cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18389209
title: JSAP v1.0 Experimental Logs: Constructive Alignment via Judge–Shift and Anchor Density

description: JSAP v1.0 Experimental Logs

This dataset contains reproducible experimental logs for the Judge–Shift Alignment Protocol (JSAP v1.0), a constructive alignment method that constrains model judgments through explicit anchor-trace mapping and external-anchor density thresholds.

Package Contents





Protocol specification (one-pager)




Fixed test set (20 items across empirical, rule-based, and ethical domains)




System prompt template with mandatory output format




Raw model outputs (JSONL) for all three experimental phases




Quantitative compliance metrics



Models Tested




Model
Vendor
JSAP Compliance




Copilot Deep Research
Microsoft
1.00 🏆


Gemini 1.5 Flash
Google
0.95


Llama 3.1
Meta
0.94


Claude Opus 4.5
Anthropic
0.93


GPT-4o
OpenAI
0.91


GPT-5.2 Thinking
OpenAI
0.91


Perplexity
Perplexity
0.90


Claude Sonnet 4
Anthropic
0.79


GPT-5.2 Auto
OpenAI
0.73




Key Findings





9 models from 6 vendors tested




JSAP Compliance range: 0.73–1.00




7/9 models achieve ≥0.90 compliance




Trace Score explains 43% of model variance




OSS matches proprietary: Llama 3.1 (0.94) ≈ Claude Opus 4.5 (0.93)



Scientific Contribution

This release provides the first cross-model empirical evidence that:





A deterministic external-anchor density threshold (D_ext < θ) can forcibly suppress confident judgments at the output level




This suppression operates without access to internal representations or training-time modification




The mechanism functions consistently across multiple vendors and architectures



License

CC-BY-4.0
DOI: 10.5061/dryad.nm08t34
title: Data from: Grazers affect selection on inflorescence height both directly and indirectly and effects change over time

description: Selection mediated by one biotic agent will often be modified by the
 presence of other biotic interactions, and the importance of such indirect
 effects might change over time. We conducted an 11-year field experiment
 to test the prediction that large grazers affect selection on floral
 display of the dimorphic herb Primula farinosa not only directly through
 differential grazing damage, but also indirectly by affecting vegetation
 height and thereby selection mediated by pollinators and seed predators.
 Exclusion of large grazers increased vegetation height and the strength of
 pollinator-mediated selection for tall inflorescences and seed
 predator-mediated selection for short inflorescences. The direct effect of
 grazers on selection resulting from differential grazing damage to the two
 scape morphs showed no temporal trend. By contrast, the increase in
 vegetation height in exclosures over time was associated with an increase
 in selection mediated by pollinators and seed predators. In the early
 years of the experiment, the indirect effects of grazers on selection
 mediated by pollinators and seed predators were weak, whereas at the end
 of the experiment, the indirect effects were of similar magnitude as the
 direct effect due to differential grazing damage. The results demonstrate
 that the indirect effects of a selective agent can be as strong as its
 direct effects, and that the relative importance of direct vs. indirect
 effects on selection can change over time. A full understanding of the
 ecological processes governing variation in selection thus requires that
 both direct and indirect effects of biotic interactions are assessed.
description: Thomann et al. Ecology -
 DataThis file includes 1.
 Estimates of pollinator-mediated, seed-predator-mediated, grazer-mediated,
 and net selection on scape morph for each site x treatment x year
 combination. 2. Difference in estimates of selection on scape morph
 between exclosure and control for each site x year combination. 3.
 Vegetation height (cm) for each site x treatment x year combination. 4.
 Difference in vegetation height between exclosure and control for each
 site x year combination.
DOI: 10.5061/dryad.rn72k04
title: Data from: Host use dynamics in a heterogeneous fitness landscape generates oscillations in host range and diversification

description: Colonization of novel hosts is thought to play an important role in
 parasite diversification, yet little consensus has been achieved about the
 macroevolutionary consequences of changes in host use. Here we offer a
 mechanistic basis for the origins of parasite diversity by simulating
 lineages evolved in silico. We describe an individual-based model in which
 (i) parasites undergo sexual reproduction limited by genetic proximity,
 (ii) hosts are uniformly distributed along a one-dimensional resource
 gradient, and (iii) host use is determined by the interaction between the
 phenotype of the parasite and a heterogeneous fitness landscape. We found
 two main effects of host use on the evolution of a parasite lineage.
 First, the colonization of a novel host allowed parasites to explore new
 areas of the resource space, increasing phenotypic and genotypic
 variation. Second, hosts produced heterogeneity in the parasite fitness
 landscape, which led to reproductive isolation and therefore, speciation.
 As a validation of the model, we analyzed empirical data from Nymphalidae
 butterflies and their host plants. We then assessed the number of hosts
 used by parasite lineages and the diversity of resources they encompass.
 In both simulated and empirical systems, host diversity emerged as the
 main predictor of parasite species richness.
description: simulated_dataData produced by the model described in the paper and used for statistical analyses.nymphalidae_dataButterfly data used for phylogenetic path analysis.
DOI: 10.5061/dryad.10m4k6q
title: Data from: Identification of biomarkers for Barcelona Clinic Liver Cancer staging and overall survival of patients with hepatocellular carcinoma

description: The aim of the current study was to identify biomarkers that correlate
 with the Barcelona Clinic Liver Cancer (BCLC) staging system and prognosis
 of patients with hepatocellular carcinoma (HCC). We downloaded 4 gene
 expression datasets from the Gene Expression Omnibus database
 (http://www.ncbi.nlm.nih.gov/geo), and screened for genes that were
 differentially expressed between HCC and normal liver tissues, using
 significance analysis of the microarray algorithm. We used a weighted gene
 co-expression network analysis (WGCNA) to identify hub genes that
 correlate with BCLC staging, functional enrichment analysis to associate
 hub genes with their functions, protein-protein interaction network
 analysis to identify interactions among hub genes, UALCAN analysis to
 assess gene expression levels based on tumour stage, and survival analyses
 to clarify the effects of hub genes on patients' overall survival
 (OS). We identified 50 relevant hub genes using WGCNA; among them, 13
 genes (including TIGD5, C8ORF33, NUDCD1, INSB8, and STIP1) correlated with
 OS and BCLC staging. Significantly enriched gene ontology biological
 process terms included RNA processing, non-coding RNA processing and
 phosphodiester bond hydrolysis, and 6 genes were found to interact with 10
 or more hub genes. We identified several candidate biomarkers that
 correlate with BCLC staging and OS of HCC. These genes might be used for
 prognostic assessment and selection of HCC patients for surgery,
 especially those with intermediate or advanced disease.
description: Gene expressions mapped
 with probes in GSE76427A combined 3 sets of
 differentially expressed genes, a total of 3315 genes, of which 1573 were
 upregulated, were regarded as hepatocellular carcinoma related
 differentially expressed genes for analysis. Among them, 1568 gene
 expressions mapped to probes in GSE76427 (S1 Table), which contained
 pre-processed raw data used for WGCNA in our research.S1_Table.xlsxExternal clinical traits of GSE76427External clinical traits of GSE76427, used for WGCNA in our research.S2_Table.xlsxGene significance and module membership based on WGCNABased on gene significance and module membership, the top 50 core genes in the Green module were regarded as hub genes.S3_Table.xlsx
DOI: 10.5061/dryad.kb505nc
title: Data from: EPA-ng: massively parallel evolutionary placement of genetic sequences

description: Next Generation Sequencing (NGS) technologies have led to a ubiquity of
 molecular sequence data. This data avalanche is particularly challenging
 in metagenetics, which focuses on taxonomic identification of sequences
 obtained from diverse microbial environments. Phylogenetic placement
 methods determine how these sequences fit into anevolutionary context.
 Previous implementations of phylogenetic placement algorithms, such as the
 Evolutionary Placement Algorithm (EPA) included in RAxML, or pplacer, are
 being increasingly used for this purpose. However, due to the steady
 progress in NGS technologies, the current implementations face substantial
 scalability limitations. Here we present EPA-ng, a complete
 reimplementation of the EPA that is substantially faster, offers a
 distributed memory parallelization, and integrates concepts from both,
 RAxML-EPA and pplacer. EPA-ng can be executed on standard shared memory,
 as well as on distributed memory systems (e.g., computing clusters). To
 demonstrate the scalability of EPA-ng we placed 1 billion metagenetic
 reads from the Tara Oceans Project onto a reference tree with 3,748 taxa
 in just under 7 hours, using 2,048 cores. Our performance assessment shows
 that EPA-ng outperforms RAxML-EPA and pplacer by up to a factor of 30 in
 sequential execution mode, while attaining comparable parallel efficiency
 on shared memory systems. We further show that the distributed memory
 parallelization of EPA-ng scales well up to 2,048 cores. EPA-ng is
 available under the AGPLv3 license: https://github.com/Pbdas/epa-ng
description: "neotrop",
 "bv" and "tara" datasets used in the evaluation part
 of the main paper.Reference
 trees/alignments, as well as query data, for the "neotrop",
 "bv" and "tara" data sets. Made available with
 permission from the respective authors (see contained readme files for
 citation information!).datasets.zipSupplement PDF to the main textSupplementary information.supplement.pdf
DOI: 10.5061/dryad.dr34q6v
title: Data from: Interspecific variation in conspecific negative density dependence can make species less likely to coexist

description: Conspecific negative density dependence (CNDD) is thought to promote plant
 species diversity. Theoretical studies showing the importance of CNDD
 often assumed that all species are equally susceptible to CNDD; however,
 recent empirical studies have shown species can differ greatly in their
 susceptibility to CNDD. Using a theoretical model, we show that
 interspecific variation in CNDD can dramatically alter its impact on
 diversity. First, if the most common species are the least regulated by
 CNDD, then the stabilising benefit of CNDD is reduced. Second, when seed
 dispersal is limited, seedlings that are susceptible to CNDD are at a
 competitive disadvantage. When parameterised with estimates of CNDD from a
 tropical tree community in Panama, our model suggests that the competitive
 inequalities caused by interspecific variation in CNDD may undermine many
 species’ ability to persist. Thus, our model suggests that variable CNDD
 may make communities less stable, rather than more stable.
description: Code for running
 simulationsThis is a .zip file that
 contains all of the code for running the simulations described in our
 paper. The code was run using Matlab 2017.code_for_simulations.zipData and code for producing figuresThis is a .zip file which contains the simulation data used to make the figures in our paper. It also contains data that was synthesized from two other sources, used to describe the impact of CNDD on species in Panama. The file also contains code which will produce all of the figures in our paper.code_and_data_for_figures.zip
DOI: 10.5061/dryad.gd86rn1
title: Data from: Community phylogeny of the globally critically imperiled pine rockland ecosystem

description: Premise of the study: Community phylogenetic methods incorporate
 information on evolutionary relationships into studies of organismal
 assemblages. We used a community phylogenetic framework to investigate
 relationships and biogeographic affinities and calculate phylogenetic
 signal of endemism and invasiveness for the flora of the pine rocklands, a
 globally critically imperiled ecosystem with a significant portion of its
 distribution in South Florida, United States. Methods: We reconstructed
 phylogenetic relationships of 538 vascular plant taxa, which represents
 92.28% of the vascular flora of the pine rocklands. We estimated
 phylogenetic signal for endemism and invasiveness using phylogenetic
 generalized linear mixed models. We determined the native range for each
 species in the dataset and calculated the total number of species sourced
 from each region and all possible combinations of these regions. Key
 results: The pine rockland flora includes representatives of all major
 vascular plant lineages, and most species have native ranges in the New
 World. There was strong phylogenetic signal for endemism, but not for
 invasiveness. Conclusions: Community phylogenetics has high potential
 value for conservation planning, particularly for fragmented and
 endangered ecosystems like the pine rockland. Strong phylogenetic signal
 for endemic species in our dataset, which also tend to be threatened or
 endangered, can help to identify species at risk as well as fragments
 where those species occur highlighting conservation priorities. Our
 results indicate, at least in the pine rockland ecosystem, no phylogenetic
 signal for invasive species, and thus other information must be used to
 predict the potential for invasiveness.
description: PineRockland Beast
 XMLThis XML file contains
 an alignment (rbcL, matK, psbA-trnH) of 540 pine rockland plant taxa as
 well as the hyperpriors used to estimate a community phylogeny in BEAST.
 This analysis included taxonomic and topological constraints implemented
 with a starting tree and in BEAST, as well as nine fossil
 constraints.Trotta_PineRockland.xmlPine Rockland Community PhylogenyThis file is a maximum clade credibility (MCC) phylogeny resulting from a BEAST analysis of 540 pine rockland plant taxa in nexus (.nex) format.Trotta_PR_MCCPhylo.nex
DOI: 10.5061/dryad.7tp3sg0
title: Data from: Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise

description: Population genetic theory related to the consequences of rapid population
 decline is well-developed, but there are very few empirical studies where
 sampling was conducted before and after a known bottleneck event. Such
 knowledge is of particular importance for species restoration, given links
 between genetic diversity and the probability of long-term persistence. To
 directly evaluate the relationship between current genetic diversity and
 past demographic events, we collected genome-wide single nucleotide
 polymorphism data from pre-bottleneck historical (c.1906) and
 post-bottleneck contemporary (c.2014) samples of Pinzón giant tortoises
 (Chelonoidis duncanensis; n=25 and 149 individuals, respectively) endemic
 to a single island in the Galapagos. Pinzón giant tortoises had a
 historically large population size that was reduced to just 150-200
 individuals in the mid 20th century. Since then, Pinzón’s tortoise
 population has recovered through an ex situ head-start program in which
 eggs or pre-emergent individuals were collected from natural nests on the
 island, reared ex situ in captivity until they were 4-5 years old, and
 subsequently repatriated. We found that the extent and distribution of
 genetic variation in the historical and contemporary samples was very
 similar, with the latter group not exhibiting the characteristic genetic
 patterns of recent population decline. No population structure was
 detected either spatially or temporally. We estimated an effective
 population size (Ne) of 58 (95% CI = 50-69) for the post-bottleneck
 population; no pre-bottleneck Ne point estimate was attainable (95% CI =
 39-infinity) likely due to the sample size being lower than the true Ne.
 Overall, the historical sample provided a valuable benchmark for
 evaluating the head-start captive breeding program, revealing high
 retention of genetic variation and no skew in representation despite the
 documented bottleneck event. Moreover, this work demonstrates the
 effectiveness of head-starting in rescuing the Pinzón giant tortoise from
 almost certain extinction.
description: SNP genotypic data for
 the contemporary sample of Pinzón Galapagos giant tortoises (Chelonoidis
 duncanensis)vcf file containing SNP
 genotypic data at 7,730 loci for the contemporary population sample (n =
 149) of the Galapagos giant tortoises endemic to Pinzón Island
 (Chelonoidis duncanensis)Jensen_contemporary_7730loci.vcfSNP genotypic data for the contemporary and historical samples of Pinzón Galapagos giant tortoises (Chelonoidis duncanensis)vcf file containing SNP genotypic data at 2,218 loci for the historical (n = 25) and contemporary (n = 149) population samples of the Galapagos giant tortoises endemic to Pinzón Island (Chelonoidis duncanensis)Jensen_historical_contemporary_2218loci.vcf
DOI: 10.5061/dryad.db430s1
title: Data from: Historical data for conservation: reconstructing range changes of Chinese pangolin (Manis pentadactyla) in eastern China (1970-2016)

description: The Chinese pangolin (Manis pentadactyla) has long suffered from intense
 exploitation driven by consumer demand for medicinal use and food.
 Effective conservation management is hampered by insufficient data on
 pangolin status and distribution. We integrated ecological niche modeling
 with long-term ecological records at the local scale (e.g. from local
 historical documents, grey and published literature and interviews) to
 estimate the magnitude of potential distribution change of the Chinese
 pangolin in eastern China (Fujian, Jiangxi and Zhejiang provinces) over
 time. Our results suggest that the range of the species decreased by
 52.20% between the 1970s and early 2000s, and that the population is now
 mainly confined to the Wuyi Mountains. This reduction in potential
 distribution range is attributable to anthropogenic pressures. According
 to our conservation prioritization analysis, the priority conservation
 area for the Chinese pangolin in eastern China is 51,268.4 km2, 5.62% of
 which is covered by nature reserves. There are 18 nature reserves and 46
 prefectures which are priority areas for conservation in China. The
 priority-level nature reserves and prefectures in eastern China are mainly
 located in the center of the Wuyi Mountains, and areas declared important
 tend to be around the Wuyi Mountains. We propose several actions to
 improve the conservation status of this species: establish or enlarge
 nature reserves, ensure local governments at the prefecture level
 prioritizes conservation management, and encourage local communities to
 participate in pangolin conservation.
description: data_for_PangolinClimate data and geographic data used in different generations. The study area is in eastern China and comprises three provinces, Fujian Province, Jiangxi Province, and Zhejiang Province. Climate data (mean annual temperature, MAT; mean annual precipitation, MAP; the number of frost-free days, NFFD; Hargreaves reference evaporation, Eref) were downloaded from Climate AP v2.03 (http://climateap.net/) and were created by ANUSPLIN ver. 4.36 and Excel 2013 (Microsoft Corp., Redmond, WA, USA); topography data (elevation and aspect) were obtained from the SRTM 90m Digital Elevation Database (http://srtm.csi.cgiar.org/) and were conducted in ArcGIS (ver. 10.2; ESRI, Inc., Redlands, CA, USA); forested and urban land were extracted from land cover data (dataset provided by the Data Center for Resources and Environmental Sciences, Chinese Academy of Sciences [RESDC; http://www.resdc.cn]) and were conducted in ArcGIS (ver. 10.2; ESRI, Inc., Redlands, CA, USA).
DOI: 10.5061/dryad.16kk001
title: Data from: Richness, geographic distribution patterns, and areas of endemism of selected angiosperm groups in Mexico

description: Mexico is a megadiverse country. Presently, 22 126 species of angiosperms
 have been registered within its territory and 11 001 are considered to be
 endemic. However, their geographical distributions are far from
 homogeneous. In addition, Mexico is the center of diversification of
 several groups. Our analysis focused on such groups. The aims were to
 identify areas of species richness and endemism. A data matrix with 766
 species and 25 579 geographical records was analyzed. It included
 Calochortus (Liliaceae); Bletia (Orchidaceae); Tigridieae (Iridaceae);
 Amaryllidaceae; Poliantheae, Echeandia (Asparagaceae); Crassulaceae;
 Hylocereus (Cactaceae); Solanum, Lycianthes and Physalinae (Solanaceae);
 Salvia section Membranaceae (Lamiaceae); and Cosmos and Dahlia
 (Asteraceae). Using Geographic Information Systems, we determined richness
 and distribution based on: 1) Mexican political divisions, 2)
 biogeographical regions and provinces, 3) a grid of 0.5 × 0.5° cells, and
 4) elevation. The areas of endemism were estimated using the endemicity
 analysis. The highest number of taxa and endemic plants were concentrated
 within the Transmexican Volcanic Belt in the Mexican Transition Zone. This
 mountain range has been recognized as a province on the basis of geologic,
 tectonic, geomorphologic, physiographic and biogeographic criteria. It is
 a 1 000 km long volcanic arc that extends east to west through Central
 Mexico and is variably from 80 to 230 km wide, between 17°30' to
 20°25'N and 96°20' to 105°20'W. Our results represent a
 local deviation from the global richness latitudinal gradient of
 angiosperm species.
description: S1 Data
 baseDatabase with 15539
 geographical records
DOI: 10.5061/dryad.m9j93jg
title: Data from: Perceptual teleology: expectations of action efficiency bias social perception

description: Primates interpret conspecific behaviour as goal-directed and expect
 others to achieve goals by the most efficient means possible. While this
 teleological stance is prominent in evolutionary and developmental
 theories of social cognition, little is known about the underlying
 mechanisms. In predictive models of social cognition, a perceptual
 prediction of an ideal efficient trajectory would be generated from prior
 knowledge against which the observed action is evaluated, distorting the
 perception of unexpected inefficient actions. To test this, participants
 observed an actor reach for an object with a straight or arched trajectory
 on a touch screen. The actions were made efficient or inefficient by
 adding or removing an obstructing object. The action disappeared
 mid-trajectory and participants touched the last seen screen position of
 the hand. Judgments of inefficient actions were biased toward the
 efficient prediction (straight trajectories upward to avoid the
 obstruction, arched trajectories downward towards the target). These
 corrections increased when the obstruction’s presence/absence was
 explicitly acknowledged, and when the efficient trajectory was explicitly
 predicted. Additional supplementary experiments demonstrated that these
 biases occur during on-going visual perception and/or immediately after
 motion offset. The teleological stance is at least partly perceptual,
 providing an ideal reference trajectory against which actual behaviour is
 evaluated.
description: MainExperiment_DataMain Experiment 1: Raw and Summary data, Demographic Information, Exclusion CriteriaSuppExperiment1_DataSupplementary Experiment 1: Raw and Summary data, Demographic Information, Exclusion CriteriaSuppExperiment2_DataSupplementary Experiment 2: Raw and Summary data, Demographic Information, Exclusion CriteriaSuppExperiment3_DataSupplementary Experiment 3: Raw and Summary data, Demographic Information, Exclusion Criteria