cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.08kprr547
title: History and practice of 8 U.S. Code §1103 notes, Sec. 102(c): Improvement of barriers at border

description: To expedite the construction of barriers along the U.S.-Mexico border, an
 extensive array of laws has been waived. This authority is codified in 8
 U.S. Code §1103 notes, Sec. 102(c) - Improvement of Barriers at Border. In
 1996 the Endangered Species Act of 1973 and the National Environmental
 Policy Act of 1969 were waived directly by Congress and in 2005 Congress
 delegated authority to the Secretary of Homeland Security to waive any law
 necessary with the REAL ID Act. Covering environmental protections,
 historic preservation, procurement procedures, religious freedoms, and
 more, waiver determinations facilitate the extensive and more rapid
 construction of border barriers. This dataset documents the history of
 this aspect of U.S. law as debated, as legislated, as proclaimed, and as
 litigated.  This dataset is designed to accompany the following
 academic paper: Madsen, Kenneth D. 2022. Institutionalising the Exception:
 Homeland Security Section 102(c) Waivers and the Construction of Border
 Barriers. Geopolitics. https://doi.org/10.1080/14650045.2022.2126766
description: Most documents in this dataset are from the U.S. government or
 other publicly available websites and are collected here to support the
 accompanying academic paper and be centrally available for future
 reference and research. Other files reflect the author's work to
 list, categorize, describe, and otherwise make sense of these collected
 documents. Many files are annotated and have relevant sections
 highlighted.
description: This dataset is organized into four sections, indicated by the
 file name prefix. File names starting with a "1" concern
 legislation in the U.S. Congress relating to Sec. 102(c) waiver authority.
 File names starting with a "2" include government documents
 cited in the accompanying academic paper. File names starting with a
 "3" document waiver determinations based on Sec. 102(c)
 authority. File names starting with a "4" summarize court
 opinions related to Sec. 102(c) waiver authority. All documents included
 are compatible with the CC0 waiver. Most are in .pdf format with relevant
 information annotated. In preparing these documents, every effort has been
 made to prepare them for long-term archival storage. As per recommended
 best practices, most files have been saved in .pdf/A format (with the
 "A" referring to standards for long-term (or archival)
 preservation). Three files are also included in Microsoft Excel format for
 added usability. For additional details and a full listing of contents,
 see file "0_dataset_CONTENTS.pdf."
DOI: 10.24400/527896/a01-2023.004
title: Antarctic Circumpolar Current (ACC) - fronts

description: The original technique, developed by Sall??e et al. (2008), assumes that iso-contours of satellite absolute dynamic topography (ADT) can be proxies for the traditional sub-surface hydrographic definition of the main Southern Ocean fronts. A recent version includes updates with the following definitions : - Polar Front (PF) is associated with the -0.30 m ADT contour - Southern (main) branch of the Subantarctic Front (SAF) with the -0.10 m ADT contour - Northern branch of the Subantarctic Front (SAF-N) with the 0 m ADT contour.
DOI: 10.5061/dryad.z612jm6d8
title: Jack-of-all-trades is parthenogenetic

description: Sex is more costly than parthenogenesis, evolutionary ecologists therefore
 wonder why sex is much more frequent than parthenogenesis in the majority
 of animal lineages. Parthenogens are as common as or even more common than
 sexuals in some ancient animal lineages such as mites and rotifers. Here,
 we analysed oribatid mites (Acari: Oribatida) as model group because these
 mites are an ancient taxon. There is evidence that the reproductive mode
 is phylogenetically conserved in oribatid mites, which makes them an ideal
 model to test hypotheses on the relationship between reproductive mode and
 species’ ecological strategies. We used oribatid mites to test the frozen
 niche variation hypothesis; we hypothesized that parthenogenetic oribatid
 mites occupy narrow specialized ecological niches. We used the geographic
 range of species as proxy for specialization as specialised species
 typically do have narrower geographic ranges than generalistic species.
 Parthenogenetic lineages have a higher probability to have broader
 geographic ranges than sexual species arguing against the frozen niche
 variation hypothesis. Our results suggest that parthenogenetic oribatid
 mite species are more generalistic than sexual species supporting the
 general purpose genotype hypothesis. Our findings indicate that
 parthenogenetic oribatid mite species possess a widely adapted
 general-purpose genotype and therefore might be viewed as
 “Jack-of-all-trades”. The data of this DRYAD file are the electronic
 Appendix of that paper ("Jack-of-all-trades is
 parthenogenetic").
description: Data on the range size of oribatid mites were assembled from
 Subías (2004, 2022; http://bba.bioucm.es/cont/docs/RO_1.pdf). The size of
 geographic regions, such as Holarctic, Palaearctic, Subtropical,
 Neotropical, was taken from Hawkins & Porter (2001; and citations
 therein), and from internet sources (for details see Appendix, Table 1;
 this DRYAD file). We included 983 species of the ca.
 11.000 described oribatid mite species of which 742 reproduce sexually and
 241 by parthenogenesis (Appendix, Table 2; this DRYAD file). The
 reproductive mode was taken from the literature (Cianciolo &
 Norton 2006; Domes et al. 2007; Fischer et al. 2010; Norton et al. 1993;
 Norton & Palmer 1991; Wehner et al. 2014; Maraun et al. 2019) or
 inferred from the reproductive mode of closely related species. Species
 were selected from Subías (2004, 2021) and overlapped in large to the
 species used in the study of Maraun et al. (2019), which included all
 major lineages of oribatid mites. For details see our
 paper in Ecology and Evolution ("Jack-of-all-trades is
 parthenogenetic") which will be resubmitted in May 2022
description: When using these data read the "README" file first
DOI: 10.5061/dryad.0k6djhb1z
title: Climate change alters sexual signaling in a desert-adapted frog

description: Climate change is altering species’ habitats, phenology, and behavior.
 Although sexual behaviors impact population persistence and fitness,
 climate change’s effects on sexual signals are understudied. Climate
 change can directly alter temperature-dependent sexual signals, cause
 changes in body size or condition that affect signal production, or alter
 the selective landscape of sexual signals. We tested whether
 temperature-dependent mating calls of Mexican spadefoot toads (Spea
 multiplicata) had changed in concert with climate in the Southwestern
 U.S.A. across 22 years. We document increasing air temperatures,
 decreasing rainfall, and changing seasonal patterns of temperature and
 rainfall in the spadefoots’ habitat. Despite increasing air temperatures,
 spadefoots’ ephemeral breeding ponds have been getting colder at most
 elevations, and male calls have been slowing as a result. However,
 temperature-standardized call characters have become faster and male
 condition has increased, possibly due to changes in the selective
 environment. Thus, climate change might generate rapid, complex changes in
 sexual signals with important evolutionary consequences.
description: Climate data were ordered from NOAA GHCND (National Oceanic and
 Atmospheric Administration, Global Historical Climatology Network Daily)
 via the Climate Data Online search tool
 (https://www.ncdc.noaa.gov/cdo-web/search?datasetid=GHCND).  These data
 are in "weatherdata.csv". Processing steps are included and
 described in the script "weather-data-analysis.R" and also
 described in the Manuscript, and include quality checks and pruning data
 columns, weather stations and dates that were not of interest to the
 study.  Frog calls and breeding pond temperatures were
 recorded in the field as described in the manuscript (see Methods and also
 Supplemental Methods). Calls were processed via Audacity and RavenPro
 software to measure call characters (e.g. call duration, call rate, etc.)
 as described in the manuscript. Temperature-standardized metrics of each
 call character were calculated as described in the manuscript. These
 processed data are in
 "multiplicata-calls-with-temp-corrections.csv" and the analyses
 that use this data are in the script
 "call-rates-over-time-analysis.R".  Some examples of original
 call recordings used in the dataset are provided as supplemental
 files.  
description: Use "weather-data-analysis.R" in R version 3.6.1 to
 analyze "weatherdata.csv"
 Use "call-rates-over-time-analysis.R" in R version
 3.6.1 to
 analyze "multiplicata-calls-with-temp-corrections.csv"
DOI: 10.6084/m9.figshare.31167931
title: DATA SET FOR RITIKA

description: DATA SET FOR RITIKA AGT FOR OESOPHAGEAL TECHNIQUE
DOI: 10.6084/m9.figshare.31167931.v1
title: DATA SET FOR RITIKA

description: DATA SET FOR RITIKA AGT FOR OESOPHAGEAL TECHNIQUE
DOI: 10.5061/dryad.9p8cz8wj2
title: Ecology of fear and its effect on seed dispersal by a neotropical rodent by Dumas Gálvez and Marisol Hernández

description: Predators exert negative effects on prey, besides the act of killing,
 generating behavioral and physiological costs, a concept known as the
 ecology of fear. Studies in scatterhoarding rodents in temperate zones
 suggests that prey use habitat structure to perceive predation risk. Less
 is known about how tropical forest rodents perceive predation risk. Here,
 we investigated whether the Central American agouti perceive predation
 risk by ocelots through olfactory cues and whether it influences the
 foraging behavior for Attalea butyracea seeds, one of its main food
 sources. By monitoring tagged seeds, we found that seed dispersal and
 pilferage was lower in sites with high density of ocelots, in line with
 the predictions of ecology of fear proposing that scared animals eat less.
 We also found that pilferage rates in high ocelot density sites seem to be
 lower during the rainy - transition period but not during dry season when
 food availability is generally low. However, we did not find evidence that
 agoutis adjust their cache spacing behavior in response to ocelot density.
 In an additional experiment to corroborate that agoutis’ responses were
 caused by ocelots’ cues, we found lower dispersal rates for seeds placed
 next to samples of urine and feces of ocelots as compared to controls,
 during the first seven days. Moreover, agoutis spent less time handling
 the seeds with ocelots’ cues. Here, we discuss potential cascading effects
 linked to the behavior of agoutis towards predation risk.
DOI: 10.5061/dryad.cfxpnvx6w
title: Linking genetic diversity and species diversity through plant-soil feedback

description: Genetic diversity and species diversity are typically studied in isolation
 despite theory showing they likely influence one another. Here, we used
 simplified communities of one or two populations of one or two species to
 test whether linkages between genetic and species diversity can be
 mediated by interactions between plants and their soil microbiota, or
 microbe-mediated plant-soil feedback (PSF). Interspecific PSF promotes the
 maintenance of species diversity when plants grow better with
 heterospecific soil microbes than with conspecific microbes. Similarly,
 intraspecific PSF promotes the maintenance of genetic diversity when
 plants grow better with heterogenotypic than with congenotypic microbes.
 In a two-generation greenhouse experiment, we conditioned the soil
 microbial community with pairs of plants that were either two individuals
 of the same species (lower species diversity) or one individual of each of
 two species (higher species diversity), and with pairs of plants that were
 either two individuals from the same population (lower genetic diversity)
 or one individual from each of two populations (higher genetic diversity).
 We then tested the effects of these microbial communities on plant growth
 in a second generation. We found that higher genetic diversity reduced the
 ability of interspecific PSF to promote plant species diversity, and for
 one of our two study species, higher species diversity reduced the ability
 of intraspecific PSF to promote plant genetic diversity. If these patterns
 occur in more diverse communities, then our results suggest that PSF may
 dampen the negative effects of diversity loss by promoting diversity at
 other levels of biological organization.
description: Methods can be found in Bolin, L. G. and J. A. Lau. 2022. Linking
 genetic diversity and species diversity through plant-soil
 feedback.
description: Descriptions of the data and R code can be found in the
 readme_Bolin_Lau_2022_dryad.txt file.
DOI: 10.5061/dryad.r7sqv9sdn
title: Hormone receptors AR, ER, PR and growth factor receptor Her-2 expression in oral squamous cell carcinoma: Correlation with overall survival, disease-free survival and 10-year survival in a high-risk population

description: Oral squamous cell carcinoma (OSCC) comprises most of head and neck
 neoplasms and is one of the highest-ranking and lethal cancers in Pakistan
 due to prevailing mouth habits. Growth and hormonal receptors act as
 prognostic markers and targets for therapy in some cancers, but their
 application in OSCC is largely unexplored. This study aimed to evaluate
 the expression of growth and hormonal receptors in OSCC patients and
 correlate it with 10-year, overall and disease-free survival. To achieve
 this objective, immunohistochemistry for Her-2, AR, ER and PR was
 performed on 100 formalin-fixed paraffin-embedded primary OSCC specimens.
 Receptor expression was correlated with mouth habits and
 clinicopathological features and patient survival was analyzed using
 Kaplan-Meier method and Cox regression univariate analysis. We observed
 that in 100 patients, there were 57 males and 43 females. Immunopositive
 Her-2 expression was observed in 21% of patients, AR in 13%, ER in 3% and
 0% for PR. Patients with betel quid/areca nut mouth habits had
 significantly absent Her-2 expression (P=0.035). Also, Her-2 negative
 patients were also negative for AR expression (P=0.002). Her-2 positive
 patients had poor 10-year survival (P=0.041). A trend of low survival and
 high recurrence rate was observed in AR positive patients, but this was
 not significant (P=0.072). No statistically relevant correlations were
 seen in the case of ER and PR. In conclusion, Her-2 may be a valuable
 marker for predicting long-term prognosis of OSCC patients.
description: Data of 100 OSCC patients was collected retrospectively from
 patient medical records and subsequent follow-up visits at clinics.
 Patient demographics, risk factor usage history, clinical characteristics
 and survival were correlated with experimental data (biomarker
 expression). Overall survival (OS) (minimum follow up 60 months) and
 10-year survival (minimum follow up 120 months) was taken as number of
 months from diagnosis until last follow-up (if alive) or date of death (if
 dead). Disease-free survival (DFS) was calculated as the number of months
 starting from surgery until date of recurrence or if no recurrence then
 until last follow-up (if alive) or date of death. SPSS version 19 (IBM,
 USA) was used for statistical analysis. Statistical tests included
 chi-square, Fisher's Exact test, logistic regression, Kaplan-Meier
 analysis and cox regression univariate analysis.
description: README file provided with this dataset details the descriptions
 for the dataset files and all the variables included in the
 files.
DOI: 10.5061/dryad.0zpc86702
title: Dispersal without drivers: Intrinsic and extrinsic variables have no impact on movement distances in a terrestrial amphibian

description: Dispersive movements are often thought to be multicausal and driven by
 individual body size, sex, conspecific density, environmental variation,
 personality and/or other variables. Yet such variables often do not
 account for most of the variation among dispersive movements in nature,
 leaving open the possibility that dispersion may be indeterministic. We
 assessed the amount of variation in 24 h movement distances that could be
 accounted for by potential drivers of displacement with a large empirical
 dataset of movement distances performed by Fowler’s Toads (Anaxyrus
 fowleri) on the northern shore of Lake Erie at Long Point, Ontario
 (2002–2021, incl.). These toads are easy to sample repeatedly, can be
 identified individually and move parallel to the shoreline as they forage
 at night, potentially dispersing to new refuge sites. Using a linear
 mixed-effect model that incorporated random effect terms to account for
 sampling variance and inter-annual variation, we found that all potential
 intrinsic and extrinsic drivers of movement accounted for virtually none
 of the variation observed among 24 h distances moved by these animals,
 whether over short or large spatial scales. We examined the idea of
 movement personality by testing variance per individual toad and found no
 evidence of individuality in movement distances. We conclude that
 deterministic variables, whether intrinsic or extrinsic, neither can be
 shown to nor are necessary to drive movements in this population over all
 spatial scales. Stochastic, short-timescale movements, such as daily
 foraging movements, can instead accumulate over time to produce large
 spatial-scale movements that are dispersive in nature.
description: The dataset comprises geo-referenced captures of individually
 identified Fowler's Toads (<em>Anaxyrus fowleri</em>)
 over 20 years (2002–2021, incl.), as well as environmental variation
 obtained for data extracted from the Environment Canada website (https://climate.weather.gc.ca/) for the Port Colborne, Ontario, weather station and US Army Corps of Engineers, Detroit District (https://www.lre.usace.army.mil/).
DOI: 10.5061/dryad.kkwh70s67
title: Gene gain/loss analysis for Bombella and related microbes

description: Synergistic effects of multiple stressors underpinned by limited nutrition
 (Dolezal and Toth, 2018). Poor nutrition is most damaging in developing
 honey bee larvae, who mature into workers unable to meet the needs of
 their colony (Scofield and Mattila, 2015). It is therefore essential that
 we better understand the nutritional landscape experienced by honey bee
 larvae. In this study, we characterize the metabolic capabilities of a
 honey bee larvae-associated bacterium, Bombella apis (formerly
 Parasaccharibacter apium), and its effects on the nutritional resilience
 of larvae. We found that B. apis is the only bacterium associated with
 larvae that can withstand the antimicrobial larval diet. Further, we found
 that B. apis can synthesize all essential amino acids and significantly
 alters the amino acid content of synthetic larval diet, largely by
 increasing the essential amino acid lysine. Analyses of gene gain/loss
 across the phylogeny suggest that four amino acid transporters were gained
 in recent B. apis ancestors. In addition, the transporter LysE is
 conserved across all sequenced strains of B. apis. This result suggests
 that amino acid export is a key feature conserved within the Bombella
 clade. Finally, we tested the impact of B. apis on developing honey bee
 larvae subjected to nutritional stress and found that larvae supplemented
 with B. apis are bolstered against mass reduction despite limited
 nutrition. Together, these data suggest an important role of B. apis as a
 nutritional mutualist of honey bee larvae.
description: Supplementary Table 1 – All
 sequenced <em>B. apis </em>strains retain the ability to
 synthesize all amino acids. Table generated from conserved core orthologs
 across the included strains showing presence/absence of amnio acid
 biosynthesis genes. ‘oid’ refers to the ortholog ID in our analysis of
 orthologous genes, ‘Name’ refers to the amino acid biosynthesis gene
 annotation, ‘Pathways/steps/scores’ refers to the biosynthetic pathway in
 which each gene is found, the enzymatic step in the pathway, and the
 GapMind score. GapMind score is either 2 (high confidence), 1 (medium
 confidence), or 0 (low confidence). In the columns below each sequenced
 strain, ‘1’ means that a given gene was identified in the corresponding
 genome and ‘0’ means that it was not identified. Supplementary Table 2- All
 <em>B. apis </em>genomes contain multiple cationic amino acid
 transporter orthologs. Gene gain/loss analysis showing all the gains and
 losses across the phylogeny of all sequenced <em>B. apis
 </em>strains and related microbes in Figure 3. ‘oid’ refers to the
 ortholog ID in our analysis of orthologous genes, ‘Name’ refers to
 proteins identified across all genomes analyzed. In the columns below each
 sequenced strain, ‘g’ means that a given gene was gained by that strain
 and ‘l’ means that it was lost. Supplementary Table 3 – Accession
 numbers for all sequenced strains used in this work.
DOI: 10.5061/dryad.6hdr7sr2n
title: The cDNA sequence data of hox genes in Daphnia similoides sinensis

description: Hox genes are important regulatory factors of transcription in metazoans,
 and are involved in the growth and development of organisms. In this
 study, the effects of Microcystis aeruginosa on Hox gene
 expression in the mothers and offspring of Daphnia similoides
 sinensis were investigated using a mixed diet of M.
 aeruginosa and Scenedesmus obliquus in two
 clones. The 14 Hox genes
 sequence were identified in D. similoides
 sinensisare through the previous transcriptome data (Zhang et
 al., 2016. DOI: 10.1038/srep34241).
DOI: 10.5061/dryad.tx95x6b0c
title: Data from: A migratory divide spanning two continents is associated with genomic and ecological divergence

description: Migratory divides are contact zones between breeding populations with
 divergent migratory strategies during the non-breeding season. These
 locations provide an opportunity to evaluate the role of seasonal
 migration in the maintenance of reproductive isolation, particularly the
 relationship between population structure and features associated with
 distinct migratory strategies. We combine light-level geolocators, genomic
 sequencing, and stable isotopes to investigate the timing of migration and
 migratory routes of individuals breeding on either side of a migratory
 divide coinciding with genomic differentiation across a hybrid zone
 between barn swallow (Hirundo rustica) subspecies in China. Individuals
 west of the hybrid zone, with H. r. rustica ancestry, had comparatively
 enriched carbon isotope values and overwintered in eastern Africa, while
 birds east of the hybrid zone, with H. r. gutturalis ancestry, had
 depleted isotope values and migrated to southern India. The two subspecies
 took divergent migratory routes around the high-altitude Karakoram Range
 and arrived on the breeding grounds over three weeks apart. These results
 indicate that assortative mating by timing of arrival and/or selection
 against hybrids with intermediate migratory traits may maintain
 reproductive isolation between the subspecies, and that inhospitable
 geographic features may have contributed to the diversification of Asian
 avifauna by influencing migratory patterns.
description: Please see the description of each file in README.txt