cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qf0bs33
title: Data from: Prior evolution in stochastic versus constant temperatures affects RNA virus evolvability at a thermal extreme

description: It is unclear how historical adaptation versus maladaptation in a prior
 environment affects population evolvability in a novel habitat. Prior work
 showed that vesicular stomatitis virus (VSV) populations evolved at
 Constant 37oC improved in cellular infection at both 29oC and 37oC; in
 contrast, those evolved under Random changing temperatures between 29oC
 and 37oC failed to improve. Here we tested whether prior evolution
 affected the rate of adaptation at the thermal-niche edge: 40oC. After 40
 virus generations in the new environment, we observed that populations
 historically evolved at random temperatures showed greater adaptability.
 Deep sequencing revealed that most of the newly evolved mutations were de
 novo. Also, two novel evolved mutations in the VSV glycoprotein and
 replicase genes tended to co-occur in the populations previously evolved
 at Constant 37oC, whereas this parallelism was not seen in populations
 with prior Random-temperature evolution. These results suggest that prior
 adaptation under Constant versus Random temperatures constrained the
 mutation landscape that could improve fitness in the novel 40oC
 environment, perhaps owing to differing epistatic effects of new mutations
 entering genetic architectures that earlier diverged. We concluded that
 RNA viruses maladapted to their previous environment could ‘leapfrog’ over
 counterparts of higher fitness, to achieve faster adaptability in a novel
 environment.
description: Gloria-Soria_BAM files BAM files from
 Illumina and Ion Torrent sequencing runs generated from each ancestral and
 evolved lineage described in this paper.
 Gloria-Soria_BAMfiles.zip
DOI: 10.5061/dryad.sm61m9s
title: Data from: A small podocnemidoid (Pleurodira, Pelomedusoides) from the Late Cretaceous of Brazil, and the innervation and carotid circulation of side-necked turtles

description: Pleurodires are less specious than cryptodires, together forming the two
 major lineages of crown-turtles. Their fossil record, however, is rich. A
 particularly large number of fossil pleurodires, many belonging to
 Podocnemidoidae, has been recovered from the Late Cretaceous Bauru Group
 outcrops in south-central Brazil. Here we describe an additional
 pleurodire from this region, Amabilis uchoensis gen. et sp. nov., based on
 a partially preserved skull. A. uchoensis is recognized as a
 Podocnemidoidae by its small entrance to the antrum postoticum and
 completely developed cavum pterygoidei, being unique among other
 non-podocnemidid podocnemidoids for its medially open fenestra postotica
 and absent basioccipital-opisthotic contact. Our cladistic analysis places
 A. uchoensis as sister-taxon to Hamadachelys + other podocnemidoids. We
 further explore the neuroanatomy of side-necked turtles with the aid of
 microcomputed tomography (µCT) of specimens of the main pleurodiran
 lineages. Our data shed light on the different carotid circulation
 patterns among pleurodires, and we propose new phylogenetic characters
 which describe neuroanatomical variation of the group. The optimization of
 these characters shows two independent acquisitions of a foramen for the
 palatal branch of the carotid in chelids and podocnemidoids, and a unique
 loss of the vidian nerve canal in chelids among turtles in general.
description: Character-taxon
 matrixThis is the
 character-taxon matrix in Nexus format used in our
 study.Hermansonetal.nexCharacter-taxon matrix (TNT)This is the character-taxon matrix in .tnt format, readable in TNT software.Hermansonetal.tnt3D surface modelsThese are the 3D models of the skull of the studied specimen. We also include a VAXML file that can be readily opened in SPIERS software, for example.Carotid 3D modelsThese are the 3D models of the carotid circulation and bones surrouding the canals for the selected species discussed in the main text. We also include a separate VAXML for each taxon that can be readily open in SPIERS software.Carotid PLY Files.zip
DOI: 10.5061/dryad.r556n3j
title: Data from: Serratia marcescens Shapes Cutaneous Bacterial Communities and Influences Survival of an Amphibian Host

description: A changing understanding of the functional interactions between microbial
 communities and their associated hosts is influencing how disease is
 perceived and ameliorated. Of the numerous host-microbiome-disease systems
 of study, the emergence of chytridiomycosis in anurans (caused by
 Batrachochytrium dendrobatidis, hereafter Bd), has been implicated in
 ongoing declines and extinction events of amphibians across the planet.
 Interestingly, there has been differential survival among amphibians in
 resisting Bd infection and subsequent disease. One factor thought to
 contribute to this resistance is the host-associated cutaneous microbiota.
 This has raised the possibility of utilizing genetically modified
 probiotics to restructure the host-associated microbiota for desired
 anti-fungal outcomes. Here, we utilize a previously described strain of
 Serratia marcescens (Sm) for manipulation of amphibian cutaneous
 microbiota. Sm was genetically altered to have a dysfunctional pathway for
 the production of the extracellular metabolite prodigiosin. This
 genetically altered strain (Δpig) and the functional prodigiosin producing
 strain (WT-pig) were compared for their microbial community and anti-Bd
 effects both in vitro and in vivo. In vitro, Bd growth was significantly
 repressed in the presence of prodigiosin. In vivo, the inoculation of both
 Sm strains was shown to significantly influence amphibian microbiota
 diversity with the Δpig-Sm treatment showing increasing α-diversity, and
 the WT-pig S. marcescens having no temporal effect on diversity.
 Differences were also seen in host mortality with Δpig-Sm exhibiting
 significantly decreased survival probability as compared to a no¬-Sm
 control in the presence of Bd. These results are important evidence for
 the potential of genetic-level manipulation of bacteria in a host
 microbial community, which may provide a way to alter disease outcomes and
 address critical frontiers in disease and microbial ecology.
description: BdvsSm Assay (color
 corrected) Data used in analysis of
 Bd vs Sm assay as per Bell et al.   
 Sm Growth
 Curves Growth curve data from
 21C for comparing WT and mutant Serratia marcescens.   
 Acris Experiment
 Data Data collected from the
 in vivo Acris blanchardi experiment.
DOI: 10.5061/dryad.v15fc6b
title: Data from: Biotransformation of chlorothalonil by strain Stenotrophomonas acidaminiphila BJ1 isolated from farmland soil

description: The chlorothalonil is a widely used fungicide while the contamination of
 soil and water environments by this chemical causes potential threats to
 the biodiversity. Given the metabolic potential of soil microorganisms,
 there is a need for developing microbiological approaches to degrade
 persistent compounds, such as chlorothalonil, in the contaminated sites.
 Here in this study, we isolated a bacterial strain (namely, BJ1) capable
 of degrading chlorothalonil from a chlorothalonil-contaminated farmland
 soil in the Shandong Province, China. Using 16S rDNA gene sequencing,
 morphological and biological characteristics, we identified the strain BJ1
 as Stenotrophomonas acidaminiphila. The strain BJ1 utilizes chlorothalonil
 as a sole carbon source. At initial concentrations of 50, 100, 200, 300 mg
 l-1, it degraded 91.5%, 89.4%, 86.5 and 83.5% of chlorothalonil after 96 h
 of inoculation under optimum conditions (30 °C and pH 7.0), respectively.
 Two metabolites, methyl-2, 5, 6-trichloro-3-cyano-4-methoxy-benzoate and
 methyl-3- cyano-2, 4, 5, 6-tetrachlorobenzoate, were detected and
 identified based on HPLC-MS analysis, which suggests that the strain BJ1
 metabolized chlorothalonil through the hydroxylation of chloro-group and
 hydration of cyano-group. The results of this study highlight the great
 potential for this bacterium to be used in chlorothalonil pollution
 remediation.
description: Data of strain BJ1
 growth and degradation of chlorothalonilData.docx
DOI: 10.5281/zenodo.18332323
title: Precision Cascade Engine — M&A Due‑Diligence Module v1.0.0 (Audit‑Certified Reproducibility Archive)

description: Abstract

 

This record releases the Precision Cascade M&A Module v1.0.0: a deterministic, audit‑grade reproducibility archive for corporate due diligence across mergers, acquisitions, divestitures, and related transactions.

 

The module converts financial, operational, legal, cyber, governance, and risk evidence into canonical truth objects governed by explicit validation, provenance, and integrity rules. It enables reproducible reconstruction of business reality without performing valuation, pricing, synergy modelling, or deal strategy.

 

The archive demonstrates how due‑diligence evidence can be validated, sealed, audited, and independently replicated under a unified, domain‑agnostic truth infrastructure.

 

Description

 

Overview

 

This archive implements a full M&A evidence standardisation and audit system using the Precision Cascade Engine.

 

Scope

 

Supported evidence includes:

 

• financial statements

• operational telemetry

• contracts and legal records

• cyber security evidence

• governance documentation

• risk and insurance data

 

 

Reference Case

 

The archive includes a complete, audit‑passed synthetic acquisition (BrightWave Technologies) demonstrating end‑to‑end due‑diligence reproducibility.

 

Relationship to the Core Engine

 

This module is a domain‑specific adaptation derived from the Precision Cascade Cosmology Engine and does not modify the underlying engine.
DOI: 10.5061/dryad.fv453k7
title: Data from: Conspecifics, not pollen, reduce omnivore prey consumption

description: Pollen can decrease (via reduced consumption) or increase (via numerical
 response) an omnivores consumption of animal prey. Although pollen can
 increase predation pressure through numerical responses of omnivores,
 pollen may also suppress predation by increasing omnivore interactions
 with conspecifics. Despite this potential, studies of the impacts of
 pollen on predation by omnivores often overlook the effect of these
 tissues on intraspecific interactions between omnivores. We designed three
 studies to examine how Spartina foliosa pollen and conspecific density
 impact scale insect prey consumption by ladybeetle (Naemia seriata)
 omnivores. First, we assessed how pollen impacts scale insect consumption
 by isolated ladybeetles. Second, we measured how pollen influences
 ladybeetle prey suppression when numerical responses were possible. Third,
 because initial experiments suggested the consumption rates of individual
 ladybeetles depended on conspecific density, we compared per capita
 consumption rates of ladybeetles across ladybeetle density. Pollen did not
 influence prey consumption by isolated ladybeetles. When numerical
 responses were possible, pollen did not influence total predation on prey
 despite increasing ladybeetle density, suggesting that pollen decreased
 per capita prey consumption by ladybeetles. The discrepancy between these
 studies is likely a consequence of differences in ladybeetle density— the
 presence of only two other conspecifics decreased per capita prey
 consumption by 76%. Our findings suggest that pollen may not alter the
 population level effects of omnivores on prey when omnivore numerical
 responses are offset by reductions in per capita predation rate.
description: Conspecifics, not
 pollen, reduce omnivore prey consumption,Raw data for the three
 primary experiments contained within the manuscript. All experiments are
 included in one file. Lab Mesocosm- Scale Density: Raw data from the six
 week lab experiment assessing how pollen affects scale insect consumption
 by isolated lady beetles. Field Manipulation- Scale Density: Raw data from
 the five-week field experiment look at the effects of ladybeetles on scale
 insect density under natural conditions (in flower and no flower
 condition). Field Maniulation- Ladybeetle: Raw data for ladybeetle
 densities in plots with and without cordgrass flowers. Laboratory Feeding
 Assay: Effects of ladybeetle conspicific density on ladybeetle scale
 insect consumption.Rinehart and
 Long_PlosOne_RawData.xlsx
DOI: 10.5061/dryad.ng94td0
title: Data from: Weighing homoplasy against alternative scenarios with the help of macroevolutionary modeling: a case study on limb bones of fossorial sciuromorph rodents

description: Homoplasy is a strong indicator of a phenotypic trait’s adaptive
 significance when it can be linked to a similar function. We assessed
 homoplasy in functionally relevant scapular and femoral traits of
 Marmotini and Xerini, two sciuromorph rodent clades that independently
 acquired a fossorial lifestyle from an arboreal ancestor. We studied 125
 species in the scapular dataset and 123 species in the femoral dataset.
 Pairwise evolutionary model comparison was used to evaluate whether
 homoplasy of trait optima is more likely than other plausible scenarios.
 The most likely trend of trait evolution among all traits was assessed via
 likelihood scoring of all considered models. The homoplasy hypothesis
 could never be confirmed as the single most likely model. Regarding
 likelihood scoring, scapular traits most frequently did not differ among
 Marmotini, Xerini, and arboreal species. For the majority of femoral
 traits, results indicate that Marmotini, but not Xerini, evolved away from
 the ancestral arboreal condition. We conclude on the basis of the scapular
 results that the forelimbs of fossorial and arboreal sciuromorphs share
 mostly similar functional demands, whereas the results on the femur
 indicate that the hind limb morphology is less constraint, perhaps
 depending on the specific fossorial habitat.
description: Woelfer_&_Nyakatura_Ecol_and_Evol_2019-R project filesThis folder contains two R projects (Femur and Scapula, respectively) and associated data, such as surface models for the femora and photos for the scapula. See README.txt for further information.Woelfer_&_Nyakatura_Ecol_and_Evol_2019.7z
DOI: 10.5061/dryad.sc30mr1
title: Data from: Genetic population structure and variation at phenology-related loci in anadromous Arctic char (Salvelinus alpinus)

description: The Arctic will be especially affected by climate change, resulting in
 altered seasonal timing. Anadromous Arctic char (Salvelinus alpinus) is
 strongly influenced by sea surface temperature (SST) delimiting time
 periods available for foraging in the sea. Recent studies of salmonid
 species have shown variation at phenology-related loci associated with
 timing of migration and spawning. We contrasted genetic population
 structure at 53 SNPs versus four phenology-related loci among 15
 anadromous Arctic char populations from Western Greenland and three
 outgroup populations. Among anadromous populations, the time period
 available for foraging at sea (&gt; 2oC) ranges from a few weeks to
 several months, motivating two research questions: 1) Is population
 structure compatible with possibilities for evolutionary rescue of
 anadromous populations during climate change? 2) Does selection associated
 with latitude or SST regimes act on phenology-related loci? In Western
 Greenland, strong isolation-by-distance at SNPs was observed and spatial
 autocorrelation analysis showed genetic patch size up to 450 km,
 documenting contingency and gene flow among populations. Outlier tests
 provided no evidence for selection at phenology-related loci. However, in
 Western Greenland, mean allele length at OtsClock1b was positively
 associated with the time of year when SST first exceeded 2oC and
 negatively associated with duration of the period where SST exceeded 2oC.
 This is consistent with local adaptation for making full use of the time
 period available for foraging in the sea. Current adaptation may become
 maladaptive under climate change, but long-distance connectivity of
 anadromous populations could redistribute adaptive variation across
 populations and lead to evolutionary rescue.
description: SNP genotypes of Arctic
 charSNP genotypes (53 loci)
 encompassing all analyzed Arctic char populations in GENEPOP
 format.SNPs_all.genPhenology-related lociGenotypes at 4 phenology-related loci in all analyzed Arctic char populations in GENEPOP format.phenology-related_loci.gen
DOI: 10.5061/dryad.4t8v4jf
title: Data from: Clinical Outcomes Associated with the use of the NexSite™ Hemodialysis Catheter with New Exit Barrier Technology: Results from a Prospective, Observational Multi-center Registry Study

description: Purpose: Decreasing the risk of catheter related bloodstream infections
 (CRBSIs) remains a key focus for improving outcomes and reducing cost of
 care for hemodialysis (HD) patients. Recent studies demonstrate CRBSI
 rates can be improved by managing bacterial colonization at the catheter
 exit site. Herein we present the results of a study documenting the
 clinical performance of the NexSite® HD catheter, a new tunneled central
 venous catheter which incorporates Exit Site Management (ESM) technology.
 Methods: We conducted an observational study using a prospective,
 multi-center registry of HD patients implanted with the NexSite® HD
 catheter. The primary endpoint for the study was CRBSI rate for a period
 up to 180-days following catheter placement. Secondary endpoints included
 device placement success rate, exit site healing, development of an exit
 site or tunnel infection, and early or late non-infectious
 catheter-related complications. All reasons for early non-elective
 catheter removal were recorded. Results: A total of 115 HD patients at 6
 sites were included in the final analysis. Cumulative catheter use was
 10,924 days with a mean duration of 95 days. Seven patients experienced
 CRBSIs during the study period resulting in a CRBSI rate of 0.64 per 1,000
 catheter-days. Seventy-four patients (64.3%) had either elective catheter
 removal (n=56) or utilized the catheter for the entire 180-day observation
 period (n=18). Thirty-five patients (30%) underwent non-elective device
 removal either due to CRBSI (n=5), low flow (n=16), exit site issues
 (n=7), or for other causes (n=7). Six patients died during the observation
 period with 1 death due to CRBSI-associated complications and the
 remaining 5 deaths attributed to non-device related causes. Conclusion:
 Our findings demonstrate that the NexSite HD catheter equipped with ESM
 technology can achieve a CRBSI rate in compliance with the NKF KDOQI
 (National Kidney Foundation Kidney Disease Outcome Quality Initiatives)
 Clinical Performance Guidelines stated goal of less than 1.0/1,000
 catheter-days when used in hemodialysis patients using current standard of
 care nursing protocols.
description: Database for NexSite™
 Catheter Registry StudyDatabased associated
 with an observational study using a prospective, multi-center registry of
 HD patients implanted with the NexSite® HD catheter. The primary endpoint
 for the study was CRBSI rate for a period up to 180-days following
 catheter placement. Secondary endpoints included device placement success
 rate, exit site healing, development of an exit site or tunnel infection,
 and early or late non-infectious catheter-related complications. All
 reasons for early non-elective catheter removal were recorded. A total of
 115 HD patients at 6 sites were included in the final
 analysis.Database for Clinical Outcomes
 Associated with the use of the NexSite™ Hemodialysis Catheter (PLOS
 ONE).xlsx
DOI: 10.5061/dryad.3n4gt77
title: Data from: Terrestrial contributions to Afrotropical aquatic food webs: the Congo River case

description: 1. Understanding the degree to which aquatic and terrestrial primary
 production fuel tropical aquatic food webs remains poorly understood, and
 quantifying the relative contributions of autochthonous and allochthonous
 inputs is methodologically challenging. Carbon and nitrogen stable isotope
 ratios (δ13C, δ15N) can provide valuable insights about contributions of
 terrestrial resources and trophic position respectively, but this approach
 has caveats when applied in typical complex natural food webs. 2. Here, we
 used a combination of C, N, and H (δ2H) stable isotope measurements and
 Bayesian mixing models to estimate the contribution of terrestrial
 (allochthonous) and aquatic (autochthonous) inputs to fish and
 invertebrate communities in the Congo River (and some tributaries). 3.
 Overall, our results show that we gained power to distinguish sources by
 using a multiple tracer approach and we were able to discriminate aquatic
 vs. terrestrial sources (esp. including hydrogen isotopes). Fish δ2H
 values were clearly correlated with their food preferences and revealed a
 high level of variation in the degree of allochthony in these tropical
 aquatic communities. 4. At the community level, it is clear that
 terrestrial C3 plants are an important source fueling the Congo River food
 web. However, in order to better constrain source contribution in these
 complex environments will require more robust constraints on stable
 isotope values of algal and methane-derived C sources.
description: Stable isotope data for
 the Congo River food webThe file is composed of
 four spreadsheets that contain information on C, N, and H isotope values
 of different food web components from the Congo River mainstream and some
 tributaries as described in Soto et al. Ecology and
 Evolution.COBAFISH dataset
 FINAL.xlsx
DOI: 10.5061/dryad.qk36k8q
title: Data from: Linking pollen foraging of megachilid bees to their nest bacterial microbiota

description: Solitary bees build their nests by modifying the interior of natural
 cavities and they provision them with food by importing collected pollen.
 As a result, the microbiota of the solitary bee nests may be highly
 dependent on introduced materials. In order to investigate how the
 collected pollen is associated with the nest microbiota, we used
 metabarcoding of the ITS2 rDNA and the 16S rDNA to simultaneously
 characterize the pollen composition and the bacterial communities of 100
 solitary bee nest chambers belonging to seven megachilid species. We found
 a weak correlation between bacterial and pollen alpha-diversity and
 significant associations between the composition of pollen and that of the
 nest microbiota, contributing to the understanding of the link between
 foraging and bacteria acquisition for solitary bees. Since solitary bees
 cannot establish bacterial transmission routes through eusociality, this
 link could be essential for obtaining bacterial symbionts for this group
 of valuable pollinators.
description: OTU tables and identities of bacteria and pollen
 Data tables with taxonomic identities and read abundances in each
 sample for pollen and larval microbiomes and nest pollens.
 Supplementary_File_1.xlsx