cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7291/d1st01
title: Microhabitats associated with solar energy development alter demography of two desert annuals

description: Political and economic initiatives intended to increase energy production
 while reducing carbon emissions are driving demand for solar energy.
 Consequently, desert regions are now targeted for development of
 large-scale photovoltaic solar energy facilities. Where vegetation
 communities are left intact or restored within facilities, ground-mounted
 infrastructure may have negative impacts on desert-adapted plants because
 it creates novel rainfall runoff and shade conditions. We used
 experimental solar arrays in the Mojave Desert to test how these altered
 conditions affect population dynamics for a closely related pair of native
 annual plants: rare Eriophyllum mohavense and common E. wallacei. We
 estimated aboveground demographic rates (seedling emergence, survivorship,
 and fecundity) over seven years and used seed bank survival rates from a
 concurrent study to build matrix models of population growth in three
 experimental microhabitats. In drier years, shade tended to reduce
 survival of the common species, but increase survival of the rare species.
 In a wet year, runoff from panels tended to increase seed output for both
 species. Population growth projections from microhabitat-specific matrix
 models showed stronger effects of microhabitat under wetter conditions,
 and relatively little effect under dry conditions (lack of rainfall was an
 overwhelming constraint). Performance patterns across microhabitats in the
 wettest year differed between rare and common species. Projected growth of
 E. mohavense was substantially reduced in shade, mediated by negative
 effects on aboveground demographic rates. Hence, the rare species was more
 susceptible to negative effects of panel infrastructure in wet years that
 are critical to seed bank replenishment. Our results suggest that altered
 shade and water runoff regimes associated with energy infrastructure will
 have differential effects on demographic transitions across annual species
 and drive population-level processes that determine local abundance,
 resilience, and persistence.
description: Please refer to Read Me.rtf file included with the data set.
description: Please refer to Read Me.rtf file included with the data set.
DOI: 10.5061/dryad.cz8w9gj2x
title: Mangrove sinkholes (cenotes) of the Yucatan Peninsula, a global hotspot of carbon sequestration

description: Mangroves are amongst the most carbon-dense ecosystems on the Planet. The
 capacity of mangrove forests to accumulate carbon has been assessed and
 reported at regional, national and global scales. However, small-scale
 sampling is still revealing ‘hot spots’ of carbon accumulation. This study
 reports one of these “hotspots” with one of the largest-recorded carbon
 stocks in the sinkholes (cenotes) of the Yucatan Peninsula, Mexico. We
 assessed soil organic carbon (SOC) stocks from deep soils (1 to 6 m) of
 mangroves associated with cenotes and measured massive amounts of SOC up
 to 2,792 Mg C ha-1, the highest value reported in the literature so far.
 This SOC is primarily derived from highly preserved mangrove roots and has
 changed little since its deposition, which started over 3,220 years ago (±
 30 BP). Most of these cenotes are owned by Mayan communities and are
 threatened by increased tourism and over-extraction and pollution of
 groundwater in the region. These hot spots of carbon sequestration, albeit
 small in area, require adequate protection and could provide valuable
 financial opportunities through carbon projects.
description: Sampling was conducted in September 2019 with SCUBA equipment
 (See Supplementary Video or https://www.youtube.com/watch?v=lGVYxnlkHu8&feature=youtu.be). We sampled two cores at Cenote Jaguar and Yaxchen, and four cores at Casa Cenote.  For each core, we used a 60 mL syringe to take one sample at each of the following depths: 0 –15, 15 – 30, 30 – 50, 50 – 100 cm, and every 100 cm until the bottom of the peat. Soil samples were analysed for soil organic carbon (SOC) and δ<sup>13</sup>C with an elemental analyser coupled with an isotope ratio mass spectrometer (EA-IRMS, Serco System, Griffith University, Brisbane, Australia) with analytical standard deviation &lt; 0.1‰.
DOI: 10.5061/dryad.r2280gbc2
title: A worldwide assessment of soil macroinvertebrate communities

description: Soil macroinvertebrate communities have been assessed worldwide using the
 standard ISO/TSBF sampling procedure. The Macrofauna database currently
 comprises 3694 sites distributed throughout 41 countries, from 55º S
 latitude to 57ºN, sea level to over 4000m in elevation, in total annual
 total rainfall regimes between 500 and &gt;3000mm and 5 to 32ºC mean
 temperature. These communities are significantly influenced by climatic
 parameters, soil texture and vegetation cover. Abundance and diversity
 were highest in tropical rain forests (1895 ± 305 individuals m-2) and
 natural savannahs (1796 ± 269), and progressively lower in
  tropical cropping systems (tree associated crops 1358 ± 101,
 pastures or transitory crops: 1178 ± 147), temperate grasslands: 583 ± 70,
 temperate forests: 529 ± 71, annual crops: 232 ± 14 and dry forest: 221 ±
 52 systems.
description: A standard method deposited at ISO was used at 3694 sites from 41
 different countries, in 10 types of plant covers to identify the main
 drivers of community structure and abundance. ISO. (2011). ISO 23611-5. Soil Quality-Sampling of Soil Invertebrates-Part 5. Sampling and Extraction of Soil Macro-invertebrates. <i>International Organization for Standardization</i>, Geneva, Switzerland.
description: This file contains the data set extracted and transformed from an
 original database to allow adapted data treatment.
DOI: 10.5061/dryad.76hdr7svh
title: Distribution pattern of entry holes of the tree-killing bark beetle Polygraphus proximus

description: Bark beetles attack their hosts at uniform intervals to avoid
 intraspecific competition in the phloem. Bark texture and phloem thickness
 also affect bark beetle attacks, and the bark characteristics are not
 spatially homogeneous; therefore, the distribution patterns of entry holes
 can demonstrate an aggregated distribution. Polygraphus proximus Blandford
 (Coleoptera: Scolytinae) is a non-aggressive phloephagous bark beetle that
 feeds on Far Eastern firs. They have caused mass mortality in Russia and
 Japan. However, the distribution pattern of entry holes of P. proximus and
 spatial relationships with bark characteristics have not been studied.
 Thus, we investigated the distribution pattern of entry holes of P.
 proximus. The distribution of entry holes was significantly uniform in
 most cases. As the attack density increased, an aggregated distribution
 pattern within a short distance (&lt; 4.0 cm) was observed. The rough
 bark had a significantly higher number of entry holes than the remaining
 bark. The distribution pattern of entry holes demonstrated a significantly
 aggregated spatial association with rough bark. Finally, rough bark around
 knots had significantly thicker phloem than the remaining barks. These
 suggest that P. proximus may preferentially attack rough bark to reproduce
 in the thicker phloem under a rough bark surface.
description: We cut down two <i>A</i>. <i>veitchii</i>
 trees at Yatsugatake Forest Station, Mountain Science Center, University
 of Tsukuba, in Minamisaku County, Nagano Prefecture, Japan on July 7,
 2020, and immediately peeled the bark. We randomly selected 18 knots and
 measured the phloem thickness of rough bark around the knots and that of
 the remaining bark near the knots.
DOI: 10.5061/dryad.rv15dv47f
title: The experimental manipulation of atmospheric drought: Teasing out the role of microclimate in biodiversity experiments

description: Drought occurrence is increasing due to anthropogenic climate change.
 Drought can negatively affect plants via reduced water belowground and
 increased evaporative demand or vapor pressure deficit (VPD) aboveground.
 Past work has shown that plant diversity can ameliorate the negative
 effects of drought in plant communities, but these results are
 inconsistent between experimental and natural drought studies. Further,
 while studies on the negative effects of reduced soil moisture on plant
 growth in drought experiments are abundant, the effects of predicted
 increases in atmospheric VPD have been neglected. We directly manipulated
 atmospheric relative humidity in a biodiversity and drought experiment at
 the California State University, Los Angeles (CA, USA) under three
 atmospheric conditions (ambient, dehumidified, and humidified), two
 treatments of native perennial grass diversity (monoculture and 8 species
 polyculture), and two soil drought treatments (control and drought). We
 assessed both polyculture plant community and individual species (Poa
 secunda) responses to atmospheric drought and soil drought. We found that
 soil drought only limits aboveground biomass production when atmospheric
 conditions are also dry. We also found that Poa secunda was limited by
 increased competition in polyculture when ambient atmospheric conditions
 were humid but was facilitated by diversity when atmospheric conditions
 were dry.
DOI: 10.5061/dryad.ngf1vhht1
title: Genomic signatures of UV resistance evolution in Escherichia coli depend on the growth phase during exposure

description: Physiological states can determine the ability of organisms to handle
 stress. Does this mean that the same selection pressure will lead to
 different evolutionary outcomes, depending on the organisms’ physiological
 state? If yes, what will be the genomic signatures of such adaptation(s)?
 We used experimental evolution in Escherichia coli followed by
 whole-genome whole-population sequencing to investigate these questions.
 The sensitivity of Escherichia coli to ultraviolet (UV) radiation depends
 on the growth phase during which it experiences the radiation. We evolved
 replicate E. coli populations under two different conditions of UV
 exposures, namely exposure during the lag and the exponential growth
 phases. Initially, the UV sensitivity of the ancestor was greater during
 the exponential phase than the lag phase. However, at the end of 100
 cycles of exposure, UV resistance evolved to similar extents in both
 treatments. Genome analysis showed that mutations in genes involved in DNA
 repair, cell membrane structure and RNA polymerase were common in both
 treatments. However, different functional groups were found mutated in
 populations experiencing lag and exponential UV treatment. In the former,
 genes involved in transcriptional and translational regulations and
 cellular transport were mutated, whereas the latter treatment showed
 mutations in genes involved in signal transduction and cell adhesion.
 Interestingly, the treatments showed no phenotypic differences in a number
 of novel environments. Taken together, these results suggest that
 selection pressures at different physiological stages can lead to
 differences in the genomic signatures of adaptation, which need not
 necessarily translate into observable phenotypic differences.
description: These datasets represent Minimum Inhibitory Concentrations (MICs)
 and growth rates of bacterial populations that have been evolved in
 presence of ultraviolet radiation. The detailed methodologies are
 presented in the paper.
DOI: 10.15468/dl.r3cdrb
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dalea pulchra",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 130 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002752-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.v9s4mw6tv
title: Sexual selection on jumping spider colour pattern: investigation with a new quantitative approach

description: How animals assess information encoded in individual colour patches have
 been extensively studied, yet the role of both individual colour patches
 and gross colour pattern (i.e. the combination of colour patches) remains
 understudied. We tested the functioning of both individual colour patches
 and gross colour pattern in sexual selection using the jumping spider
 Siler semiglaucus as a study system. We first quantified sexual dimorphism
 in S. semiglaucus in both individual patches and gross colour pattern
 using the newly developed quantitative colour pattern analysis (QCPA)
 framework. After detecting sexual differences in colour coverage and
 pattern contrast, we manipulated the abdomen colour pattern of males and
 had them engage in both female mate choice and male contest trials.
 Females spent more time watching males with lower pattern contrast and
 greater red coverage during mate assessment, suggesting that they evaluate
 information from both individual patches and gross colour pattern of
 males. However, male colour pattern had no significant effect on the
 outcomes of male contests. Thus, we suggest that the observed sexual
 colour pattern dimorphism evolved primarily through female mate choice in
 S. semiglaucus. This is the first study to use QCPA framework to quantify
 sexual dimorphism in within-pattern conspicuousness from an intraspecific
 perspective in invertebrates. Our study also highlights the importance of
 both individual colour patches and gross colour pattern in sexual
 selection.
DOI: 10.5061/dryad.ht76hdrdv
title: Influence of early thermal-oxidative ageing on the structure and properties of polyoxymethylene copolymer

description: Thermal-oxidative ageing of polyoxymethylene (POM) copolymer in oven at
 100 °C for 1, 2, 3, 5, 7, 10, 14 and 21 days and the influence of early
 thermal-oxidative on POM structure and properties were studied by
 means of wide-angle X-ray diffraction (WAXD), Fourier transform infrared
 spectroscopy (FTIR), differential scanning calorimetry (DSC) and
 tensile test. Based on the results, we found that the early
 thermal-oxidative ageing of POM copolymer can be divided into
 three regions. The first region is the initial three days. In
 this region, some molecular chains
 rearranged, resulting in internal stress
 relaxation, increased of crystallinity degree and grain size due
 to the perfection of crystal structure; both extended chain
 crystal (ECC) and folded chain crystal (FCC) increased
 and ECC grew faster than FCC. The second region is from 3 days to 10 days
 and in this region chain scission took place in amorphous region and led
 to chemi-crystallization. The last region is after 10 days. In this
 region, the structure and performance of POM copolymer reached a stable
 situation at this stage. In this work, the difference between skin and
 core were also analyzed.
description: The data was collected by experiments. The
 data was processed manually by excel and software
 (Jade、Omnic、Origin).
DOI: 10.5061/dryad.v6wwpzgv6
title: Data from: The history of foot-and-mouth disease virus serotype C: the first known extinct serotype?

description: Foot-and-mouth disease (FMD) is a highly contagious animal disease caused
 by an RNA virus subdivided into seven serotypes that are unevenly
 distributed in Asia, Africa and South America. Despite the challenges of
 controlling FMD, since 1996 there have been only two outbreaks attributed
 to serotype C, in Brazil and in Kenya, in 2004. This review describes the
 historical distribution and origins of serotype C and its disappearance.
 The serotype was first described in Europe in the 1920s, where it mainly
 affected pigs and cattle but as a less common cause of outbreaks than
 serotypes O and A. No serotype C outbreaks have been reported in Europe
 since vaccination stopped in 1990. FMD virus is presumed to have been
 introduced into South America from Europe in the 19th century, although
 whether serotype C evolved there or in Europe is not known. As in Europe,
 this serotype was less widely distributed and caused fewer outbreaks than
 serotypes O and A. Since 1994, serotype C had not been reported from South
 America until four small outbreaks were detected in the Amazon region in
 2004. Elsewhere, serotype C was introduced to Asia, in the 1950s to the
 1970s, persisting and evolving for several decades in the Indian
 subcontinent and for eighteen years in the Philippines. Serotype C virus
 also circulated in East Africa between 1957 and 2004. Many serotype C
 viruses from European and Kenyan outbreaks were closely related to vaccine
 strains, including the most recently recovered Kenyan isolate from 2004.
 International surveillance has not confirmed any serotype C cases,
 worldwide, for over 15 years, despite more than 2000 clinical submissions
 per year to reference laboratories. Serology provides limited evidence for
 absence of this serotype, as unequivocal interpretation is hampered by
 incomplete intra-serotype specificity of immunoassays and the continued
 use of this serotype in vaccines. It is recommended to continue
 strengthening surveillance in regions of FMD endemicity, to stop
 vaccination against serotype C and to reduce working with the virus in
 laboratories, since inadvertent escape of virus during such activities is
 now the biggest risk for its reappearance in the field.
description: This data package includes the FMDV Serotype C VP1 coding
 sequqnces (.fasta file) and .xml BEAST input file required to reproduce
 the analyses of the following paper: Paton DJ, Di Nardo A, et al - The
 history of foot-and-mouth disease virus serotype C: the first known
 extinct serotype?
DOI: 10.5061/dryad.vq83bk3rp
title: Machine learning to extract muscle fascicle length changes from dynamic ultrasound images in real-time

description: B-mode ultrasound has become one-off, if not the main way of measuring
 muscle fascicle fiber lengths non-invasively. Yet, the gold standard for
 tracking these is still time-intensive hand-tracking, and even with
 semi-automated approaches, the process takes time and has to be done post
 hoc. Hence, towards greatly improving current processing capabilities
 by tracking these muscle fasicle lengths in real-time,
 we trained and optimized machine learning models with collected B-mode
 ultrasound data. We focused on soleus muscle ultrasound data given the
 relationships existing between soleus and whole body energetics
 while walking and our intention to use these measurements in the
 loop. To ensure these data were representative of different
 muscle fiber loading and displacement levels, we collected B-mode
 ultrasound data from the soleus muscle of six participants performing five
 defined ankle motion tasks: (a) seated, constrained ankle plantarflexion,
 (b) seated, free ankle dorsi/plantarflexion, (c) weight-bearing, calf
 raises (d) walking, and then a (e) mix. We collected 24-seconds
 of 60 frames-pre-second data for each
 task using Telemed, ArtUs EXT-1H,
 LV8-5N60-A2 ultrasound probe wrapped to the right calf
 with 3M Vetrap Bandaging Tape. The probe was aligned so that both
 aponeuroses were as close to horizontal as possible in the live ultrasound
 video feed.   
description:  *** Machine learning to extract muscle fascicle       
   <br>  *** length changes from dynamic ultrasound
 images  <br>  *** in real-time                                     
                         # All provided data is
 ultrasound data in .mat format # The .mat files are the
 result after processing .tvd files <br>   from EchoWaveII with the
 Matlab code provided by UltraTrack # The .mat files can
 be read by UltraTrack where you'll be <br>   able to both see
 the ultrasound images and do semi-automated<br>   muscle fascicle
 tracking # All data focused on soleus muscle
 # Data includes 5 Tasks, 6 Subjects, and around ~24
 seconds <br>   per task  # Tasks are a)
 constrained ankle contractions, b) free ankle <br>   dorsiflexion
 and plantarflexion, c) calf raises, d) walking,<br>   and e)
 mix # File names will include subject numbers (s1, s2,
 s3, s4, s5,<br>   , s6) and tasks (constrained, free, raises,
 walking, zmix)<br>   For example:
 "s4_walking.mat" # All data we used is
 included (all 5 tasks for each of the<br>   6 subjects)
DOI: 10.5061/dryad.bnzs7h498
title: Data from: Abundance data applied to a novel model invertebrate host sheds new light on parasite community assembly in nature

description: Understanding how environmental drivers influence the assembly of parasite
 communities, in addition to how parasites may interact at an
 infracommunity level, are fundamental requirements for the study of
 parasite ecology. Knowledge of how parasite communities are assembled will
 help to predict the risk of parasitism for hosts, and model how parasite
 communities may change under variable conditions. However, studies
 frequently rely on presence-absence data and examine multiple host species
 or sites, metrics which may be too coarse to characterise nuanced
 within-host patterns. We utilised a novel host system, the freshwater
 mussel Anodonta anatina, to investigate the drivers of community structure
 and explore parasite interactions. In addition, we aimed to highlight
 consistencies and inconsistencies between presence-absence and abundance
 data. Our analysis incorporated 14 parasite taxa and 720 replicate
 infracommunities. Using redundancy analysis, a joint species distribution
 model and a Markov random fields approach, we modelled the impact of both
 host-level and environment-level characteristics on parasite structure, as
 well as parasite-parasite correlations after accounting for all other
 factors. This approach was repeated for both the presence and abundance of
 all parasites. We demonstrated that the regional species pool, individual
 host characteristics (mussel length and gravidity) and predicted
 parasite-parasite interactions are all important but to varying degrees
 across parasite species, suggesting that applying generalities to parasite
 community construction is too simplistic. Further, we showed that
 presence-absence data fails to capture important density-dependent effects
 of parasite load for parasites with high abundance, and in general
 performs poorly for high-intensity parasites. Host and parasite traits, as
 well as broader environmental factors, all contribute to parasite
 community structure, emphasising that an integrated approach is required
 to study community assembly. However, care must be taken with the data
 used to infer patterns, as presence-absence data may lead to incorrect
 ecological inference.
description: Sixty individuals of the duck mussel <i>Anodonta
 anatina</i> (Linnaeus 1758) were sampled from the same location at
 the Old West River at Stretham (52.3343° N, 0.2243°E), a lower reach of
 the River Great Ouse (UK), at monthly intervals from February 2019 to
 February 2020 (12 collections, N = 720 mussels). Parasites were identified
 and counted (S3), host and environment traits recorded (S4), and parasite
 life-history traits reported (S5).  In addition, we
 attach three additional 'Results' files
 ("differences.csv", "meananderror.csv",
 "modeldiff.csv"), necessary to faithfully reproduce the figures
 in the manuscript (as the Bayesian model processes mean that output will
 be subtly different between runs).