cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26166427.v3
title: Supplementary material to: 'Changing feeding levels reveal plasticity in elasmobranch life history strategies'

description: Lucas S, Berggren P, Barrowclift E, Smallegange IM. 2024. Changing feeding levels reveal plasticity in elasmobranch life history strategies. <i>Preprint</i>. Life history strategies are shaped by phylogeny, environmental conditions and individual energy budgets, and have implications for population performance. Here, we used an approach that merges demography with energy budget theory to structure life history traits of 151 elasmobranch species into life history strategies for two contrasting feeding levels. We assessed how phylogeny and habitat impacted life history strategies, and tested if these strategies predict population performance and conservation status. Elasmobranch life history strategies are structured along the fast-slow continuum and reproductive strategy axes. However, species’ positions in this life history space were not fixed, but instead moved in an anticlockwise ‘whirlpool’ manner along the two axes in response to an increase in feeding level. We also found that population growth rate does not necessarily inform on a species demographic resilience. Finally, only at the higher feeding level does the fast-slow continuum predict IUCN conservation status, with the slowest species at the highest risk of extinction. Our analyses reveal plasticity in species life history strategies, and warn against extrapolating the fast-slow continuum and reproductive strategy framework from one environment to another when predicting a species’ response to (climate) change, perturbations, and, particularly in case of elasmobranchs, (over)exploitation.
DOI: 10.3535/rph-fls-dfm
title: Ancyrochitina? sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xzx-c62-32x
title: Rhabdochitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ds8-72z-b8r
title: Conochitina cf. tuba

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wmx-ta7-1bv
title: †Pollicina Koken, 1895

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14067047.v1
title: Chronos: Gene Fitness Effect Inference from CRISPR

description: Dataset provided in support of "Chronos: a model of cell population dynamics in CRISPR knockout screens that improves inference of gene dependency" by Dempster et al. Includes the jupyter notebook Analysis.ipynb together with all files needed to generate the panels in that manuscript. Also includes MAGeCK-MLE, CRISPRCleanR, CERES, and Chronos inference of gene fitness effects for the genome-wide pan-cancer CRISPR knockout experiments Project Achilles (public 20Q2) and Project Score.<br><br>To conserve space and speed up data loading, large matrices are provided as hdf5 files where dim_0 stores row names, dim_1 stores column names, and data stores the matrix as a 2D array. UTF8 encoding was used. Python users can load the matrices as Pandas dataframes using read_hdf5 from the Chronos package at https://github.com/broadinstitute/chronos. <br><br>
DOI: 10.3535/71m-2se-pds
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/p3p-syt-2xm
title: †Siphonotreta Verneuil, 1845

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/2ml-er1-zz1
title: Bivalvia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8y5-zap-h8w
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.15147009.v1
title: covid19 vaccine adults

description: covid19 vaccine adults
DOI: 10.3535/vlc-42t-zmv
title: Stony meteorites

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.25486414.v3
title: GeoTool-GPT

description: None
DOI: 10.3535/dgk-7be-hpx
title: Hyolithes sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pht-r1l-xk4
title: Hainholz meteorite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/qy8-war-8n2
title: Conochitina cf. linearistriata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.13241972.v2
title: DEB-IPM project. Database of DEB-IPM model parameters.

description: <b>What is the DEB-IPM project about?</b> How can we predict how populations respond to the ever greater changes in their environment? Within this project, we want to know which characteristics of organisms relate to population responses to environmental change. One way to find out is to analyse life history patterns using demographic models. However, depending on whether you model individual life histories from phenomenological descriptions (Salguero-Gomez et al. 2016; Paniw et al. 2018; Capdevila et al 2020) or from mechanistic descriptions using energy budget models (Smallegange et al. in press; Smallegange & Berg 2019), different predictions are obtained. <br>The DEB-IPM project aims to (i) unravel if energy budget descriptions of individual life histories consistently return different predictions on population responses to environmental change compared to when individual life histories are represented by statistical functions, (ii) understand why that is the case, and (iii) identify the most accurate way to predict population responses to novel environmental change. To this end, we support Bachelor, Master and PhD student projects in which students answer their own research questions, while at the same time expanding the DEB-IPM database to ultimately conduct large, cross-taxonomical life history analyses.
DOI: 10.3535/876-sf6-pfl
title: Bivalvia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x36-vzq-bct
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.26039245.v1
title: for review: · <b>Abrupt physico-chemical changes in the limnology of </b><b>Pyrenean mountain lakes necessitates urgent management actions</b>

description: for reviewing: <b>Abrupt physico-chemical changes in the limnology of </b><b>Pyrenean mountain lakes necessitates urgent management actions</b>
DOI: 10.17632/8ghkg576n7
title: Data for "Insights on the contradiction between the affinity and capacity of ferrihydrite towards As(III) and As(V): Surface reaction revisited"

description: This dataset is raw data associated with the paper entitled "Insights on the contradiction between the affinity and capacity of ferrihydrite towards As(III) and As(V): Surface reaction revisited" by Yuhong Huang et al.. The 15 worksheets in the excel file contain all table contents and data for all figures.
DOI: 10.3535/h4j-bv9-pc8
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.28703168
title: The foam cell-derived exosomes exacerbate ischemic white matter injuryvia transmitting metabolic defectsto microglia

description: HMC3 were treated with modified OGD accompanied with NC-Exos or AS-Exos. HMC3 cells were collected into TRIZOL to extract total RNA. Libraries were constructed using eukaryotic common transcriptome libraries, and sequencing was performed using Novaseq-PE150 platform.
DOI: 10.3535/v1c-6k8-115
title: †Pollicina Koken, 1895

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xxf-26l-ja7
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.26974309.v1
title: Trait-specific responses and environmental thresholds to Phosphorus addition in forests.zip

description: These dataset consists of both the source data and R-code to produce figures and analyze datasets.
DOI: 10.6084/m9.figshare.28703168.v1
title: The foam cell-derived exosomes exacerbate ischemic white matter injuryvia transmitting metabolic defectsto microglia

description: HMC3 were treated with modified OGD accompanied with NC-Exos or AS-Exos. HMC3 cells were collected into TRIZOL to extract total RNA. Libraries were constructed using eukaryotic common transcriptome libraries, and sequencing was performed using Novaseq-PE150 platform.
DOI: 10.17866/rd.salford.25376203.v1
title: Interview transcripts for doctoral thesis <i>Words from Word Watchers: Experiences with the Occult in Mauritius</i>

description: These are confidential interview transcripts and notes to evidence the stated findings for <i>Words from World Watchers</i>. These serve as extended appendices for the doctoral thesis submission and are shared privately to the supervisory and examiner team.
DOI: 10.3535/54g-0a9-pen
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/g11-4qt-d6e
title: Ramochitina? sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vb5-388-jlt
title: Monroe meteorite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rta-p52-hnc
title: Ramochitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/76j5vnvb6h
title: Maturation and persistence of the anti-SARS-CoV-2 memory B cell response. Sokal and Chappert et al.
DOI: 10.3535/j9a-405-kgg
title: Anthochitina sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/qxb-qjf-jy4
title: Conochitina aff. postrobusta

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.27000574.v2
title: Routine surveillance data on the isolation and antimicrobial susceptibilities of VRE from 15 Japanese hospitals from 2018 to 2021

description: Anonymized surveillance data of VRE analyzed in the following paper:Enhanced automated detection of outbreaks of a rare antimicrobial-resistant bacterial speciesYumiko Hosaka, Aki Hirabayashi, Adam Clark, Meghan Baker, Motoyuki Sugai, John Stelling, Koji YaharaPLOS One, in revision
DOI: 10.3535/5tb-cqw-k0c
title: Specimen from Tallinn University of Technology

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xa7-qz1-338
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.12383639.v3
title: hygrip.h5

description: Complete data-set, that comprises the task signal (a dynamically varying force signal that is displayed visually), co-located brain signals in form of electroencephalography (EEG) and near-infrared spectroscopy (NIRS) that captures a higher spatial resolution oxygenation cortical response, the muscle activity of the grip muscles, the force generated at the grip sensor, as well as confounding sources, such as breathing and eye movement activity during a motor task. In total, 14 right-handed subjects performed a uni-manual dynamic grip force task within 25-50% of each hand's maximum voluntary contraction.
DOI: 10.3535/0gb-1wq-e9e
title: Halite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/g04-y4d-kpv
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.17122718.v1
title: Timing map response time series

description: Responses time series of voxels in each timing map region of interest.
DOI: 10.60893/figshare.apl.27020485.v1
title: Supplementary Material

description: Supplementary material is available regarding: the laser characteristics, the calculation of the Allan deviation, the detector and laser noise and the data processing used to obtain the absorption spectrum.
DOI: 10.3535/f0m-1q5-kbh
title: New Concord meteorite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v9w-9da-j8s
title: Conochitina? sp. 6

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.26210288.v1
title: Regulation of Diabetic Cardiomyopathy Through Mitochondrial Import of Long Non-Coding RNAs

description: Evaluating if nuclear genome-encoded lncRNA presence in cardiac mitochondria is disrupted as a result of diabetes mellitus in a manner that disrupted mitochondrial genome regulation through miRNA availability
DOI: 10.3535/2z0-0vq-15f
title: Basalt

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zjg-55h-vq7
title: Melaphyre

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1147465.v2
title: WebRDS data collected in the Netherlands and Thailand to study contact patterns relevant for the spread of close-contact pathogens.

description: Web based respondent driven sampling conducted among students in Thailand and the Netherlands, to investigate contact patterns relevant for the spread of close-contact infections.
DOI: 10.3535/lyl-hb6-b2t
title: Pyrophyllite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zsm-lce-sg1
title: †Leptaena Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/22q-dgk-5fw
title: Dolomite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fv7-jmp-bc6
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.9736028.v1
title: Consentimiento informado

description: Consentimiento informado
DOI: 10.3535/94y-75t-smv
title: Pyrophyllite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zcc-jyk-lma
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14429108.v1
title: Additional file 6 of Eudiplozoon nipponicum (Monogenea, Diplozoidae) and its adaptation to haematophagy as revealed by transcriptome and secretome profiling

description: Additional file 6: Table S6. Spreadsheet presenting E. nipponicum KEGG Orthologues and pathways. Pathways are linked with K number and quantified by the sum of TPM values of all included transcripts (also presented) and the ratio between the TPM value and the number of transcripts.
DOI: 10.6084/m9.figshare.28012925.v2
title: Attachment of amphibian fossils location.xlsx

description: The amphibian fossil in China.
DOI: 10.6084/m9.figshare.966113.v1
title: Discrete levels and limits of free choice

description: What turns individuals, groups and organizations into 'human machinery' ?
DOI: 10.3535/8t7-z3q-9tv
title: Breccia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.12370550.v2
title: Isotope and chemical assessment of natural water in the Jaffna Peninsula in northern Sri Lanka for groundwater development aspects

description: The demand for fresh groundwater in the Jaffna peninsula in northern Sri Lanka, has been increasing as the only water source for domestic and agricultural needs. Isotopic and hydro-chemical assessment on groundwater recharge and quality was done with the objective of assisting groundwater management plans. Water samples were collected in pre and post monsoon periods for isotope analyses (<sup>2</sup>H, <sup>18</sup>O and <sup>3</sup>H) and major ions. Isotope data provide evidence that the groundwater is predominantly recharged by inter-monsoon (convectional) and North-East monsoon rains. Different residence times of shallow groundwater were found. The study revealed that the groundwater quality is mainly deteriorated due to dissolution of geogenic elements. However, in some instances, seawater intrusion and evaporation have caused lowering of groundwater quality. More saline groundwater is found in deeper levels in the karstic limestone aquifer system. Fresh water is available in coastal sandy aquifers in the eastern part of the peninsula. The impact of rainfall variations and agricultural activities are contributory factors for producing variations in the quality of groundwater. The current study suggests artificial groundwater recharge for the development and utilization of groundwater resources through small scale tanks/reservoirs or ponds in the areas where direct rain recharge occurs.
DOI: 10.6084/m9.figshare.27991232.v2
title: <b>Intrinsic and extrinsic factors affecting the evolution of virulence in the HIV-associated opportunistic human fungal pathogen </b><b><i>Cryptococcus neoformans</i></b>

description: The fungus <i>Cryptococcus neoformans</i> is considered the leading cause of mortality in immunocompromised patients. While extensive research has unveiled the molecular epidemiology of <i>Cryptococcus neoformans</i>, the influence of genetic and environmental factors on genotype-phenotype correlations remains poorly understood. Specifically, it remains unclear whether the genetic and environmental variability observed across isolates from diverse sources has significant implications for the pathogen's virulence. In this study, we analyzed 105 Chinese <i>C. neoformans </i>isolates, including 54 from HIV-infected patients, 44 from HIV-uninfected individuals and 7 from a natural environment. Multilocus sequence typing (MLST) revealed that sequence type (ST) 5 predominates across all clinical isolates; however, genotypic diversity was notably higher in isolates from HIV-uninfected individuals and the natural environment, whereas HIV-infected isolates exhibited restricted genetic variation. Furthermore, isolates from HIV-uninfected individuals exhibited significantly enhanced virulence traits, including elevated capsule production, increased melanin production, improved survival in human cerebrospinal fluid (CSF), reduced phagocytic uptake, and higher mortality in both <i>Galleria mellonella</i> and murine models of cryptococcosis. Importantly, these pathogenic phenotypes were correlated with CD4<sup>+</sup> T cell counts, highlighting the critical role of host immunity in shaping <i>C. neoformans</i> virulence. Whole-genome sequencing and genome-wide association studies (GWAS) further revealed that variations in genes involved in carbohydrate metabolism, such as <i>CDA3</i> and<i> GPD1</i>, may drive host-specific virulence evolution. Our findings provide compelling evidence for a genotype-phenotype correlation, demonstrating that both genetic and environmental factors shape the virulence of <i>C. neoformans</i>, with significant implications for understanding host-pathogen interactions and guiding therapeutic strategies.<br>
DOI: 10.3535/7e7-2wx-7rp
title: Ancyrochitina sp. 3

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/dj7-98e-df5
title: Breccia

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.57841/casdc.0005221
title: ALS患者的人体成分数据集
DOI: 10.6084/m9.figshare.13157585.v4
title: Interactive Clustering of Cooking Recipe Instructions:Towards the Automatic Detection of Events Involving Kitchen Devices

description: Abstract: Cooking recipes are a rich source of semantic information. They contain instructions for food preparation tasks, specifying the actions that should be carried out which typically involve various ingredients and kitchen devices. In an IoT scenario, instructions in cooking recipes can form the basis for automatically controlling kitchen devices without any programming. However, as these instructions are written in natural language, they first need to be transformed or parsed into machine-interpretable commands. As a step towards this, we investigate methods for identifying the various types of actions (events) that kitchen devices are involved in. We cast this problem as a clustering task, whereby recipe instructions involving a given device of interest, are automatically grouped according to the type of event described. Each sentence in every instruction is represented by its embedding vector which is computed using a BERT-based model, specifically one pre-trained using a Roberta architecture. We cluster these sentence embeddings using our newly proposed interactive machine learning (IML)-based framework underpinned by the HDBScan clustering technique. We demonstrate that our IML framework can detect events in sentences with satisfactory accuracy, reaching almost the same level as human performance.
DOI: 10.6084/m9.figshare.14573538.v1
title: Deposit for "Siblings matter: Family heterogeneity improves associative learning later in life"

description: This deposit includes all the data and R-code for the analysis presented in the main manuscript as well as the supplementary file. <br>
DOI: 10.6084/m9.figshare.14923842.v1
title: fMRI data for finger tapping

description: Single subject fMRI data for finger tapping with a right hand
DOI: 10.3535/h4q-mmp-r5s
title: Specimen from Tallinn University of Technology

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zyr-6k1-js6
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.12738164.v1
title: Appendix 4.1 Sentiment analysis on WeChat posts

description: Sentiment analysis on WeChat posts
DOI: 10.3535/l0k-5g7-e6m
title: †Eochonetes Reed, 1917

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ys1-6cp-ahb
title: Eisenackitina invenusta

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/6t2-brt-b5k
title: Belonechitina postrobusta

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v0c-b7b-xga
title: Favars meteorite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/cep-pjq-67p
title: Stibnite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/m0k-ghz-lwm
title: Ullmannite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.