cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/ddr5h589xt.1
title: Brief Report: A pharmacokinetic study of single-dose periungual methotrexate injections that induced multi month remission of Nail Psoriasis in five patients.

description: This dataset contains supplementary methods and results for the article "Brief Report: A pharmacokinetic study of single-dose periungual methotrexate injections that induced multi month remission of Nail Psoriasis in five patients.", published to Journal of American Academy of Dermatology .
DOI: 10.5061/dryad.bg79cnpfb
title: Data for: Antigen footprint governs activation of the B cell receptor

description: Antigen binding by B cell receptors (BCR) on cognate B cells elicits a
 response that eventually leads to production of antibodies. However, it is
 unclear what the distribution of BCRs is on the naïve B cell and how
 antigen binding triggers the first step in BCR signaling. Using DNA-PAINT
 super-resolution microscopy, we find that most BCRs are present as
 monomers, dimers, or loosely associated clusters on resting B cells, with
 a nearest-neighbor inter-Fab distance of 20-30 nm. We leverage a Holliday
 junction nanoscaffold to engineer monodisperse model antigens with
 precision-controlled affinity and valency, and find that the antigen
 exerts agonistic effects on the BCR as a function of increasing affinity
 and avidity. Monovalent macromolecular antigens can activate the BCR at
 high concentrations, whereas micromolecular antigens cannot, demonstrating
 that antigen binding does not directly drive activation. Based on this, we
 propose a BCR activation model determined by the antigen footprint.
description: Please see the README document ("README.md") and the
 accompanying published article: Ferapontov et al. 2023. Antigen footprint
 governs activation of the B cell receptor. Nature
 Communications.
description: Please see the README document ("README.md") and the
 accompanying published article: Ferapontov et al. 2023. Antigen footprint
 governs activation of the B cell receptor. Nature
 Communications.
DOI: 10.5061/dryad.0zpc86727
title: Data for: High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display

description: Tyrosine kinases and SH2 (phosphotyrosine recognition) domains have
 binding specificities that depend on the amino acid sequence surrounding
 the target (phospho)tyrosine residue. Although the preferred recognition
 motifs of many kinases and SH2 domains are known, we lack a quantitative
 description of sequence specificity that could guide predictions about
 signaling pathways or be used to design sequences for biomedical
 applications. Here, we present a platform that combines
 genetically-encoded peptide libraries and deep sequencing to profile
 sequence recognition by tyrosine kinases and SH2 domains. We screened
 several tyrosine kinases against a million-peptide random library and used
 the resulting profiles to design high-activity sequences. We also screened
 several kinases against a library containing thousands of human
 proteome-derived peptides and their naturally-occurring variants. These
 screens recapitulated independently measured phosphorylation rates and
 revealed hundreds of phosphosite-proximal mutations that impact
 phosphosite recognition by tyrosine kinases. We extended this platform to
 the analysis of SH2 domains and showed that screens could predict relative
 binding affinities. Finally, we expanded our method to assess the impact
 of non-canonical and post-translationally modified amino acids on sequence
 recognition. This specificity profiling platform will shed new light on
 phosphotyrosine signaling and could readily be adapted to other protein
 modification/recognition domains.
description: These data were collected as described in the methods sections of
 the associated manuscript. After peptide display, selection, and
 paired-end Illumina deep sequencing (using a MiSeq or NextSeq), paired-end
 reads were merged using the software FLASH (version FLASH2-2.2.00, PMID:
 21903629), trimmed using Cutadapt (version 3.5, DOI:
 10.14806/ej.17.1.200), and then further processed using in-house Python
 code (https://github.com/nshahlab/2022_Li-et-al_peptide-display).
description: FLASH (version FLASH2-2.2.00, PMID: 21903629), trimmed using
 Cutadapt (version 3.5, DOI: 10.14806/ej.17.1.200), and then further
 processed using in-house Python code (https://github.com/nshahlab/2022_Li-et-al_peptide-display).
DOI: 10.5281/zenodo.17382444
title: Operationalizing AI Ethics in the Public Sector: A Cross-Context Replication in Brazil

description:  Background: AI ethics encompasses principles such as privacy, fairness, transparency, accountability, and safety that guide the responsible design and use of AI systems. Responsible AI (RAI) translates these principles into actionable practices across the AI lifecycle. In Brazil, the General Data Protection Law (LGPD) provides a privacy baseline, but there is no national AI ethics framework; meanwhile, Generative AI (GenAI) introduces new socio-technical and governance risks.  Objective: This study replicates and extends  the research by Pant et al. [24] to examine how Brazilian public organizations perceive, interpret, and implement AI ethics. It aims to identify awareness levels, institutional governance maturity, and capability gaps in the context of GenAI adoption. Method. A mixed-method, cross-sectional survey was conducted with 87 civil servants from federal, state, and municipal agencies. The questionnaire adapted Pant et al.’s instrument to the Brazilian context, incorporating LGPD references and GenAI-specific items. Quantitative data were analyzed descriptively, while open-ended responses underwent qualitative content analysis with open coding and constant comparison. Results. Awareness of AI ethics is moderate and concentrated on compliance-oriented principles, whereas participatory dimensions such as Fairness and Contestability remain limited. Governance maturity is low: only 18.6% of organizations have dedicated ethics roles or committees, and over half report never conducting training. Perceived GenAI risks are high across ethics, privacy, and data protection. The main barriers include a lack of AI knowledge, the absence of AI-specific regulation for privacy and data protection, and limited tools to apply LGPD principles. A comparison with Pant et al. shows that, while both studies identify an awareness–practice gap, its cause in Brazil lies primarily in institutional governance immaturity rather than practitioner capability. Conclusion. Brazilian public organizations demonstrate growing recognition of AI ethics but face structural barriers to operationalization. Advancing toward Responsible and Trustworthy AI requires institutional scaffolding—ethics roles, policies, and training programs—alongside regulatory clarification to align GenAI governance with LGPD principles. The study contributes cross-context empirical evidence on AI ethics governance in the Global South and outlines practical levers for embedding ethics-by-design in public-sector AI initiatives.
DOI: 10.5281/zenodo.17382443
title: Operationalizing AI Ethics in the Public Sector: A Cross-Context Replication in Brazil

description:  Background: AI ethics encompasses principles such as privacy, fairness, transparency, accountability, and safety that guide the responsible design and use of AI systems. Responsible AI (RAI) translates these principles into actionable practices across the AI lifecycle. In Brazil, the General Data Protection Law (LGPD) provides a privacy baseline, but there is no national AI ethics framework; meanwhile, Generative AI (GenAI) introduces new socio-technical and governance risks.  Objective: This study replicates and extends  the research by Pant et al. [24] to examine how Brazilian public organizations perceive, interpret, and implement AI ethics. It aims to identify awareness levels, institutional governance maturity, and capability gaps in the context of GenAI adoption. Method. A mixed-method, cross-sectional survey was conducted with 87 civil servants from federal, state, and municipal agencies. The questionnaire adapted Pant et al.’s instrument to the Brazilian context, incorporating LGPD references and GenAI-specific items. Quantitative data were analyzed descriptively, while open-ended responses underwent qualitative content analysis with open coding and constant comparison. Results. Awareness of AI ethics is moderate and concentrated on compliance-oriented principles, whereas participatory dimensions such as Fairness and Contestability remain limited. Governance maturity is low: only 18.6% of organizations have dedicated ethics roles or committees, and over half report never conducting training. Perceived GenAI risks are high across ethics, privacy, and data protection. The main barriers include a lack of AI knowledge, the absence of AI-specific regulation for privacy and data protection, and limited tools to apply LGPD principles. A comparison with Pant et al. shows that, while both studies identify an awareness–practice gap, its cause in Brazil lies primarily in institutional governance immaturity rather than practitioner capability. Conclusion. Brazilian public organizations demonstrate growing recognition of AI ethics but face structural barriers to operationalization. Advancing toward Responsible and Trustworthy AI requires institutional scaffolding—ethics roles, policies, and training programs—alongside regulatory clarification to align GenAI governance with LGPD principles. The study contributes cross-context empirical evidence on AI ethics governance in the Global South and outlines practical levers for embedding ethics-by-design in public-sector AI initiatives.
DOI: 10.5061/dryad.08kprr567
title: Evaluating niche changes during invasion with seasonal models in Capsella bursa‐pastoris

description: Premise Researchers often use ecological niche models to predict where
 species might establish and persist under future or novel climate
 conditions. However, these predictive methods assume species have stable
 niches across time and space. Furthermore, ignoring the time of occurrence
 data can obscure important information about species reproduction and
 ultimately fitness. Here, we assess and compare ecological niche models
 generated from full-year averages to seasonal models  Methods In
 this study, we generate full-year and monthly ecological niche models for
 Capsella bursa-pastoris in Europe and North America to see if we can
 detect changes in the seasonal niche of the species after long-distance
 dispersal.  Key Results We find full-year ecological niche models
 have low transferability across continents and there are continental
 differences in the climate conditions that influence the distribution of
 C. bursa-pastoris. Monthly models have greater predictive accuracy than
 full-year models in cooler seasons but no monthly models are able to
 predict North American summer occurrences very well. Conclusions The
 relative predictive ability of European monthly models compared to North
 American monthly models suggests a change in the seasonal timing between
 the native range to the non-native range. These results highlight the
 utility of ecological niche models at finer temporal scales in predicting
 species distributions and unmasking subtle patterns of evolution.
description: Here, we present the mean Partial Area Under the Curve (pAUC)
 value for comparisons of European monthly models on North American
 occurrences. We evaluated the performance of models using a pAUC analysis
 to focus on the most informative metrics of predictive ability for our
 study. We chose an admissible omission error rate of 0.15 for each model
 and 300 bootstrapped iterations. We evaluated the European models’
 predictive ability on North American occurrences of <em>C.
 bursa-pastoris</em> to test for a seasonal niche shift. Each month
 of North American occurrences was evaluated against all twelve models
 resulting in 144 evaluations of the European model's predictive
 ability on North American occurrence records.
DOI: 10.17632/9v4j8h43my
title: Preservice Teachers' Motivations to Become a Teacher and their Professional Qualifications

description: This dataset includes a total of 797 freshman preservice teachers' responses across 21 teacher education programs in different regions of Türkiye by employing non-random sampling approach. Data was collected with an online form given the widespread geographical location of 21 teacher education programs. (Respondents are 632 female, 158 male whereas seven participants chose not to disclose their gender). The average age for participants was 20,75 (SD=3,35).
DOI: 10.17632/9v4j8h43my.1
title: Preservice Teachers' Motivations to Become a Teacher and their Professional Qualifications

description: This dataset includes a total of 797 freshman preservice teachers' responses across 21 teacher education programs in different regions of Türkiye by employing non-random sampling approach. Data was collected with an online form given the widespread geographical location of 21 teacher education programs. (Respondents are 632 female, 158 male whereas seven participants chose not to disclose their gender). The average age for participants was 20,75 (SD=3,35).
DOI: 10.17632/x9c8yj325z
title: Characterisation of gas liquid two phase flow transition

description: The data set describes two phase flow characterisation in L shaped pipe.
DOI: 10.5061/dryad.qbzkh18nb
title: Data for: Endo-lysosomal assembly variations among Human Leukocyte Antigen class I (HLA-I) allotypes

description: The extreme polymorphisms of HLA-I proteins enable the presentation of
 diverse peptides to cytotoxic T lymphocytes (CTL). The canonical
 endoplasmic reticulum (ER) HLA-I assembly pathway enables presentation of
 cytosolic peptides, but effective intracellular surveillance requires
 multi-compartmental antigen sampling. Endo-lysosomes are generally sites
 of HLA class II assembly, but human monocytes and monocyte-derived
 dendritic cells (moDCs) also contain significant reserves of
 endo-lysosomal HLA-I molecules. We hypothesized variable influences of
 HLA-I polymorphisms upon outcomes of endo-lysosomal trafficking, as the
 stabilities and peptide occupancies of cell surface HLA-I are variable.
 Consistent with this model, when the endo-lysosomal pH of moDCs is
 disrupted, HLA-B allotypes display varying propensities for reductions in
 surface expression, with HLA-B*08:01 or HLA-B*35:01 being among the most
 resistant or sensitive respectively, among eight tested HLA-B allotypes.
 Perturbations of moDC endo-lysosomal pH result in redistribution of
 HLA-B*35:01, but not HLA-B*08:01, to LAMP1+ compartments and increase
 HLA-B*35:01 peptide receptivity. These findings reveal the intersection of
 the vacuolar cross-presentation pathway with a constitutive assembly
 pathway for some HLA-B allotypes. Notably, cross-presentation of epitopes
 derived from two soluble antigens was also more efficient for B*35:01
 compared to B*08:01, even when matched for T cell response sensitivity,
 and more affected by cathepsin inhibition. Thus, HLA-I polymorphisms
 dictate the degree of endo-lysosomal assembly, which can supplement ER
 assembly for constitutive HLA-I expression and increase the efficiency of
 cross-presentation.
description: Flow Cytometry, Microscopy and T cell assays.
description: Data can be accessed using FLow Jo and Image J.
DOI: 10.57745/eg2wai
title: 2019-09-16.tar
DOI: 10.17632/x9c8yj325z.1
title: Characterisation of gas liquid two phase flow transition

description: The data set describes two phase flow characterisation in L shaped pipe.
DOI: 10.57745/ls5ekz
title: 2019-09-17.tar
DOI: 10.57745/e5c3h6
title: 2019-09-18.tar
DOI: 10.57745/you7u5
title: 2019-09-19.tar
DOI: 10.5061/dryad.2fqz612t3
title: Data from: Evolutionary constraints mediate extinction risk under climate change

description: Mounting evidence suggests that rapid evolutionary adaptation may rescue
 some organisms from the impacts of climate change. However, evolutionary
 constraints might hinder this process, especially when different aspects
 of environmental change generate antagonistic selection on genetically
 correlated traits. Here, we use individual-based simulations to explore
 how genetic correlations underlying the thermal physiology of ectotherms
 might influence their responses to the two major components of climate
 change—increases in mean temperature and thermal variability. We found
 that genetic correlations can influence population dynamics under climate
 change, with declines in population size varying three-fold depending on
 the type of correlation present. Surprisingly, populations whose thermal
 performance curves were constrained by genetic correlations often declined
 less rapidly than unconstrained populations. Our results suggest that
 accurate forecasts of the impact of climate change on ectotherms will
 require an understanding of the genetic architecture of the traits under
 selection.
description: All data uploaded to this page was generated using
 individual-based simulations. The details on how it was generated can be
 found in the manuscript and in the code that is publically available in
 the following GitHub repository:
 https://github.com/ggcostoya/tpc_genetic_correlations
description: All metadata and instructions on the usage of this dataset is
 publically available in the following GitHub repository:
 https://github.com/ggcostoya/tpc_genetic_correlations
DOI: 10.57745/csqgoh
title: 2019-09-20.tar
DOI: 10.57745/ofjjmw
title: 2019-09-21.tar
DOI: 10.57745/0d2rnj
title: 2019-09-22.tar
DOI: 10.57745/9ltjmr
title: 2019-09-23.tar
DOI: 10.57745/kfnpj7
title: 2019-09-24.tar
DOI: 10.57745/dnwhud
title: 2019-09-25.tar
DOI: 10.57745/dixpau
title: README.md

description: :unav
DOI: 10.57745/uxcwoc
title: Corrected version of the DARPA OpTC dataset

description: There are some errors in the DARPA OpTC dataset (https://github.com/FiveDirections/OpTC-data) related to unique identifiers and some other properties of events. This dataset is a (partially) corrected version of the dataset that should be used instead of the original version. More information are available here: https://correctedoptc.inria.fr/
DOI: 10.7272/q6cf9nc5
title: Data for: Growth cone advance requires EB1 as revealed by genomic replacement with a light-sensitive variant

description: A challenge in analyzing dynamic intracellular cell biological processes
 is the dearth of methodologies that are sufficiently fast and specific to
 perturb intracellular protein activities. We previously developed a
 light-sensitive variant of the microtubule plus end-tracking protein EB1
 by inserting a blue light-controlled protein dimerization module between
 functional domains. Here, we describe an advanced method to replace
 endogenous EB1 with this light-sensitive variant in a single genome
 editing step, thereby enabling this approach in human induced pluripotent
 stem cells (hiPSCs) and hiPSC-derived neurons. We demonstrate that acute
 and local optogenetic EB1 inactivation in developing cortical neurons
 induces microtubule depolymerization in the growth cone periphery and
 subsequent neurite retraction. In addition, advancing growth cones are
 repelled from areas of blue light exposure. These phenotypes were
 independent of the neuronal EB1 homolog EB3, revealing a direct dynamic
 role of EB1-mediated microtubule plus end interactions in neuron
 morphogenesis and neurite guidance.
description: This dataset contains raw data and analysis used to produce
 figures and conclusions associated with bioRxiv/eLife manuscript. Detailed
 description of the data collection and analysis methodology can be found
 in the associated manuscript.
description: Raw microscopy data are provided as Nikon ND2 files that are
 native to Nikon Elements microscopy software. ND2 files can also be opened
 with ImageJ/Fiji with the Bioformats plugin (Note: metadata may not be
 imported correctly into ImageJ), or with a freely available Nikon Elements
 Viewer. Data analysis on which manuscript figures are
 based are provided as Microsoft Excel spreadsheets. Raw
 sequence data are provided in AB1 and SEQ file formats.
DOI: 10.5061/dryad.hx3ffbgjj
title: The climatic drivers of long-term population changes in rainforest montane birds

description: Climate-driven biodiversity erosion is escalating at an alarming rate. The
 pressure imposed by climate change is exceptionally high in tropical
 ecosystems, where species adapted to narrow environmental ranges exhibit
 strong physiological constraints. Despite the observed detrimental effect
 of climate change on ecosystems at a global scale, our understanding of
 the extent to which multiple climatic drivers affect population dynamics
 is limited. Here, we disentangle the impact of different climatic
 stressors on 47 rainforest birds inhabiting the mountains of the
 Australian Wet Tropics using hierarchical population models. We estimate
 the effect of spatiotemporal changes in temperature, precipitation,
 heatwaves, droughts, and cyclones on the population dynamics of rainforest
 birds between 2000–2016. We find a strong effect of warming and changes in
 rainfall patterns across the elevational-segregated bird communities, with
 lowland populations benefiting from increasing temperature and
 precipitation, while upland species show an inverse strong negative
 response to the same drivers. Additionally, we find a negative effect of
 heatwaves on lowland populations, a pattern associated with the observed
 distribution of these extreme events across elevations. In contrast,
 cyclones and droughts have a marginal effect on spatiotemporal changes in
 rainforest bird communities, suggesting a species-specific response
 unrelated to the elevational gradient. This study demonstrated the
 importance of unravelling the drivers of climate change impacts on
 population changes, providing significant insight into the mechanisms
 accelerating climate-induced biodiversity degradation.
DOI: 10.5061/dryad.kwh70rz7v
title: Data from: Leaf-cutting ant nests support less dense and impoverished seed assemblages in a human-modified Caatinga dry forest

description: Regenerating forests make up an increasingly large portion of tropical
 landscapes worldwide and regeneration dynamics may be influenced by
 leaf-cutting ants (LCA), which proliferate in disturbed areas and collect
 seeds for fungus culturing. Here we investigate how LCA influence seed
 fate in human-modified areas of Caatinga dry forest. We evaluate the seed
 deposition and predation on Atta opaciceps nests, foraging habitat
 surrounding nest and control habitat away of nest influence of 15 colonies
 located along a forest cover gradient during the rainy and dry season. For
 each habitat, four 50-cm2 plots were established and all seeds on the soil
 surface were collected along one year. We recorded 13,628 seeds
 distributed among 47 species and 36.57% of the total seeds did not show
 any sign of predation. Nest mound habitats supported low-density and
 species-poor seed assemblages, which were taxonomically distinct from the
 control habitats. These effects only occurred in the rainy season. The
 proportion of undamaged seeds were similar across the habitats. While
 forest cover did not influence seed assemblage in terms of species
 richness or seed predation, it did interact with habitat type via
 increments in seed abundance as forest cover increased across the nests.
 Forest cover also affected seed composition, but only in the rainy season.
 These results indicate that LCA decrease seed deposition in areas under
 their influence, particularly on the nest mounds. As LCA profit from human
 disturbance in the Caatinga, their role as seed ‘sinks’ should be enhanced
 in disturbed Caatinga patches, particularly during the rainy season, when
 most of the plant recruitment occurs. Our findings reinforce the
 importance of LCA as drivers of forest dynamics and resilience in
 human-modified landscape.