&lt;0.001). In contrast, the prevalence of adults
 (mostly mothers) with overweight and obesity was high (65%) and similar in
 the two study areas. Wealth (b = 0.01; SE 0.0; p=0.003) and income (b =
 0.29; SE 0.11; p=0.009) predicted higher BMI z-score in pre-adolescents.
 Conclusions In Nairobi, pre-adolescent overweight was already highly
 prevalent in the middle-income area, while the proportion of women with
 overweight/obesity was high also in the low-income area. These results
 suggest that a lifestyle promoting obesity is prevalent even in lower
 income areas  in urban Kenya, and this is a strong justification
 for promoting healthy lifestyles across all socio-economic classes.
description: This cross-sectional study was conducted among of 9-14 years old
 pre-adolescents and their guardians living in low- (Embakasi) and
 middle-income (Langata) sub-counties. The sociodemographic characteristics
 were collected using a validated questionnaire. Weight, height, mid-upper
 arm circumference, and waist circumference were measured using standard
 approved protocols.  Socioeconomic characteristics of the residential
 sites were accessed using Wealth Index, created by using Principal
 Component Analysis.  Statistical analyses were done by analysis of
 variance (continuous variables, comparison of areas) and with logistic and
 linear regression models.
DOI: 10.5061/dryad.31zcrjdq0
title: Simultaneous determination method of 10 organophosphate esters in oyster, an environmental indicator organism

description: Oyster is a common indicator organism of environment pollution. A method
 was built to simultaneously determine ten common commercial
 organophosphate ester flame retardants in oysters. After the careful
 optimization of conditions, the organophosphate esters (OPEs) in oyster
 sample were extracted with hexane assisted by ultrasound, purified with
 NH2 solid-phase extraction column, eluted with the mixture solution of
 dichloromethane and ethyl acetate at the ratio of 1:1 (v/v), and finally
 detected by gas chromatography coupled with tandem triple quadrupole mass
 spectrometry (GC–MS/MS). All the ten compounds in the concentrations
 ranging from 0.5 ng·mL-1 to 100 ng·mL-1 showed good linearity with their
 R2 higher than 0.9991. The limits of detection and limits of
 quantification for the organophosphate esters were from 0.03 ng·g-1 to
 0.47 ng·g-1 (dry weight) and from 0.1 ng·g-1 to 1.56 ng·g-1 (dry weight),
 respectively. At the three spiking levels with five replicates, recoveries
 of organophosphate esters ranged from 82% to 108% with the relative
 standard deviation ranging from 0.9% to 6.4%. In the samples collected
 from mariculture farms, nine OPE compounds were detected in oysters with
 the concentration ranging from 6.52 ng·g-1 to 22 ng·g-1 (dry weight). It
 indicated the method was suitable for OPEs determination in oysters.
description: 0.5 g of oyster sample was
 weighed into a 50 mL centrifuge tube and then equilibrated for
 30 min followed by the addition of 50
 μL mixture of internal standards (1
 μg·mL-1). After the
 addition of 3 g of anhydrous sodium sulphate and 10 mL of hexane, the
 mixture in the centrifuge tube was vortexed for 2 min (IKA MS3 Basic, IKA
 Works GmbH & Co, Germany), ultrasonically treated for 30 min
 (KQ-250E, Kun Shan Ultrasonic Instruments Co., Ltd, China), and then
 centrifuged for 10 min at 5500 rpm at 4℃ (Anke DL-6000B, Shanghai Anting
 Scientific Instruments Factory, China). The supernatant was transferred to
 another 50 mL tube. The extraction process was repeated and the
 supernatant of the two extractions was then applied to the NH2 cartridge
 which has been preconditioned with 3 mL of DCM/EA (1:1, v/v) and 3 mL of
 hexane. After rinsing with 3 mL of hexane, the target compounds were
 eluted with 6 mL of DCM/EA (1:1, v/v). The eluent was dried under a gentle
 nitrogen flow and reconstituted in 1 mL of EA.