cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25040777.v1
title: Bayesian Integrative Region Segmentation in Spatially Resolved Transcriptomic Studies

description: The spatially resolved transcriptomic study is a recently developed biological experiment that can measure gene expressions and retain spatial information simultaneously, opening a new avenue to characterize fine-grained tissue structures. In this article, we propose a nonparametric Bayesian method named BINRES to carry out the region segmentation for a tissue section by integrating all the three types of data generated during the study—gene expressions, spatial coordinates, and the histology image. BINRES is able to capture more subtle regions than existing statistical partitioning models that only partially make use of the three data modes and is more interpretable than neural-network-based region segmentation approaches. Specifically, due to a nonparametric spatial prior, BINRES does not require a prespecified region number and can learn it automatically. BINRES also combines the image and the gene expressions in the Bayesian consensus clustering framework and thus flexibly adjusts their label alignment contribution weights in a data-adaptive manner. A computationally scalable extension is developed for large-scale studies. Both simulation studies and the real application to three mouse spatial transcriptomic datasets demonstrate that BINRES outperforms the competing methods and easily achieves the uncertainty quantification of the integrative partition. The R package of the proposed method is publicly available at https://github.com/yinqiaoyan/BINRES. Supplementary materials for this article are available online.
DOI: 10.3535/r5j-y53-tna
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ycm-r76-sqy
title: Bryozoa

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.22823351.v2
title: Tetranychus_urticae

description: Gene, transcript and intron level classifications, by species
DOI: 10.3535/fth-07s-t4g
title: †Batostoma granulosum Bassler, 1911

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q3p-ldm-a02
title: †Cliftonia Foerste, 1909

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.26065153.v1
title: Dataset and Code for Laferriere et al. (2024) (Lunar Hydration Exosphere)

description: Figures includes the jupyter notebook used to create the figures in the manuscript, Supplemental includes the jupyter notebook used to create the supplemental figures from the manuscript. Lunar_processes.py is the python code which encompasses our ballistic transport model. The Repository zipfile contains all of the model run results. The directory is separated into the two particles (H2O, OH), and then each of those contains the results from the exosphere model runs, full model runs, and relevant tests as discussed in the manuscript.
DOI: 10.3535/ave-1n1-ncf
title: †Phylloporina Ulrich, 1887

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/k44-v5z-zhx
title: †Stigmatella massalis Bassler, 1911

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.20146637.v1
title: Raw_dataset_Sylvia_Dobbs_leaky_gut.zip

description: 1D NMR spectra used for the statistical analysis of fecal extracts samples from patients with Parkinsons' disease.
DOI: 10.6084/m9.figshare.23657841.v1
title: <strong>Beyond observation: genomic traits and machine learning algorithms for predicting fungal lifestyles</strong>

description: Figure S1. Distribution and proportion (%) of TE families in 638 genome assemblies. The bubble size represents the proportion of the TE in the genome. The bar represents the proportion of total TE size to the genome size. Figure S2. Composition and abundance of functional protein groups in 638 genome assemblies. The bubble size represents the number of the protein group. The bar represents the proportion of the secretome size to the total number of proteins per genome. Table S1. A summary table containing genome information of 638 genome assemblies, lineage information, and statistics of TE categories, basic genomic features and functional protein groups. Table S2. Taxonomic and lifestyle coverage of 638 Sordariomycete genomes. Table S3. General statistics of sequencing technologies, assembly completeness and TE sizes of 638 Sordariomycete genomes. Table S4. Pearson Correlations of 25 basic genomic features. Table S5. Comparative analysis results of 25 basic genomic features. Table S6. Pearson Correlations of 24 functional protein features. Table S7. Comparative analysis results of 24 functional protein features. Table S8. Predictive accuracies of six machine learning algorithms. Table S9. Predicted results of 85 undetermined genomes and the observed lifestyles of phylogenetically close groups.
DOI: 10.6084/m9.figshare.25012433.v1
title: Optimization of <i>Rhizobium rhizogenes</i>-mediated transformation, regeneration and characterization of <i>Malus domestica</i> Borkh. Ri lines

description: <b>This study explored the establishment and optimization of Ri technology for apple breeding, using the bacterium </b><b><i>Rhizobium rhizogenes</i></b><b> to obtain Ri lines with compact shoots and stronger root systems. The transformation and shoot regeneration for </b><b><i>Malus domestica</i></b><b> cultivars was studied in detail. Various </b><b><i>R. rhizogenes</i></b><b> strains, scion and rootstock genotypes, explant types, wounding methods and explant orientations were tested for hairy root induction. Most of the 16 tested strains, especially those with plasmid type III, induced hairy roots in the rootstock genotype ‘M26’. Although apple genotypes differed in response, in most of them roots were successfully induced using strains ATCC 15834, LMG 63 and LMG 150, with leaf blades outperforming petioles as explants. Wounding by scratching or sonication further improved transformation efficiency, as did placing leaf blades with their abaxial side upward on root induction medium. The majority (94%) of roots formed in one transformation experiment were tested PCR-positive for at least one T-DNA gene. Shoot regeneration experiments investigated salt concentrations, gelling agents, cytokinin types, concentrations, and a resting period on hormone-free medium. Shoot regeneration was highly genotype-dependent varying between 0 and 83%, whereas only minor, non-significant effects were observed for the treatments tested. Copy numbers of T-DNA genes were estimated using digital PCR for the first time in apple Ri lines. In the greenhouse, two Ri lines showed compact shoots and shorter leaves, but no enhanced root system. The improved protocol provides a valuable tool for breeders and scientists to obtain and further use Ri lines.</b>
DOI: 10.17632/8jrxyxkcvw
title: Circadian clock controls rhythms in ketogenesis by interfering with PPAR transcriptional network

description: The file contains row data for the manuscript "Circadian clock controls rhythms in ketogenesis by interfering with PPAR transcriptional network" Volha Mezhnina, Oghogho P. Ebeigbe, Nikkhil Velingkaar, Allan Poe, Yana Sandlers and Roman V Kondratov.
DOI: 10.3535/161-1wv-3gh
title: †Diplotrypa petropolitana Nicholson, 1879

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/92z-e6p-32n
title: Porifera Grant, 1836

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.8044370.v1
title: Quantitative genetic parameters for growth and wood properties in Eucalyptus urograndis - SNP marker data

description: <b>Data File for</b><b>:</b> <b>Lima et al. 2019.</b> Quantitative genetic parameters for growth and wood properties in Eucalyptus “urograndis” hybrid using near-infrared phenotyping and genome-wide SNP-based relationships. PlosOne (accepted) <b>SNP_markers.txt</b> Genotype data for 33,398 Single nucleotide polymorphisms (SNPs) for 970 trees sampled (numbered from 1 to 1,000) in the study. Genotypes are identified as 0 = homozygous for the major frequency allele; 1 = heterozygous; 2= homozygous for the minor frequency allele. SNP markers identification contains chromosome number and bp position (ex. EuBR01s12827, SNP on chromosome 1 at position 12,827 bp)
DOI: 10.3535/ckd-17z-6qh
title: †Hallopora Bassler, 1911

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vfw-6fc-l3r
title: Halite

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.23734104.v1
title: Microenvironment has little effect on the litter decomposition rate of temperate trees

description: Remaining total and ash-free dry mass, nitrogen (N) content, phosphorus (P) content, and carbon to nitrogen ratio (C/N) of the litter of eight tree species in the Arboretum of the Universidad Austral de Chile, expressed as % of the initial content. Initial values correspond to winter time (0). Harvests were performed in spring (4), summer (7) and autumn (9). Constants of decay are estimated.
DOI: 10.3535/bvy-td7-l5k
title: †Anaphragma mirabile cognatum Bassler, 1911

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/p3y-saw-ep0
title: †Dianulites fastigiatus Eichwald, 1829

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/fle-8af-rtv
title: †Monotrypa jewensis Bassler, 1911

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/07x-82q-pfe
title: †Hemiphragma Ulrich, 1893

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/2cl-ldf-9yt
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1577673.v2
title: resting state fMRI dataset of conduct disorder

description: The 4 dataset of conduct disorder patients from 1 to 4 used in this study.
DOI: 10.6084/m9.figshare.22336315.v2
title: bursty and telegraph

description: <strong>This is the data used in my article</strong>: Deep Koopman Neural Network Based Process Monitoring for Industrial Biosystems. <br> n_fixed_p_nums_0_500: bursty n_fixed_p_nums_0_60: telegraph
DOI: 10.3535/6qm-w4w-4ch
title: †Bythopora subgracilis (Ulrich, 1893)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/724-psn-vym
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.12745214.v3
title: High SARS-CoV-2 seroprevalence in Health Care Workers but relatively low numbers of deaths in urban Malawi

description: This data set contains demographic data and SARS-CoV-2 serology data from an asymptomatic health care worker population in Blantyre, Malawi. The data was collected between 22nd May 2020 to 19th June 2020. SARS-CoV-2 anti-Spike (S2) and anti-Nucleoprotein (NP) were detected using the Mologic/Omega Diagnostic ELISA (UK).
DOI: 10.3535/8h1-07s-8d3
title: †Bythopora subgracilis (Ulrich, 1893)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/91f-4hz-6sk
title: †Hemiphragma Ulrich, 1893

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.10220714.v1
title: MOESM10 of Characterization of nAChRs in Nematostella vectensis supports neuronal and non-neuronal roles in the cnidarianâ bilaterian common ancestor

description: Additional file 10: Table S3. Edited amino acid alignment consisting of transmembrane domains and double cysteines necessary for acetylcholine binding. A protein alignment of confirmed bilaterian muscarinic and nicotinic acetylcholine receptors, GABAergic receptors, a confirmed Hydra muscarinic acetylcholine receptor, a potential N. vectensis nicotinic acetylcholine receptor and a cnidarian nicotinic acetylcholine receptor. Protein sequences were edited to consist of the four conserved transmembrane domains (TM1â TM4) and the double cysteines necessary for acetylcholine binding (denoted by asterisks).
DOI: 10.3535/0y3-c6h-7p1
title: †Revalopora revalensis (Dybowski, 1877)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/e7r-61w-8lp
title: †Favositella exserta Bassler, 1911

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/8w3tsjyjmm
title: Data for: Paleomagnetism and the Stability of Dharwar Craton, India

description: This supplementary material reproduces analyses discussed in the paper "Paleomagnetism and Stability of Dharwar Craton, India".
DOI: 10.3535/754-1hy-5c3
title: †Strophomena Blainville, 1824

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rpk-37l-cmr
title: †Oanduella bassleri Männil, 1958

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1573006.v2
title: ASCE Survey Data on Water Managers Raw Data
DOI: 10.3535/hnc-874-lc5
title: Teichichnus isp.

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.11368307.v1
title: Fig4 exp3

description: fluorescence images of GFP expressing cells
DOI: 10.3535/kmw-a9v-gsm
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/thc-xcf-2zf
title: Bryozoa

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/14d-qtb-y52
title: †Goldfussitrypa esthoniae (Bassler, 1911)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wzx-90l-ray
title: †Hallopora Bassler, 1911

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.12009789.v1
title: 1 microsecond simulation of nCoV 6LU7 using the dimeric form,

description: This protein was simulated without its cocrystallized ligand. Simulation time was 1 microsecond. The protein was parametrized using ff19SB and OPC water. <br>Trajectories are shared as dcd charms files without water or counterion molecules.
DOI: 10.6084/m9.figshare.12792029.v5
title: OCT raw scans - HR

description: OCT scans at two lateral resolutions (40 um, 40 um, 2.18 um <i>x,y,z</i> respectively, labeled LR) and (11.1 um ,11.1 um and 2.18 um, labeled HR) were taken every 3 days in a 15 days experiment. LR scans have dimension 250 x 250 x 1024 pixels and are contained in folders name large. HR scans are 900 x 900 x 1024 pixels and are contained in folders names B1 (for the FFM) and B5 (for the SFM). Both HR and LR scans covered a total volume of 10 mm x 10 mm x 2.2 mm. 66 x 3 low resolution (LR) scans covered an area of 0.4 m x 0.025 m in a tiled pattern. 3 x 3 high resolution (HR) scans were taken at the extremes of the same area of interest. Each scan (in .raw format) has a relative .json metadata file named accordingly. Files are labeled with the date and time of acquisition, while the last part of the file name identifies the tile. Days of biofilm development and replicate for each acquisition date are reported in the OCTScans_metadata.xls file.<br>
DOI: 10.6084/m9.figshare.9900089.v1
title: The Multiple Tensions of Organizational Hybridism: A Look at the Translation Perspective and Open Strategy in a Social Enterprise

description: Abstract Purpose: In this research we seek to understand how a social enterprise deals with the multiple tensions of organizational hybridism to achieve its strategic objectives. Design/methodology/approach: A qualitative single-case study was performed using longitudinal and in-depth data collection. For the analysis and interpretation of the data an abductive logic and narrative analysis were used. Findings: We concluded that the actors were involved in various openness practices for inclusion, transparency, flexibility, and horizontalization in the strategic process. We also found evidence that the practices of opening up the strategy support a translation process, thus minimizing the tensions of organizational hybridism. This translation process was redefined in the context of hybridism. Originality/value: This research showed that actor-network theory, in particular the translation perspective, is indicated for the study of social enterprises. Concerning the process of opening up the strategy, it is suggested that the process of horizontalizing relationships and flexibility is necessary in the strategic process, in addition to inclusion and transparency. Another contribution is related to the translation process in hybrid organizations, suggesting a reduction of the political imposition of roles and identities.
DOI: 10.3535/688-l68-edy
title: †Eridotrypa aedilis (Eichwald, 1855)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bwk-dgh-f3s
title: †Phragmoporella maculata (Bassler, 1911)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4rc-pk9-7rp
title: †Homotrypa Ulrich, 1882

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/yj7-3qj-rpn
title: †Ceramoporella Ulrich, 1882

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/8fj-2gs-gpx
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/tmj-z7k-5zl
title: †Ceramoporidae Ulrich, 1882

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.4632280.v1
title: HIF Data Odisha (1) (1) (1).xlsx

description: Data for published paper in PLOS Currents Disasters on Demand Survey for Disaster Microinsurance in Odisha.
DOI: 10.3535/nmr-84n-t7c
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/sk0-ag6-912
title: †Pilina Koken, 1925

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1t4-rln-edl
title: Porifera Grant, 1836

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/6zb-eh0-yrd
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.6991478.v1
title: Genetic Testing and Pregnancy Outcome Analysis of 362 Fetuses with Congenital Heart Disease Identified by Prenatal Ultrasound

description: Abstract Background: Congenital heart defects (CHD), as the most common congenital anomaly, have been reported to be associated with chromosomal abnormalities. Currently, patients with CHD are routinely offered karyotyping and chromosomal microarray (CMA) testing, but the genotype-phenotype relationship has not yet been fully established. Objective: To determine the type and frequency of chromosomal abnormalities in fetuses with CHD and to analyze pregnancy outcomes of fetuses with heart abnormalities caused by different genetic factors. Methods: A total of 362 cases of CHD were enrolled from 2009 to 2016. Detailed ultrasound and laboratory examinations, including karyotyping and CMA, were performed. Outcome was obtained from discharge summaries. Results: Of the 362 fetuses, 220 were found with an isolated CHD, and 142 had CHD with extracardiac anomaly. Among these 362 fetuses, 140 were identified with a genetic cause, including 111 cases with aneuploidy, 10 cases with abnormality of chromosomal structure by karyotyping and 19 cases with pathogenic or likely pathogenic copy-number variations (CNVs) by CMA. The detection rate is close to 38.7%. Only one (identified as trisomy 18 syndrome) in 140 positive cases resulted in perinatal death, with the others being induced. The remaining 222 cases had negative results for both genetic testing and of these cases, 56 resulted in induced labor, and 77 had natural childbirth or caesarean births. The pregnancy outcome of the remaining 89 cases was uncertain. Conclusions: Karyotyping and CMA are effective and accurate prenatal genetic techniques for identifying fetal chromosomal abnormalities associated with cardiac defects, and this can assist clinical doctors to perform appropriate genetic counselling with regard to the etiology and outcome of CHD.
DOI: 10.3535/gt9-hek-d4q
title: Hedstroemophyllum

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zx6-km2-7hg
title: †Heterotrypa Nicholson, 1879

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

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/s18-5y0-nwn
title: †Batostoma Ulrich, 1882

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.5644357.v1
title: Morphological affinities of Homo naledi with other Plio-Pleistocene hominins: a phenetic approach

description: ABSTRACT Recent fossil material found in Dinaledi Chamber, South Africa, was initially described as a new species of genus Homo, namely Homo naledi. The original study of this new material has pointed to a close proximity with Homo erectus. More recent investigations have, to some extent, confirmed this assignment. Here we present a phenetic analysis based on dentocranial metric variables through Principal Components Analysis and Cluster Analysis based on these fossils and other Plio-Pleistocene hominins. Our results concur that the Dinaledi fossil hominins pertain to genus Homo. However, in our case, their nearest neighbors are Homo habilis and Australopithecus sediba. We suggest that Homo naledi is in fact a South African version of Homo habilis, and not a new species. This can also be applied to Australopithecus sediba.
DOI: 10.17632/hrvt43kpxn
title: Data for: Regional landscape change triggered by Andean uplift: the extinction of Sparassodonta (Mammalia, Metatheria) in South America.

description: Data for all analyses carried out in the referenced work.
DOI: 10.3535/7mn-0mw-4h7
title: limestone

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/nal-p18-vk3
title: Rhabdinopora flabelliformis flabelliformis (Eichwald, 1840)

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.8142992.v1
title: Fig03 brining experiment rawdata.csv

description: Raw data and descriptive statistic data (univariate diagram) of figure 03 performed with the Add-In XLSTAT 2009.1.02 is provided as CSV. The data include file name, sample name, type of treatment, area, calculated N2O amounts and statistical values.
DOI: 10.3535/q0b-mb2-x8f
title: limestone

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vcn-j2d-g59
title: limestone

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17632/5zdc953zdg
title: Data Variabel Independen Harian

description: Data Indeks keyakinan konsumen indonesia, curah hujan kota bandung, inflasi indonesia, hari libur nasional indonesia