cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/y9j999yk25
title: Blind cavefish retain functional connectivity despite loss of retinal input

description: Sensory systems display remarkable plasticity and are under strong evolutionary selection. The Mexican cavefish, Astyanax mexicanus, consists of eyed river-dwelling surface populations, and multiple independent cave populations which have converged on eye loss, providing the opportunity to examine the evolution of sensory circuits in response to environmental perturbation. Functional analysis across multiple transgenic populations expressing GCaMP6s showed that functional connectivity of the optic tectum largely did not differ between populations, except for the selective loss of negatively correlated activity within the cavefish tectum, suggesting positively correlated neural activity is resistant to an evolved loss of input from the retina. Further, analysis of surface-cave hybrid fish reveals that changes in the tectum are genetically distinct from those encoding eye-loss. Together, these findings uncover the independent evolution of multiple components of the visual system and establish the use of functional imaging in A. mexicanus to study neural circuit evolution.

The uploaded data consists of .mat files containing time-lapse flourescence intensity data and related supplementary data, for experiments oultine in the associated article. Time-lapse images were collected on either a confocal Nikon A1 (light stimulus experiments) or two-photon Nikon A1R (spontaneous activity recordings). Following acquisition, time-lapse images were motion corrected using the "moco" plugin in ImageJ/FIJI. Following motion correction, time-lapse images were processed in MATLAB using the calcium imaging processing toolbox published in Romano et al., 2017 (DOI: 10.1371/journal.pcbi.1005526). Further details on the formatting of this dataset can be found in that publication.
DOI: 10.3535/jkc-zh1-vsg
title: Grewingkia sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pkk-ag5-f3e
title: Tryplasma sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4mq-jlf-qp8
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hmq-vp9-sqb
title: Brachyelasma sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/s83-n73-2xy
title: †Dianulites petropolitanus Dybowski, 1877 ()

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/kxb-h01-yq2
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/msg-cx9-k9b
title: †Chaetetes Fischer, 1830

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/59g-r4f-18z
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/jsj-qsk-lny
title: Kenophyllum sp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4kk-872-fz8
title: †Dalmanella Hall & Clarke, 1892

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/7prmw6v233
title: The degradation of TGR5 mediated by Smurf1 contributes to diabetic nephropathy

description: Source data for Western blots (unedited gels/images)
DOI: 10.3535/jtp-qea-5yq
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pyv-jl8-681
title: Favosites gothlandicus Lamarck

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/2sg3v7zpcn
title: HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis

description: Unprocessed microscopy images, gels, and blots
DOI: 10.3535/2c3-asm-572
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/k6b-g7j-cz6
title: †Dianulites petropolitanus Dybowski, 1877 ()

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mdt-thc-fzm
title: †Asaphidae

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.12727670.v1
title: Why do Benguela Niños lead Atlantic Niños?

description: Model data used for the paper "Why do Benguela Niños lead Atlantic Niños?", by S. Illig, M.L. Bachèlery and J. Lübbecke
DOI: 10.6084/m9.figshare.20464383.v1
title: Genotypes from two wood ant species and three hybrid populations

description: This VCF file contains 1,659,532 single nucleotide polymorphisms (SNPs) genotyped across 59 wood ant individuals, please see the reference below for more details (including metadata). Whole-genome sequencing was carried out on Illumina Novaseq 6000 (150 base pairs, paired-end reads), targeting 15× per individual. We trimmed raw Illumina reads and adapter sequences with TRIMMOMATIC (v0.38; parameters LEADING:3, TRAILING:3, MINLEN:36) and mapped trimmed reads against the reference genome (10.1093/jhered/esac019) using BWA MEM (v0.7.17). We then removed duplicates using PICARD TOOLS (v2.21.4). SNPs were then jointly called across all samples with FREEBAYES (v1.3.1, population priors disabled with -k option) and the resulting VCF file was normalized using VT (v0.5). We excluded both sites located at less than two base pairs from indels and sites supported by only Forward or Reverse reads using BCFTOOLS (v1.10). We decomposed multi-nucleotide variants using vcfallelicprimitives from VCFLIB (v1.0.1). The next steps were carried out with BCFTOOLS. Biallelic SNPs with quality equal or higher than 30 were kept. Individual genotypes with (<em>i</em>) genotype qualities lower than 30 and/or (<em>ii</em>) with depth of coverage lower than eight were coded as missing data. Sites displaying more than 50% missing data over all samples were discarded. Genotyping errors due to e.g., misaligned reads were removed using a filter based on excessive heterozygosity. To do so, we used an approach similar to Pfeifer <em>et al</em>. (2018) and excluded sites displaying heterozygote excess after pooling all samples (P &lt; 0.01, --hardy command from VCFTOOLS v0.1.16). We then filtered sites based on individual sequencing depth distributions, setting as missing sites where depth was lower than half or higher than twice the mean value of the individual considered. Finally, sites with more than 15% missing data over all samples were discarded.
DOI: 10.6084/m9.figshare.2060673.v1
title: Learning APAs in adults

description: Figure and Dataset related to the manuscript "Shift of the muscular inhibition latency during on-line acquisition of Anticipatory Postural Adjustments". The manuscript has been submitted in PlosOne (<b>PONE-D-15-25300R1).</b>
DOI: 10.3535/405-pqc-ba2
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.26991112.v1
title: Additional file 2 of Functional connectivity of cognition-related brain networks in adults with fetal alcohol syndrome

description: Additional file 2.Detailed naming of regions of interest and order key (overall and within networks)
DOI: 10.17632/23vmgmwryg
title: Asymptotic energy and wave function of one-electron molecular orbital

description: Abstract A program for the calculation of one-electron molecular energy and wave function for large inter nuclear distance R is reported. Asymptotic expansion of the energy and the wave function in inverse powers of R is obtained by solving the recurrence formula. Title of program: MOAS Catalogue Id: ACPQ_v1_0 Nature of problem The program calculates asymptotic expansion of the energy and the wave function of one-electron molecular orbital in inverse powers of inter nuclear distance R up to 1/R^N term in the energy (up to 1/R^N-2 term in the wave function). Versions of this program held in the CPC repository in Mendeley Data ACPQ_v1_0; MOAS; 10.1016/0010-4655(94)90008-6 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)
DOI: 10.17632/ng7v3bmsyw
title: A place-based framework for assessing resettlement capacity in the context of displacement induced by climate change

description: Two datasets used in the paper titled "A place-based framework for assessing resettlement capacity in the context of displacement induced by climate change". The datasets are on expert validation and illustration of the climate change resettlement capacity (CCRC) framework.
DOI: 10.3535/jsd-01x-4dt
title: Lingula Bruguière, 1791

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/nq0-qcj-ezj
title: Actinolite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.27061255.v1
title: GWAS summary statistics for major depression (PGC MDD2025)

description: Genome-wide summary statistics of major depression from the Psychiatric Genomics Consortium (2025)<br>Meta-analysed summary statistics for:Multi-ancestries, excluding 23andMe [DIV]European-ancestries, excluding 23andMe [EUR]European ancestries, excluding 23andMe and UK Biobank [EUR]European ancestries, top 10k SNPs [EUR]Clinical/interview phenotypes [EUR]Electronic health record / register phenotypes [EUR]Questionnaire symptom phenotypes [EUR]<br>
DOI: 10.3535/7kk-91m-2vg
title: Orthoclase

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/dfd-w2p-t8b
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/02a-aw2-hnp
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vje-hw3-l57
title: †Diplotrypa petropolitana Nicholson, 1879

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/lc8-x6e-3ea
title: Gypsum

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/9q6-gzp-g2d
title: †Dalmanella Hall & Clarke, 1892

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zgq-xk7-sfg
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.26342137.v1
title: <b>Human Phosphorylation Pathway Profiling Array</b><b> dataset evaluating the effect of </b><b>TNO155 treatment on</b><b> oral squamous cell carcinoma cells</b>

description: Processed data from phosphorylation arrays of DMSO-treated (control) and TNO155-treated OSCC lines, raw data for plotting of Figure 3C in the manuscript entitled "<b>TNO155 is a selective SHP2 inhibitor to target </b><b><i>PTPN11</i></b><b>-dependent oral squamous cell carcinoma</b>".Kit used:Human Phosphorylation Pathway Profiling Array C55 kit (Raybiotech, Inc. AAH-PPP-1-4)Analysis:Densitometric analysis of the array spots was performed using Carpentier G. Protein Array Analyzer (2010)[17] for ImageJ software (v.1.53, RRID:SCR_003070).
DOI: 10.3535/1s4-kjw-h4n
title: †Sinuites Koken, 1896

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/cxk-wf2-w0w
title: Glauconite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.28626650.v1
title: HPA axis SR Supplemental File

description: We hypothesized that the chronic administration of the novel GR receptor modulator CORT113176 during chronic sleep restriction (SR) and opioid abstinence would reveal important effects on the HPA axis giving insight into mechanisms of the interaction of SR and opioid abstinence. Using our rat model of persistent sleep loss during chronic opioid abstinence, we evaluated the effect of chronic CORT113176 administration on diurnal HPA axis dynamics and adrenal function, as well as the expression of critical mRNAs in the hypothalamic PVN and pituitaries in male and female rats. We concluded that the response of the HPA axis to CORT113176 during SR and opioid abstinence is not predictable by sex or sleep state because it can act both as an antagonist and agonist in the brain and pituitary, and an agonist in the adrenal gland in a sexually dimorphic manner.
DOI: 10.3535/gx5-r53-7vw
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/n92-nat-v25
title: Wagnerite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/cqp-q65-c26
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fmp-s0q-qj6
title: rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v0h-4yw-5sv
title: Clinochlore

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14694879.v1
title: Plant and soil nitrogen in oligotrophic boreal forest habitats with varying moss depths: does exclusion of large grazers matter?"

description: These data accompany the article "Plant and soil nitrogen in oligotrophic boreal forest habitats with varying moss depths: does exclusion of large grazers matter?" published in Oecologia (doi: 10.1007/s00442-021-04957-0).<br>
DOI: 10.3535/2mj-lr1-bww
title: Minerals

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v6h-zwd-bl0
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/d46wxf4b62
title: Vibration Anesthesia for Facial Injections: A Systematic Review and Meta-Analysis

description: Supplementary data for the manuscript entitled "Vibration Anesthesia for Facial Injections: A Systematic Review and Meta-Analysis".
DOI: 10.3535/5vs-k8q-67e
title: †Diplotrypa petropolitana Nicholson, 1879

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/cjh-8gm-4q1
title: †Diplotrypa petropolitana Nicholson, 1879

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/kv2-kh7-bgf
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sav-zyb-j80
title: Cyclocrinites C.E.I. von Eichwald, 1840

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/bsm3s864fv
title: Miller et al 2023 "p53 inhibitor iASPP is an unexpected suppressor of KRAS and inflammation driven pancreatic cancer"

description: Raw imaging data that was used to generate the figures for Miller et al 2023 " p53 inhibitor iASPP is an unexpected suppressor of KRAS and inflammation driven pancreatic cancer" . Please refer to the paper in Cell Death & Differentiation for more explanation.
The data discussed in Miller et al publication have been deposited in NCBI's Gene Expression Omnibus (GEO) and are accessible through GEO Series accession number GSE226595 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226595). Any additional information required to reanalyse the data reported in this paper is available from the lead contacts upon request..
DOI: 10.3535/6dn-d65-ttv
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/gya-jq6-yt7
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/c6x-5j0-m5e
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ehq-nas-j03
title: Hauyne

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/j2w-6bs-e42
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/s8v-blf-0az
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/jxe-lap-q2j
title: Gneiss

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q16-enp-50d
title: Bryozoa

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.28082405.v4
title: Association of domain-specific physical activity with nocturia: a population-based study

description: Nocturia is the most prevalent lower urinary tract symptom (LUTS) and is closely associated with various diseases and social burdens. Research on the relationship between physical activity and various diseases has progressed significantly. However, the association between nocturia and physical activity has received limited attention in prior studies. Thus，this study aimed to investigate the relationship between different domains of physical activity (e.g., occupation-related physical activity [OPA], transportation-related physical activity [TPA], and leisure-time physical activity [LTPA]) and nocturia. We included 5516 participants from the cross-sectional National Health and Nutrition Examination Survey (NHANES) conducted between 2007 and 2012，employing survey-weighted logistic regression, restricted cubic splines (RCS), subgroup analysis, and sensitivity analysis to assess the relationship between different domains of physical activity and nocturia.<b> </b>Multivariable logistic regression analysis revealed a significant negative correlation between PA, LTPA, and nocturia. Specifically, PA (OR: 0.7523, 95% CI: 0.6307–0.8974, P = 0.002) and LTPA (OR: 0.7664, 95% CI: 0.6314–0.9304, P = 0.007) were negatively associated with nocturia. The RCS curve demonstrated non-linear relationships between PA, LTPA, and nocturia. Additionally, subgroup analyses and sensitivity analyses further validated this association.<b> </b>Based on this cross-sectional study, we suggested that PA and LTPA are associated with a reduced risk of nocturia in adults aged 20 years and older in the United States. This underscoring the importance of physical activity in preventing and managing nocturia may provide valuable guidance for clinical practice.
DOI: 10.6084/m9.figshare.6269705.v2
title: Data repository Hypoxia, Exercise and Attention

description: The Frankfurt Attention Inventory 2 (FAIR-2) was performed at four testing points (D1, 14, 16, 18). 80 participants were assigned to 4 groups (HYP+EX, HYP, EX, and NOR).HYP = hypoxia; EX = exercise, NOR = normoxia<br>
DOI: 10.17632/7bkb7fymvg
title: Data for: Experimental Analysis of Fiber Optic Responses in Ionizing Radiation Environments for Distributed Sensing Applications

description: This dataset is from a distributed sensing fiber optic with a gamma irradiation dose of 1 MGy.
DOI: 10.3535/avz-723-6eb
title: Faujasite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ybd-yt2-c32
title: Almandine

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/593-mbm-ann
title: Natrolite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xf1-qaz-ek3
title: Minerals

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.11839512.v1
title: Quality assessment of abortion care from the users’ perspective: dimensional structure of the QualiAborto-Pt questionnaire

description: Abortion complications are a major public health problem, and studies to assess the quality of abortion care require adequate measurement tools. This study is a continuation of such an instrument’s refinement, the QualiAborto-Pt questionnaire. Using data from a survey of 2,336 women hospitalized for abortion complications in 19 hospitals in three state capitals in Northeast Brazil (Salvador - Bahia, Recife - Pernambuco, and São Luís - Maranhão), we implemented a series of exploratory and confirmatory factor analyses based on a 55-item prototype. The analyses indicate a structure with 17 items in five dimensions: reception, orientation, inputs/physical environment, technical quality, and continuity of care. All the items in the final model displayed acceptable reliability, absence of content redundancy, and factor specificity, as well as theoretical consistency with the respective dimensions. The solution also shows discriminant factor validity. Despite some persistent issues for further analysis and clarification, this version merits recommendation for use in Brazil.
DOI: 10.3535/6sy-jtc-5b6
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/elk-rm7-215
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.20496825.v1
title: Single-cell RNA-seq analysis of the goldfish retina

description: This is the single-cell RNA-seq data of the goldfish retina.
DOI: 10.6084/m9.figshare.28639523.v2
title: Neutrophil Extracellular Trap-borne C3-Driven Endothelial Dysfunction in <i>Klebsiella pneumoniae</i> Liver Abscess

description: <i>Klebsiella pneumoniae</i> (<i>K</i><i>.</i><i> pneumoniae</i>) liver abscess (KPLA) is a severe bacterial infection that is frequently complicated by intrahepatic thrombophlebitis and extrahepatic metastatic infections leading to high mortality rates. This study investigates the role of neutrophil extracellular traps (NETs) in endothelial injury and disease progression in KPLA. Our findings reveal that KPLA patients with intrahepatic thrombophlebitis are more prone to developing sepsis and extrahepatic migratory infections. <i>K. pneumoniae</i> induces NET formation via the TLR4-PI3Kα-AKT signaling pathway, and C3 deposition on NETs significantly contributes to endothelial injury. In a KPLA mouse model, increased C3 levels were observed in the liver, with NETs carrying substantial amounts of C3, disrupting the endothelial barrier and exacerbating liver injury. Treatment with the C3 inhibitor AMY-101 reduced C3 deposition on NETs, alleviated endothelial damage, significantly improved survival, and reduced extrahepatic dissemination, inflammatory infiltration, and lung injury while also suppressing systemic inflammation. Our findings underscore the pivotal role of C3 in NET-mediated endothelial damage and the pathogenesis of KPLA. Thus, targeting C3 deposition on NETs may be a promising therapeutic strategy to reduce endothelial injury, thrombosis, and extrahepatic infections in KPLA without compromising neutrophil antimicrobial function.
DOI: 10.3535/606-lpp-11j
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/p87vppcwdm
title: Data for: Euro area sovereign yield spreads as determinants of private sector borrowing costs

description: The file contains EViews workfiles. Please contact the authors if any other type of files are required.
DOI: 10.3535/jsl-f58-4vd
title: sedimentary rocks

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