cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/343nrfcbp4
title: Purification of enzymatically active Xrn1 for removal of non-capped mRNAs from in vitro transcription reactions and evaluation of mRNA decapping status in vivo

description: Karolina Drążkowska1,#, Rafał Tomecki2,3,#,*, and Agnieszka Tudek2,*

1Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Poland
2Laboratory of RNA Processing and Decay, Institute of Biochemistry and 
Biophysics, Polish Academy of Sciences, Warsaw, Poland
3Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland

#Karolina Drążkowska and Rafał Tomecki contributed equally to this work

*Correspondence should be addressed to Agnieszka Tudek or Rafał Tomecki

Abstract

The cap is a 7-methylguanosine attached to the first messenger RNA (mRNA) nucleotide with a 5'-5' triphosphate bridge. This conserved eukaryotic modification confers stability to the transcripts and is essential for translation initiation. The specific mechanisms that govern transcript cytoplasmic longevity and translatability were always of substantial interest. Multiple works aimed at modeling mRNA decay mechanism, including the onset of decapping, which is the rate-limiting step of mRNA decay. Additionally, with the recent advances in RNA-based vaccines, the importance of efficient synthesis of fully functional mRNA has increased. Non-capped mRNAs arising during in vitro transcription are highly immunogenic, and multiple approaches were developed to reduce their levels. Efficient and low-cost methods for elimination of non-capped mRNAs in vitro are therefore essential to basic sciences and to pharmaceutical applications. Here, we present a protocol for heterologous expression and purification of catalytically active recombinant Xrn1 from Thermothelomyces (Myceliophthora) thermophilus (Tt_Xrn1). We also describe protocols needed to verify the enzyme quality, and provide an overview of its potential applications.
DOI: 10.3535/b9k-2sg-6me
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/gp2-jpc-zb2
title: Illaenus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4j0-hp7-371
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5f2-w6b-z60
title: †Orthis Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/qg0-f82-12a
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.13704559.v7
title: Supplemental materials

description: Supplemental tables and figures
DOI: 10.6084/m9.figshare.14761527.v1
title: DelphiCalcFig8.xlsx

description: Organized data for determination of Phase-shift (DelPhi0) Graph presenting Delphi determination (16 set)
DOI: 10.3535/bbm-h1x-gyl
title: †Subulites Emmons, 1842

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/k2l-llk-pz5
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.25826845.v1
title: <b>急性亚硝酸盐暴露会导致肠道菌群失调和虾中致病</b><b><i>性光细菌</i></b><b>在虾中</b>

description: 的代表性菌株的组装基因组<i>Photobacterium damselae </i>subsp.<i> damselae</i> 本研究中分离并获得了
DOI: 10.3535/2e9-rmp-pne
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/qhb-kn0-sz2
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1177953.v1
title: Dados da pesquisa sobre a satisfação dos trabalhadores em empresas de diferentes setores

description: Esse banco de dados será utilizado ao longo do livro AnalisaR. Ele se originou à partir de duas pesquisas conduzidas para verificar a satisfação de trabalhadores em empresas de diferentes áreas.
DOI: 10.3535/7d9-amw-yfs
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ad4-anh-7h3
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/f4k-ypg-20z
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.24590568.v1
title: Drone-Person Tracking in Uniform Appearance Crowd (D-PTUAC)

description: Drone-person tracking in uniform appearance crowds poses unique challenges due to the difficulty in distinguishing individuals with similar attire and multi-scale variations. To address this issue and facilitate the development of effective tracking algorithms, we present a novel dataset named D-PTUAC (Drone-Person Tracking in Uniform Appearance Crowd). The dataset comprises 138 sequences comprising over 121K frames, each manually annotated with bounding boxes and attributes. During dataset creation, we carefully consider 17 challenging attributes encompassing a wide range of viewpoints and scene complexities. These attributes are annotated to facilitate the analysis of performance based on specific attributes. Extensive experiments are conducted using 44 state-of-the-art (SOTA) trackers, and the performance gap demonstrate the need for a dedicated end-to-end aerial visual object tracker that accounts the inherent properties of aerial environment.<br>
DOI: 10.6084/m9.figshare.27861894.v1
title: Dataset Questionnaire Bali THK (English).doc

description: Tri Hita KaranaQuestionnaire (English)
DOI: 10.3535/bfq-clw-r7f
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x1q-t0x-hg7
title: †Murchisonia d'Archiac & Verneuil, 1841

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.9894371.v1
title: Figshare File 4

description: Proteomics data from the growth experiment (the proteomics without 13C label). The first column contains the protein identifier (Uniprot accession), followed by the protein length, then the total number of unique peptides detected for that protein across all biological and technical replicates (‘No. Unique Peptides Across All Replicates). The subsequent columns contain the total spectral counts and Normalized Spectral Abundance Factor values for each mass spectrometry analysis, (e.g., Early Exp 1, the first technical replicate for early exponential stage). Table is in .xlsx format.
DOI: 10.3535/q0n-t9p-bjj
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/tnl-w33-cbl
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.22178141.v1
title: Proteomics_fulldataset_log2FOT_r3489c180.csv

description: Proteomics_fulldataset_log2FOT_r3489c180.csv
DOI: 10.3535/50j-v2l-v5m
title: †Orthis Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/m67-q5z-qdq
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/bkl-fea-hz1
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xey-3r4-pl8
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.24784485.v1
title: D9-P5-DailyTemp-pH

description: The pH was recorded once daily along with the EC. The temperature was recorded every 10 seconds.
DOI: 10.3535/2e4-d4l-8c5
title: †Orthis Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/lwb-pnq-wdv
title: †Orthis Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/dk9-x53-eyf
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/rrn-12k-xn8
title: Platycladus Spach

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

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xm8-atz-760
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.7315040.v1
title: Data

description: Data used for the systematic review
DOI: 10.3535/2pk-kmj-kn4
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/2wd-zm7-bdx
title: †Oepikina Salmon, 1942

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.28497716.v1
title: survey dataset.xlsx on Effect of Industry 4.0 on Social and Environmental Sustainability in Multinational Manufacturing Industries.

description: The dataset is a response from a survey carried out on the effect of industry 4.0 pillars (i.e. technologies) on multinational manufacturing organizations' environmental and social sustainability in Lagos State, Nigeria. The survey was open to the targeted population between March and October 2024. Thirty-eight questionnaires were returned and filled based on each of the questionnaire sections distributed among the multinational manufacturing companies in Lagos state. Section A of the questionnaire addresses the socio-demography of the respondents, section B assesses the rate of implementation of Industry 4.0 technologies and section C assesses the impact of Industry 4.0 on social and environmental sustainability.
DOI: 10.3535/aw8-0vk-gf2
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ctp-z7k-w40
title: †Orthis Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.27301509.v2
title: GO analysis

description: Transcriptome profiling across 11 different tissues in Pisum sativum.
DOI: 10.3535/vfg-5r7-y0k
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/yk7-myt-dyp
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.21382773.v1
title: RiMod-FTD Metadata

description: Metadata and other information for the RiMod-FTD datasets. <br> https://www.rimod-ftd.org/
DOI: 10.6084/m9.figshare.25827706.v1
title: <b>Substrates mimicking the blastocyst geometry revert pluripotent stem cell to naivety</b>

description: Naïve pluripotent stem cells (nPSCs) have the highest developmental potential among PSCs, but their <i>in vivo </i>existence in blastocysts is transient. Here, inspired from nature, we designed blastocyst motif substrate to achieve the <i>in vitro</i> reversion of PSCs to a naïve state. The substrate features randomly varied microstrucutres encompassing, but not being limited to, geometry of blastocyst.
DOI: 10.3535/0lc-4mj-78c
title: sedimentary rocks

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

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/7ge-273-zc5
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wfy-f4x-h99
title: rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/h68-hm1-r8d
title: Mesofavosites similis Sokolov

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/lq1-qk7-pnb
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1321884.v1
title: AD Model Builder and AutoHotkey Code for Evaluating Genetic Stock Identification Software

description: AD Model Builder .tpl and .dat files and AutoHotkey script for conducting simulations described in Brenden, T.O., J.R. Bence, W. Liu, I. Tsehaye, and K.T. Scribner. In press. Comparison of the accuracy and consistency of likelihood-based estimation routines for genetic stock identification. Methods in Ecology and Evolution combined.ahk - AutoHotkey script for running ONCOR and SPAM main.dat - AD Model Builder .dat file containing factors and factor levels to evaluate during simulations main.tpl - AD Model Builder .tpl file which is the driver program that loops over the factor levels and repeatedly calls the simulation program to produce a dataset and calls the other estimation routines to analyze the dataset mixbayes.tpl - AD Model Builder .tpl that implements the conditional penalized maximum likelihood estimation routine. This file also generate the files (baseline, mixture, control program) needed to run SPAM and ONCOR mixbayes_MLE.tpl - AD Model Builder .tpl that implements the condition maximum likelihood estimation routine. sim.tpl - AD Model Builder .tpl that simulates the actual source population and mixture data for a given combination of factor levels These files are provided without warranty of any kind and in no event shal the authors be liable for any claim, damages or any liabilit.
DOI: 10.6084/m9.figshare.3521282.v1
title: Appendix B. Results of mark-resight models (Tables B1–B12) and occupancy models (Tables B13–B16) for bobcats and pumas on the Western Slope and Front Range, Colorado, USA.

description: Results of mark-resight models (Tables B1–B12) and occupancy models (Tables B13–B16) for bobcats and pumas on the Western Slope and Front Range, Colorado, USA.
DOI: 10.3535/2qm-g0p-sjf
title: rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/mhb-wl7-wbf
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/6y5-p2h-m4p
title: †Diplotrypa Nicholson, 1879

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zgl-qnc-n7x
title: gravel

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.24265198.v6
title: The genome assembly and annotation of <i>Puccinia striiformis</i> f. sp.<i> </i><i>tritici</i> isolate AZ2

description: Stripe rust fungus <i>Puccinia striiformis</i> f. sp. <i>tritici</i> (<i>Pst</i>) is a destructive pathogen of wheat worldwide. PacBio HiFi sequencing technology and a trio-binning approach were combined to generate a fully haplotype-resolved and nearly gap-free genome assembly of <i>Pst</i> isolate AZ2, which was derived from <i>Pst</i> isolate A153 crossing with isolate XZ-2. AZ2A and AZ2B represent the two haplotypes of AZ2. AZ2mt represents the mitochondrial genome of AZ2.AZ2A.genomic.fa.gz and AZ2B.genomic.fa.gz include the genome sequences of haplotype A and B of AZ2.AZ2A.cds.fa.gz and AZ2B.cds.fa.gz include the CDS sequences of haplotype A and B of AZ2.AZ2A.proteins.fa.gz and AZ2B.proteins.fa.gz include the amino acid sequences of haplotype A and B of AZ2.AZ2A.anno.gff3.gz and AZ2B.anno.gff3.gz include the gene annotations of haplotype A and B of AZ2.AZ2mt.genomic.fa.gz includes the mitochondrial genome sequence of AZ2.
DOI: 10.3535/1ja-z08-c2s
title: igneous rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/w3y-v7c-rlq
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.7514789.v1
title: Simulation model of DO and BOD integrating river and reservoir applied to the Tietê River

description: ABSTRACT A simulation model of DO and BOD combining rivers and reservoirs, was developed in the software Microsoft Office Excel and used in the Tietê river, stretch between Pirapora do Bom Jesus and Salto, known to be polluted due to the receipt of the remaining organic load contribution to Metropolitan Region of São Paulo. The calibration used to monitored data and optimization tools. They were simulated 12 scenarios characterized by the combination of the variables: discharged flow (700, 411 and 130 m3/s), level of the reservoir (691 and 688 m), and input concentration of BOD to Pirapora reservoir (37 and 56 mgO2/L). With these analysis of the scenarios was possible to evaluate the impacts of reservoir operation on the water quality of the Tietê River downstream of this dam. The results indicated that the water quality to input on reservoir protrudes towards the operational aspects. Reduce the contribution that organic load refers to a long-term planning. A short-term alternative is to minimize the impacts operate with low discharge reservoir (130 m3/s), while keeping the normal level (691 m). Thus, when the input concentration of BOD is high (56 mgO2/L), the stretch between Pirapora do Bom Jesus and Cabreúva is anoxic and the region of Salto presents DO and BOD concentrations of 3 and 20 mgO2/L, respectively. When normal (37 mgO2/L), is not found anaerobic conditions throughout the simulated stretch and the region of Salto presents concentrations of 6 mgO2/L and BOD equal to 17 mgO2/L.
DOI: 10.3535/0ps-65h-8rk
title: rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1e6-f7d-hhf
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.27266412.v1
title: UAV altimeter Flight data

description: GNSS-R and LiDAR data togeter with GNSS buoy data, used in the paper "Sea Surface Height measurements by UAV altimeters using Nadir LiDAR and low-cost GNSS Reflectometry".F1, F2, F3 are for Flights 1,2,3 respectively. Time, H_U, d_L, d_G, H_B are included in files.F1s.zip, F2s.zip, F3s.zip are zip files for Flights 1, 2, 3, respectively, that includes results of different GNSS system sets.
DOI: 10.3535/77z-bza-yk5
title: rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/r3d-38q-44e
title: igneous rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/b5t-tsh-nn9
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/r1q-zvy-n37
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.17045/sthlmuni.4254335.v1
title: Scripts for logistic regression of ASE genomic determinants.

description: Script used in Steige et al. 2017 PNAS for estimating the impact of genomic features on allele specific expression in Capsella grandiflora using logistic regression.<br> * The folders contains an jupyter notebook (ypython) that runs the analysis by downloading the input from figshare * A html reports of the analysis performed in the paper * a r script from the jupyter notebook
DOI: 10.3535/3le-pld-1c8
title: †Asaphidae

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ee3-dqd-3jx
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5281/zenodo.15114104
title: GeoEcoMar Macrozoobenthos BRIDGE-BS June 2023

description: The dataset contains macrozoobenthos data collected in June 2023, from 6 stations located in the South of the Romanian Black Sea area. The sampling was performed within H2020 BRIDGE-BS Project with the aim of monitoring and data collection, in line with the project objectives, bringing together the expertise and competences required for implementing planned activities. The sediment samples were taken with a Box corer (the sampling size - 0.1 m2) and Van-Veen grab (the sampling size - 0.125 m2). The sediment was preserved in buffered formalin 4% , then sieved through a 1 mm and 0.5 mm mesh sieve and subsequently stored in 70% ethanol. The database comprises taxonomic and quantitative data (density and wet weight biomass per square meter) for 68 macrobenthic species and 2 supraspecific groups.
DOI: 10.5281/zenodo.15114105
title: GeoEcoMar Macrozoobenthos BRIDGE-BS June 2023

description: The dataset contains macrozoobenthos data collected in June 2023, from 6 stations located in the South of the Romanian Black Sea area. The sampling was performed within H2020 BRIDGE-BS Project with the aim of monitoring and data collection, in line with the project objectives, bringing together the expertise and competences required for implementing planned activities. The sediment samples were taken with a Box corer (the sampling size - 0.1 m2) and Van-Veen grab (the sampling size - 0.125 m2). The sediment was preserved in buffered formalin 4% , then sieved through a 1 mm and 0.5 mm mesh sieve and subsequently stored in 70% ethanol. The database comprises taxonomic and quantitative data (density and wet weight biomass per square meter) for 68 macrobenthic species and 2 supraspecific groups.
DOI: 10.6084/m9.figshare.19149308.v1
title: In-Scanner Timing and Behavior Files

description: We examined memory and fMRI activity for photos of indoor and outdoor scenes across four time periods to examine these neural changes more carefully. Participants (N = 21) studied scenes 1 hour, 1 day, 1 week, or 1 month before scanning. During scanning, participants viewed scenes, made old/new recognition memory judgments, and gave confidence ratings.
DOI: 10.3535/5tb-qra-02n
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/6fa-3s3-768
title: Platycladus Spach

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ch3-0fd-b5w
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vge-29d-bc8
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5pl-j82-cvh
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/th3-4bd-4jq
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/g4q-w4w-3q1
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vc2-rx0-1ac
title: sedimentary rocks

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.19152587.v2
title: Survey data of children's attitudes towards trees and the use of wood

description: raw dataset in Excel that served as the basis of statistical analysis
DOI: 10.3535/cak-2xe-1gm
title: rocks

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