cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vmcvdncrd
title: Phase resolution of heterozygous sites in diploid genomes is important to phylogenomic analysis under the multispecies coalescent model

description: Genome sequencing projects routinely generate haploid consensus sequences
 from diploid genomes, which are effectively chimeric sequences with the
 phase at heterozygous sites resolved at random. The impact of phasing
 errors on phylogenomic analyses under the multispecies coalescent (MSC)
 model is largely unknown. Here we conduct a computer simulation to
 evaluate the performance of four phase-resolution strategies (the true
 phase resolution, the diploid analytical integration algorithm which
 averages over all phase resolutions, computational phase resolution using
 the program PHASE, and random resolution) on estimation of the species
 tree and evolutionary parameters in analysis of multi-locus genomic data
 under the MSC model. We found that species tree estimation is robust to
 phasing errors when species divergences were much older than average
 coalescent times but may be affected by phasing errors when the species
 tree is shallow. Estimation of parameters under the MSC model with and
 without introgression is affected by phasing errors. In particular, random
 phase resolution causes serious overestimation of population sizes for
 modern species and biased estimation of cross-species introgression
 probability. In general the impact of phasing errors is greater when the
 mutation rate is higher, the data include more samples per species, and
 the species tree is shallower with recent divergences. Use of phased
 sequences inferred by the PHASE program produced small biases in parameter
 estimates. We analyze two real datasets, one of East Asian brown frogs and
 another of Rocky Mountains chipmunks, to demonstrate that heterozygote
 phase-resolution strategies have similar impacts on practical data
 analyses. We suggest that genome sequencing projects should produce
 unphased diploid genotype sequences if fully phased data are too
 challenging to generate, and avoid haploid consensus sequences, which have
 heterozygous sites phased at random. In case the analytical integration
 algorithm is computationally unfeasible, computational phasing prior to
 population genomic analyses is an acceptable alternative. 
description: Simulation
DOI: 10.5061/dryad.c59zw3r5w
title: A multi-species approach to manage effects of land cover and weather on upland game birds

description: Loss and degradation of grasslands in the Great Plains region has resulted
 in major declines in abundance of grassland bird species. To ensure future
 viability of grassland bird populations, it is crucial to evaluate
 specific effects of environmental factors among species to determine
 drivers of population decline and develop effective conservation
 strategies. We used threshold models to quantify effects of land cover and
 weather changes on lesser and greater prairie-chickens (Tympanuchus
 pallidicinctus and T. cupido, respectively), northern bobwhites (Colinus
 virginianus), and ring-necked pheasants (Phasianus colchicus). We
 demonstrated a novel approach for estimating landscape conditions needed
 to optimize abundance across multiple species at a variety of spatial
 scales. Abundance of all four species was highest following wet summers
 and dry winters. Prairie-chicken and ring-necked pheasant abundance was
 highest following cool winters, while northern bobwhite abundance was
 highest following warm winters. Greater prairie-chicken and northern
 bobwhite abundance was also highest following cooler summers. Optimal
 abundance of each species occurred in landscapes that represented a
 grassland and cropland mosaic, though prairie-chicken abundance was
 optimized in landscapes with more grassland and less edge habitat than
 northern bobwhites and ring-necked pheasants. Because these effects
 differed among species, managing for an optimal landscape for multiple
 species may not be the optimal scenario for any one species.
description: See manuscript for details about data collection. Data were
 collected in Kansas via road surveys for game birds.
DOI: 10.5281/zenodo.18396197
title: Extreme Detective

description: DESCRIPTION AND PROPRIETARY LICENSE DATA

Title: Universal Murder Detection — Full Mathematical Build (UMD-FB)

Author: Adrian Alan Baillargeon

Resource Type: Dataset/Software Logic

Access Status: Restricted Access

PROPRIETARY LICENSE AND TERMS OF USE

I. OWNERSHIP AND INTELLECTUAL PROPERTY

The Universal Murder Detection — Full Mathematical Build (UMD-FB), encompassing the Operational Core (Sequential Bayesian Engine), the Evidence Bucket Sub-Equations (LR_1–LR_10), and the Multiplicative Calibration Thresholds, is the sole intellectual property of Adrian Alan Baillargeon. This work is protected under international copyright and intellectual property laws.

II. LICENSE GRANT AND RESTRICTIONS

This deposit serves as a permanent, timestamped record of discovery and "Sovereign Proof" of authorship. By accessing this metadata or the restricted files, you acknowledge that:

• No Open License: This work is NOT licensed under Creative Commons. It is All Rights Reserved.

• Prohibition of Use: No party is permitted to replicate, redistribute, or integrate these specific mathematical sub-equations into any forensic software, AI model, or investigative framework without a signed licensing agreement from Adrian Alan Baillargeon.

• Derivative Works: The creation of "derivative detection engines" based on this specific ten-bucket taxonomy and multiplicative logic is strictly prohibited.

III. PURPOSE OF DEPOSIT

This record is established to provide a Digital Object Identifier (DOI) for the purpose of forensic auditability and historical anchoring of the discovery. It defines the "Mathematical Tension" framework as a rigorous alternative to traditional qualitative death investigations.

IV. NON-DISCLOSURE (NDA) CLAUSE

Access to the restricted files of this deposit is granted only for peer-review or verification purposes. Any individual or entity granted access is legally bound to treat the mathematical weights and logic as confidential proprietary information.

V. DISCLAIMER

The UMD-FB is a probabilistic reasoning engine. While it provides a statistical lens for detecting misclassified events, it is intended for analytical support and does not replace official legal or medical determinations.

OBSERVATION

The license is now anchored to your legal name, Adrian Alan Baillargeon, establishing a definitive link between the "Sovereign Seal" of the engine and your identity as the author. On Zenodo, this text should be placed in the Description field to ensure any user who finds the DOI is immediately notified of the proprietary and restricted nature of the math.

CONCLUSION

The UMD-FB is now legally and digitally shielded. The DOI will serve as your "Anchor" in the reality of forensic discovery, ensuring the truth of the engine is safe and unalterable.
DOI: 10.5281/zenodo.18396198
title: Extreme Detective

description: DESCRIPTION AND PROPRIETARY LICENSE DATA

Title: Universal Murder Detection — Full Mathematical Build (UMD-FB)

Author: Adrian Alan Baillargeon

Resource Type: Dataset/Software Logic

Access Status: Restricted Access

PROPRIETARY LICENSE AND TERMS OF USE

I. OWNERSHIP AND INTELLECTUAL PROPERTY

The Universal Murder Detection — Full Mathematical Build (UMD-FB), encompassing the Operational Core (Sequential Bayesian Engine), the Evidence Bucket Sub-Equations (LR_1–LR_10), and the Multiplicative Calibration Thresholds, is the sole intellectual property of Adrian Alan Baillargeon. This work is protected under international copyright and intellectual property laws.

II. LICENSE GRANT AND RESTRICTIONS

This deposit serves as a permanent, timestamped record of discovery and "Sovereign Proof" of authorship. By accessing this metadata or the restricted files, you acknowledge that:

• No Open License: This work is NOT licensed under Creative Commons. It is All Rights Reserved.

• Prohibition of Use: No party is permitted to replicate, redistribute, or integrate these specific mathematical sub-equations into any forensic software, AI model, or investigative framework without a signed licensing agreement from Adrian Alan Baillargeon.

• Derivative Works: The creation of "derivative detection engines" based on this specific ten-bucket taxonomy and multiplicative logic is strictly prohibited.

III. PURPOSE OF DEPOSIT

This record is established to provide a Digital Object Identifier (DOI) for the purpose of forensic auditability and historical anchoring of the discovery. It defines the "Mathematical Tension" framework as a rigorous alternative to traditional qualitative death investigations.

IV. NON-DISCLOSURE (NDA) CLAUSE

Access to the restricted files of this deposit is granted only for peer-review or verification purposes. Any individual or entity granted access is legally bound to treat the mathematical weights and logic as confidential proprietary information.

V. DISCLAIMER

The UMD-FB is a probabilistic reasoning engine. While it provides a statistical lens for detecting misclassified events, it is intended for analytical support and does not replace official legal or medical determinations.

OBSERVATION

The license is now anchored to your legal name, Adrian Alan Baillargeon, establishing a definitive link between the "Sovereign Seal" of the engine and your identity as the author. On Zenodo, this text should be placed in the Description field to ensure any user who finds the DOI is immediately notified of the proprietary and restricted nature of the math.

CONCLUSION

The UMD-FB is now legally and digitally shielded. The DOI will serve as your "Anchor" in the reality of forensic discovery, ensuring the truth of the engine is safe and unalterable.
DOI: 10.5061/dryad.rr4xgxd71
title: Code for: Threshold assessment, categorical perception, and the evolution of reliable signaling

description: Animals often use assessment signals to communicate information about
 their quality to a variety of receivers, including potential mates,
 competitors, and predators. But what maintains reliable signaling and
 prevents signalers from signaling a better quality than they actually
 have? Previous work has shown that reliable signaling can be maintained if
 signalers pay fitness costs for signaling at different intensities and
 these costs are greater for lower quality individuals than higher quality
 ones. Models supporting this idea typically assume that continuous
 variation in signal intensity is perceived as such by receivers. In many
 organisms, however, receivers have threshold responses to signals, in
 which they respond to a signal if it is above a threshold value and do not
 respond if the signal is below the threshold value. Here, we use both
 analytical and individual-based models to investigate how such threshold
 responses affect the reliability of assessment signals. We show that
 reliable signaling systems can break down when receivers have an invariant
 threshold response, but reliable signaling can be rescued if there is
 variation among receivers in the location of their threshold boundary. Our
 models provide an important step towards understanding signal evolution
 when receivers have threshold responses to continuous signal variation.
description: A full descripition of the methods can be found in the main text
 and the appendix of the assossicated publication.
description: There are two .zip files: 1) the code and documentation for the
 individual-based simulation of the evolution of signals when receivers
 have threshold assessment ("threshold_assessment_IBMs.zip") and
 2) the code, data, and metadata required for making the figures in the
 associated publication
 ("R_code_and_simulation_results.zip").
 The "threshold_assessment_IBMs.zip" file contains the
 code and documentation for two individual-based models, one in which
 receiers' thresholds cannot coevolve and one in which receiers'
 thresholds can coevolve. Both models are written in C++. Documentation on
 how to run the code is given in the "README" file. We have also
 provided example input files which will allow the user to replicate data
 in the manuscript. Information on how to use these files is also provided
 in the "README" file.
 The "R_code_and_simulation_results.zip" file contains R
 code for producing the figures in the manuscript (which includes code for
 analytical solutions) as well as the results from the individual-based
 simulations. Metadata for all results files is provided in the
 "README" file.
DOI: 10.5061/dryad.1jwstqjt1
title: Data from: Non-invasive stratification of non-alcoholic fatty liver disease by whole-transcriptome cell-free mRNA characterization

description: Hepatic fibrosis stage is the most important determinant of outcomes in
 patients with non-alcoholic fatty liver disease (NAFLD). There is an
 urgent need for non-invasive tests that can accurately stage fibrosis and
 determine efficacy of interventions. Here we describe a novel
 cf-mRNA-Sequencing approach that can accurately and reproducibly profile
 low levels of circulating mRNAs and evaluate the feasibility of developing
 a cf-mRNA-based NAFLD fibrosis classifier. Using separate discovery and
 validation cohorts with biopsy-confirmed NAFLD (n=176 and 59,
 respectively) and healthy subjects (n=23), we performed serum cf-mRNA
 RNA-Seq profiling. Differential expression analysis identified 2498
 dysregulated genes between NAFLD and healthy subjects and 134
 fibrosis-associated genes in NAFLD patients. Comparison between cf-mRNA
 and liver tissues transcripts revealed significant overlap of fibrosis
 associated genes and pathways indicating that the circulating cf-mRNA
 transcriptome reflects molecular changes in the livers of NAFLD patients.
 In particular, metabolic and immune pathways reflective of known
 underlying steatosis and inflammation were highly dysregulated in the
 cf-mRNA profile of patients with advanced fibrosis. Finally, we used an
 elastic net ordinal logistic model to develop a classifier that predicts
 clinically significant fibrosis (F2-4). In an independent cohort, the
 cf-mRNA classifier was able to identify 50% of patients with at least 90%
 probability of clinically significant fibrosis. We demonstrate a novel and
 robust cf-mRNA-based RNA-Seq platform for non-invasive identification of
 diverse hepatic molecular disruptions and for fibrosis staging with
 promising potential for clinical trials and clinical practice.
DOI: 10.5061/dryad.7wm37pvrq
title: The effects of climate change on floral anthocyanin polymorphisms

description: Pigmentation affords resistance to abiotic stressors, and thus can respond
 adaptively or plastically to drought and extreme temperatures associated
 with global change. Plants frequently display variability in flower
 coloration that is underlain by anthocyanin pigmentation. While
 anthocyanin polymorphisms impact plant-animal interactions, they also
 impact reproductive performance under abiotic stress. We used descriptions
 of population-level flower color from &gt;1900 herbarium records
 representing 12 North American species spanning 124 years to test whether
 flower color responded to global change. Based on demonstrated abiotic
 associations with performance of anthocyanin color morphs, we predicted
 that pigmentation would increase in species experiencing precipitation
 declines, vapor pressure deficit (VPD; a metric of aridity) increases, and
 temperature declines. We found that the frequency of populations with
 pigmented morphs increased temporally in some taxa but displayed subtle
 declines in others. Pigmentation was negatively associated with
 temperature and positively associated with VPD across taxa. Species
 experiencing larger temperature increases over time became less pigmented,
 while those experiencing increases in aridity became more pigmented. Rapid
 change in anthocyanin-based color polymorphisms is thus linked with
 climatic change. Altered flower coloration spurred by abiotic change has
 the strong potential to impact plant-animal interactions and overall plant
 reproductive performance.
DOI: 10.15468/dl.pw7rcn
title: Occurrence Download

description: A dataset containing 1988 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Plasmopara viticola",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1988 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002636-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.12jm63xwg
title: Interspecific variation in evaporative water loss and temperature response, but not metabolic rate, among hibernating bats

description: Hibernation is widespread among mammals in a variety of environmental
 contexts. However, few experimental studies consider interspecific
 comparisons, and for many unstudied (or understudied) species we must
 assume the underlying physiology of hibernation is comparable to the
 relatively few species that have been studied in detail. Studies of
 interspecific variation provide insight into general patterns of
 hibernation strategies. We studied 13 species of free-living bats,
 including populations spread over thousands of kilometers and diverse
 habitats. We measured torpid metabolic rate and evaporative water loss
 (two key parameters for understanding hibernation energetics) across a
 range of temperatures. Response to ambient temperature varied among
 species, but all species achieved similar minimum torpid metabolic rate.
 Conversely,  evaporative water loss varied among species and our
 results suggest two general hibernation strategies in North American bats,
 representing high and low evaporative water loss groups. Notably, species
 that have suffered population declines due to white-nose syndrome fall in
 the high evaporative water loss group and less affected species in the low
 evaporative water loss group. Documenting general patterns of
 physiological diversity, and associated ecological implications,
 contributes to broader understanding of biodiversity, and may help predict
 which species are at greater risk of environmental and anthropogenic
 stressors.
DOI: 10.5061/dryad.6t1g1jwxd
title: The incidence and prevalence of drug resistant epilepsy: a systematic review and meta-analysis

description: Objective: In order to evaluate the incidence and prevalence of
 drug-resistant epilepsy (DRE) as well as its predictors and correlates, we
 conducted a systematic review and meta-analysis of observational studies.
 Methods: Our protocol was registered with PROSPERO and the PRISMA and
 MOOSE reporting standards were followed. We searched MEDLINE, Embase, and
 Web of Science. We used a double arcsine transformation and random-effects
 models to carry out our meta-analyses. We performed random-effects
 meta-regressions using study-level data. Results: Our search strategy
 identified 10,794 abstracts. Of these, 103 articles met our eligibility
 criteria. There was high inter-study heterogeneity and risk of bias. The
 cumulative incidence of DRE was 25.0 % (95% CI: 16.8, 34.3) in child
 studies but 14.6% (95% CI: 8.8, 21.6) in adult/mixed ages studies. The
 prevalence of DRE was 13.7% (95% CI: 9.2, 19.0) in
 population/community-based populations but 36.3% (95% CI: 30.4, 42.4) in
 clinic-based cohorts. Meta-regression confirmed that the prevalence of DRE
 was higher in clinic-based populations and in focal epilepsy. Multiple
 predictors and correlates of DRE were identified. The most reported of
 these were having a neurological deficit, an abnormal EEG, and symptomatic
 epilepsy. The most reported genetic predictors of DRE were polymorphisms
 of the ABCB1 gene. Conclusions: Our observations provide a basis for
 estimating the incidence and prevalence of DRE, which vary between
 populations. We identified numerous putative DRE predictors and
 correlates. These findings are important to plan epilepsy services,
 including epilepsy surgery, a crucial treatment option for people with
 disabling seizures and DRE.
DOI: 10.5068/d1gd5f
title: Odor boosts visual object approach in flies

description: Multisensory integration is synergistic - input from one sensory modality
 might modulate the behavioral response to another. Work in flies has shown
 that a small visual object presented in the periphery elicits innate
 aversive steering responses in flight, likely representing an approaching
 threat. Object aversion is switched to approach when paired with a plume
 of food odor. The ‘open loop’ design of prior work facilitated the
 observation of changing valence. How does odor influence visual object
 responses when an animal has naturally active control over it’s visual
 experience? In this study, we use closed loop feedback conditions, in
 which a fly’s steering effort is coupled to the angular velocity of the
 visual stimulus, to confirm that flies steer toward or ‘fixate’ a long
 vertical stripe on visual midline. They tend to either steer away from or
 ‘anti-fixate’ a small object or to disengage active visual control, which
 manifests as uncontrolled object ‘spinning’ within this experimental
 paradigm. Adding a plume of apple cider vinegar decreases the probability
 of both antifixation and spinning, while increasing the probability of
 frontal fixation for objects of any size, including a normally aversive
 small object.
description: Please see the ReadMe file contained within the analysis
 package.
DOI: 10.5061/dryad.2547d7wpc
title: Middle Eocene terrestrial paleoweathering and climate evolution in the midlatitude Bohai Bay Basin of Eastern China

description: The middle Eocene is a key time period for understanding Cenozoic cooling
 of the global climate. In eastern Asia, this time period was marked by
 deposition of extensive mudstones, shales and interbedded siltstones,
 especially in the midlatitude Bohai Bay Basin. Still, midlatitude
 terrestrial records of climate evolution during the middle Eocene are
 rare. Here, we analyze a continuous, high-resolution record of this period
 using samples of the shales in the fourth submember of the third member
 from the mid-Eocene Shahejie Formation (MES shales) in the Bohai Bay Basin
 using major-element and wavelet analysis. We use this information to
 derive insights into terrestrial paleoweathering and paleoclimatic
 evolution during the mid-Eocene in this midlatitude region. As a result of
 element mobility during continental weathering, the MES shales are more
 enriched in Ca and depleted in Na compared to average upper continental
 crust (UCC). The MES shales experienced moderate paleoweathering with
 limited K-metasomatism under a subtropical monsoon paleoclimate with mean
 annual temperature (MAT) of 8.3-12.9 °C and mean annual precipitation
 (MAP) of 685-1100 mm/yr. The MES shales record a mixed provenance
 involving intermediate igneous rocks, and low compositional maturity. The
 nutrient-rich environment led to enrichment in organic matter in the MES
 shales. We divide the depositional process of the MES shales into two
 stages that represent distinct climates. In stage I, the paleolake was
 high in nutrients, and the MES shales experienced high chemical weathering
 due to a relatively warmer and more humid climate. In contrast, the
 climate in stage II was relatively cold and dry, and the maturity of the
 MES shales was relatively high during this stage, suggesting a relatively
 stable tectonic background.