cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18299002
title: ENCODE LR-RNA-seq models and expression values

description: In this object are the following files:

 



filt_ab_tpm_mouse.tsv / filt_ab_tpm_human.tsv: Expression levels in TPM for each transcript in human and mouse

lr_mouse_library_data_summary.tsv / lr_human_library_data_summary.tsv: Metadata for each dataset in human and mouse

cerberus.gtf / mouse_cerberus.gtf: Transcript models in GTF format

human_ucsc_transcripts.gtf / mouse_ucsc_transcripts.gtf: Transcript models for transcripts that passed expression filtering (>= 1 TPM in at least one library; transcripts from known 

human_protein_summary.tsv / mouse_protein_summary.tsv: Summary of protein coding predictions, including ORF locations and NMD status

human_triplets.h5  / mouse_triplets.h5: Cerberus H5 objects (see here for specification) that detail the TSSs, ICs, and TESs used in each transcript, as well as the triplets calculated globally and for individual samples. 

human_swan_graph.p  / mouse_swan_graph.p: SwanGraph pickled python objects.
DOI: 10.5061/dryad.v9s4mw758
title: Data for: First evidence of yearly allochrony in a terrestrial vertebrate: A case study of an annual chameleon

description: Isolation through differences in reproductive timing, known as allochrony,
 is a unique life history trait that can lead to the separation of a
 population into two distinct populations. Yearly allochrony, where
 reproductive events are separated between years, is extremely rare and has
 been documented less than ten times. It requires a single reproductive
 event at a fixed age and a life cycle of two years or more. Among
 terrestrial vertebrates, documented examples of yearly allochrony are
 non-existent. Our study reveals that Chamaeleo chamaeleon musae possesses
 the potential for allochronic separation. These chameleons reproduce one
 year after hatching, with only 0.2% of the population surviving to a
 second reproductive season. Their eggs require 11 months to hatch. This
 combination of factors results in two distinct subpopulations: one that
 incubates eggs during even years while adults reproduce in odd years, and
 another that follows the reverse pattern. This separation prevents
 intermixing between the two subpopulations. Chamaeleo chamaeleon
 musae is currently the only known terrestrial vertebrate exhibiting yearly
 allochrony. Population and evolutionary ecologists must consider yearly
 allochrony when studying animal life cycles, given its significant
 implications for speciation, species conservation, and monitoring
 programs.
description: # Data for: First evidence of yearly allochrony in a terrestrial
 vertebrate: A case study of an annual chameleon
 [https://doi.org/10.5061/dryad.v9s4mw758](https://doi.org/10.5061/dryad.v9s4mw758) ## Description of the data and file structure ### Files and variables #### File: MARK\_Output.zip **Description:**  All MARK output files used in the analysis. #### File: SurveyData.csv **Description:** This file contains raw survey data from Chameleon surveys. ##### Variables * sessions: survey session * Julian C: days since last November (Julian date) * Mass: grams (g) * Head length: millimeters (mm) * Tail: length, millimeters (mm) * SV: snout-vent length, millimeters (mm) * sex: M/F * Finger new: individual chameleon ID * floor age group: age group (g0 = &lt;1 year, g1 = 1–2 years, g2 = 2–3 years) The NA values in the data set represent data that were not measured, due to one of the following reasons: (1) technical limitations during data collection; (2) the variable was added to the protocol at a later stage (e.g., Head length); or (3) the individual was already sampled in the same month and was not measured again to avoid disturbance. * ## Code/software Required software: Microsoft Excel, R
DOI: 10.5061/dryad.rfj6q57jw
title: Data from: Interacting phenotypic plasticities: Do male and female responses to the sociosexual environment interact to determine fitness?

description: Socially induced plasticity in reproductive effort is a widely documented
 phenomenon. However, few empirical studies have examined how male and
 female plastic responses to the social environment might interact in
 determining fitness outcomes. In field crickets, Teleogryllus oceanicus,
 males respond to rival song by increasing expenditure on seminal fluid
 proteins that enhance competitive fertilization success at the cost of
 reduced embryo survival. It remains unknown whether plastic responses in
 females could moderate the effects of male competitiveness on offspring
 performance. Here we used a fully factorial design to explore the
 interacting effects on fitness of male and female plasticity to the
 sociosexual environment. We found that female crickets exposed to male
 song increased the number of eggs produced during early life reproduction,
 which came at a cost of reduced offspring size. There was evidence, albeit
 weak, that interacting effects of male and female sociosexual environment
 contributed to variation in the hatching success of eggs laid by females.
 Lifetime offspring production was unaffected by the sociosexual
 environments to which upstream male and female plastic responses were
 made. Our data offer a rare test of the theoretical expectation
description: # Data from: Interacting phenotypic plasticities: Do male and female
 responses to the sociosexual environment interact to determine fitness?
 [https://doi.org/10.5061/dryad.rfj6q57jw](https://doi.org/10.5061/dryad.rfj6q57jw) ## Description of the data and file structure The file Simmons & Lovegrove2024.xlsx contains the data to reproduce the analyses presented in Simmons & Lovegrove, Interacting phenotypic plasticities: Do male and female responses to the sociosexual environment interact to determine fitness? Evolution, 2024.  Male and female crickets from two sociosexual environments (song/no-song) were paired in all possible combinations: ### Files and variables #### File: Simmons\_\_\_Lovegrove\_2024.xlsx  Treatment A: male song / female song Treatment B: male song / female no-song Treatment C: male no-song / female song Treatment D: male no-song / female no-song The experiment was conducted in two blocks, block 1 and block 2. For each case the environment (S/NS) for the male and female in each pair is given, along with data on the male’s weight (mg), male’s pronotum width (mm), female’s weight (mg), female’s pronotum width (mm), the sperm viability (proportion sperm alive) for males, the number of eggs laid by females in weeks 1-3 (eggswkn), the average weight of eggs (mg) laid in weeks 1-3 (avg wt wkn), the proportion of eggs hatching in weeks 1-3 (hatch wkn), the total number of offspring hatched during the female’s lifespan, and the female’s lifespan in weeks. Empty cells indicate missing values.
DOI: 10.5281/zenodo.18386774
title: Experimental_PLSpectroscopy_WP3_FORTH

description: This dataset was generated as part of DYNASTY project activities (specifically WP3, samples preparation, data production and data analysis), to support the characterization of the physical properties of van der Waals heterojunctions. Photoluminescence (PL) emission spectroscopy measurements were conducted to evaluate the behavior and emissive properties of WS2/graphite heterojunctions
DOI: 10.5281/zenodo.18386775
title: Experimental_PLSpectroscopy_WP3_FORTH

description: This dataset was generated as part of DYNASTY project activities (specifically WP3, samples preparation, data production and data analysis), to support the characterization of the physical properties of van der Waals heterojunctions. Photoluminescence (PL) emission spectroscopy measurements were conducted to evaluate the behavior and emissive properties of WS2/graphite heterojunctions
DOI: 10.15468/dl.s5tzyb
title: Occurrence Download

description: A dataset containing 5608 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is North America",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Syrphidae"
 ]
}

 The dataset includes 5608 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004108-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fydr48
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Norway",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is December",
 "OccurrenceStatus is Present",
 "TaxonKey is Megaptera novaeangliae",
 "Year 2015-2015"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004110-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15139/s3/kao2mk
title: Data Management and Sharing Plan for: Characterizing the Immunopathology of PCD-Related CRS

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5281/zenodo.18319032
title: Données d'exemple Agri-STAMP pour le département de la Martinique (972)

description: Ce dépôt contient les données d'exemple utilisées par le modèle Agri-STAMP v1.1.x pour exécuter une simulation de démonstration sur le département de la Martinique (972).
DOI: 10.5281/zenodo.18319031
title: Données d'exemple Agri-STAMP pour le département de la Martinique (972)

description: Ce dépôt contient les données d'exemple utilisées par le modèle Agri-STAMP v1.1.x pour exécuter une simulation de démonstration sur le département de la Martinique (972).
DOI: 10.5061/dryad.q573n5ts2
title: Data from: Evolutionary tempo, supertaxa and living fossils

description: A relationship between the rate of molecular change and diversification
 has long been discussed, on both theoretical and empirical grounds.
 However, the effect on our understanding of evolutionary patterns is yet
 to be fully explored. Here we develop a new model, the Covariant
 Evolutionary Tempo (CET) model, with the aim of integrating patterns of
 diversification and molecular evolution within a framework of a
 continuously changing ‘tempo’ variable that acts as a master control for
 molecular, morphological and diversification rates. Importantly, tempo
 itself is treated as being variable at a rate proportional to its own
 value. This model predicts that diversity is dominated by a small number
 of extremely large clades at any historical epoch including the present;
 that these large clades are expected to be characterised by explosive
 early radiations accompanied by elevated rates of molecular evolution; and
 that extant organisms are likely to have evolved from species with
 unusually fast evolutionary rates. Under such a model, the amount of
 molecular change along a particular lineage is essentially independent of
 its height, which weakens the molecular clock hypothesis. Finally, our
 model explains the existence of ‘living fossil’ sister groups to large
 clades that are species poor and exhibit slow rates of morphological and
 molecular change. Our results demonstrate that the observed historical
 patterns of evolution can be modelled without invoking special
 evolutionary mechanisms or innovations that are unique to specific times
 or taxa, even when they are highly non-uniform.
description: # Evolutionary tempo, supertaxa and living fossils
 [https://doi.org/10.5061/dryad.q573n5ts2](https://doi.org/10.5061/dryad.q573n5ts2) ## Description of the data and file structure **BuddMannTempoSI.R** provides the R code necessary to create the figures for Budd and Mann "Evolutionary tempo, supertaxa and living fossils". It contains only a code supplement. There are no data associated with this paper. Required R packages are: deSolve, ReacTran, and parallel. Once these are installed, sourcing the file will then reproduce the figures of the paper.  ## Code/software R studio can be used to run the code and reproduce the results.
DOI: 10.5061/dryad.dncjsxm7z
title: Data from: Tracking free water in human body by magnetic resonance imaging: New insights on the network pathways

description: Water is the most indispensable material for life. Although extensive
 research has been carried out at the microscopic level, including studies
 focusing on transport and molecular effects, the macroscopic water system
 of the human body is still unclear. In this study, the distribution of
 free water in the human body under natural conditions was non-invasively
 depicted by magnetic resonance hydrography sequences. Spatial saturation
 technique was used to explore the dynamic properties of free water.
 Imaging and post-processing results reveal that abundant free water formed
 a macroscopic network consisting of interconnected pathways. The slow-flow
 trajectories of some waterways were captured in the saturation band. The
 free water channels enclosed or bordered the space around blood vessels
 and nerves or traversed the tissues. This spatial relationship is similar
 to the fluid flow patterns in the interstitial space in the periphery and
 the glymphatic system of the brain, suggesting potential physiological
 functions and pathological variations.
description: The scanning process and imaging parameters of MRI are described
 in the related paper. The raw data is in DICOM format and contains
 personal information about the subjects. In order to protect the privacy
 of human subjects and comply with their wishes, we present part of the
 (2D) scan results in the form of video. The sequences are further
 reconstructed in 3D, and the video can be found in the supplementary
 material. One of this work's contributions is the establishment of
 standardized free water scanning processes, which can help researchers
 conduct validation and generalization.
description: # Data from: Tracking free water in human body by magnetic resonance
 imaging: New insights on the network pathways
 [https://doi.org/10.5061/dryad.dncjsxm7z](https://doi.org/10.5061/dryad.dncjsxm7z) ## Description: We used magnetic resonance (MR) hydrography (MRF) to capture the free water network in the human body under natural state. Implementation steps and parameters were described in detail in associated publication. The original sequence data contained subject information. For privacy reasons, we only presented the imaging results here, in the form of video. The reproduction of the imaging results could be realized in the MR unit by referring to the sequence and parameter selection given in the publication. ## Files: * Folder *s1/s2/s3* : Free water imaging videos from three anonymous subjects. * Folder *knee/nape* : Observation sites of free water in human body. * Mp4 *3D_'sequencename'_MIP* : Common 3D MR sequences after maximum intensity projection (MIP), including NerveView, time-of-flight (TOF) artery, and TOF vein. Details can be found in publication. * Mp4 *MRF_with/without_saturationband_MIP* : MRF sequence was proposed for free water imaging. Saturation bands were introduced for exploratory experiments to characterize the dynamics of free water. Details can be found in publication.
DOI: 10.5281/zenodo.15282832
title: LecNet-  A Legal Citation Network Benchmark Dataset

description: Legal document analysis plays a critical role in modern judicial systems, particularly for case retrieval, classification, and recommendation tasks. While datasets like COLIEE have significantly advanced the research in this domain, the lack of large-scale datasets tailored to the Indian judicial system has limited progress. To address this gap, we introduce the Indian Legal Case Citation Network (LeCNet) Benchmark dataset as the first of its kind for the Indian judiciary. The dataset is a gold standard and expert-curated in itself as it has been created using the mentioned citation cases from a source document. LeCNet comprises 26,308 nodes representing case judgments and 67,108 edges representing citation relationships between the case nodes. Each node is described with rich features of document embeddings that incorporate contextual information from the case documents. In this paper, we consider link prediction for a legal citation recommendation. We have performed extensive experiments on the dataset with different AI models for dataset validation. The Mean Reciprocal Rank (MRR) metric is used for model evaluation. Our experiments show promising results for graph structure models that are capable of inferencing dynamic relationships between nodes effectively. The obtained results also demonstrate the utility of our dataset highlighting the importance of graphical networks over textual representations.
DOI: 10.5281/zenodo.15282833
title: LecNet-  A Legal Citation Network Benchmark Dataset

description: Legal document analysis plays a critical role in modern judicial systems, particularly for case retrieval, classification, and recommendation tasks. While datasets like COLIEE have significantly advanced the research in this domain, the lack of large-scale datasets tailored to the Indian judicial system has limited progress. To address this gap, we introduce the Indian Legal Case Citation Network (LeCNet) Benchmark dataset as the first of its kind for the Indian judiciary. The dataset is a gold standard and expert-curated in itself as it has been created using the mentioned citation cases from a source document. LeCNet comprises 26,308 nodes representing case judgments and 67,108 edges representing citation relationships between the case nodes. Each node is described with rich features of document embeddings that incorporate contextual information from the case documents. In this paper, we consider link prediction for a legal citation recommendation. We have performed extensive experiments on the dataset with different AI models for dataset validation. The Mean Reciprocal Rank (MRR) metric is used for model evaluation. Our experiments show promising results for graph structure models that are capable of inferencing dynamic relationships between nodes effectively. The obtained results also demonstrate the utility of our dataset highlighting the importance of graphical networks over textual representations.
DOI: 10.5281/zenodo.15283173
title: TCRvdb
DOI: 10.5281/zenodo.15283174
title: TCRvdb
DOI: 10.15468/dl.qc8t5k
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Isleria hauxwelli (P.L.Sclater, 1857))",
 "Country is one of (American Samoa, Australia, Christmas Island, Cocos (Keeling) Islands, Cook Islands, Fiji, French Polynesia, Guam, Heard Island and McDonald Islands, Kiribati, Marshall Islands, Micronesia (Federated States of), Nauru, New Caledonia, New Zealand, Niue, Norfolk Island, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn, Samoa, Solomon Islands, Tokelau, Tonga, Tuvalu, United States Minor Outlying Islands, Vanuatu, Wallis and Futuna)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016401-250525065834625/datasets/export for details.
DOI: 10.15468/dl.keyase
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Isleria hauxwelli (P.L.Sclater, 1857))",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016400-250525065834625/datasets/export for details.
DOI: 10.15468/dl.mfn7s4
title: Occurrence Download

description: A dataset containing 200 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Acacia caven (Molina) Molina",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 200 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010249-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28497380
title: Code_Data.zip

description: This is a record of the code and data used to generate the results in the manuscript "Three-year assessment of integrated vector management in Attica, Greece: Results from surveillance and control activities".
DOI: 10.6084/m9.figshare.28497380.v4
title: Code_Data.zip

description: This is a record of the code and data used to generate the results in the manuscript "Three-year assessment of integrated vector management in Attica, Greece: Results from surveillance and control activities".
DOI: 10.6084/m9.figshare.28497380.v3
title: Code_Data.zip

description: This is a record of the code and data used to generate the results in the manuscript "Three-year assessment of integrated vector management in Attica, Greece: Results from surveillance and control activities".
DOI: 10.17026/ss/wxdb0c
title: Silver transports from Vera Cruz to Europe during the Napoleonic wars
title: Table of shipments in the years 1805-1808 by the firms of Hope & Co. and Barings and of the firm Gordon & Murphy.

description: These data come from a research on international bankers that acted as diplomatic agents between Spain, France, England and the United States during the Napoleonic Wars. In the period 1805-1808, the bankers of Hope & Co. and Baring were involved in silver shipments from Vera Cruz to Europe. The research answered questions as: what motivated them to undertake this complex undertaking, how did they manage to carry out this operation despite the war situation and what were the effects of their involvement? In the table a list of the relevant shipments is presented.
description: The data are based on the author's research for his master thesis at Leiden University under the supervision of professor Cátia Antunes.
DOI: 10.15468/dl.9fub7c
title: Occurrence Download

description: A dataset containing 6443 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-203.60580 -57.71583,-133.79092 -57.71583,-133.79092 -29.80183,-203.60580 -29.80183,-203.60580 -57.71583))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ozothamnus leptophyllus"
 ]
}

 The dataset includes 6443 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011418-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.