cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14883639.v1
title: An integrated DNA and RNA variant detector identifies a highly conserved three base exon in the <i>MAP4K5</i> kinase locus

description: RNA variants that emerge from editing and alternative splicing form important regulatory stages in protein signalling. In this report, we apply an integrated DNA and RNA variant detection workbench to define the range of RNA variants that deviate from the reference genome in a human melanoma cell model. The RNA variants can be grouped into (i) classic ADAR-like or APOBEC-like RNA editing events and (ii) multiple-nucleotide variants (MNVs) including three and six base pair in-frame non-canonical unmapped exons. We focus on validating representative genes of these classes. First, clustered non-synonymous RNA edits (A-I) in the <i>CDK13</i> gene were validated by Sanger sequencing to confirm the integrity of the RNA variant detection workbench. Second, a highly conserved RNA variant in the <i>MAP4K5</i> gene was detected that results most likely from the splicing of a non-canonical three-base exon. The two RNA variants produced from the <i>MAP4K5</i> locus deviate from the genomic reference sequence and produce V569E or V569del isoform variants. Low doses of splicing inhibitors demonstrated that the MAP4K5-V569E variant emerges from an SF3B1-dependent splicing event. Mass spectrometry of the recombinant SBP-tagged MAP4K5<sup>V569E</sup> and MAP4K5<sup>V569del</sup> proteins pull-downs in transfected cell systems was used to identify the protein-protein interactions of these two MAP4K5 isoforms and propose possible functions. Together these data highlight the utility of this integrated DNA and RNA variant detection platform to detect RNA variants in cancer cells and support future analysis of RNA variant detection in cancer tissue.
DOI: 10.6084/m9.figshare.14446345
title: Global identification of RsmA/N binding sites in <i>Pseudomonas aeruginosa</i> by <i>in vivo</i> UV CLIP-seq

description: <i>Pseudomonas aeruginosa</i> harbours two redundant RNA-binding proteins RsmA/RsmN (RsmA/N), which play a critical role in balancing acute and chronic infections. However, <i>in vivo</i> binding sites on target transcripts and the overall impact on the physiology remains unclear. In this study, we applied <i>in vivo</i> UV crosslinking immunoprecipitation followed by RNA-sequencing (UV CLIP-seq) to detect RsmA/N-binding sites at single-nucleotide resolution and mapped more than 500 binding sites to approximately 400 genes directly bound by RsmA/N in <i>P. aeruginosa</i>. This also verified the ANGGA sequence in apical loops skewed towards 5ʹUTRs as a consensus motif for RsmA/N binding. Genetic analysis combined with CLIP-seq results suggested previously unrecognized RsmA/N targets involved in LPS modification. Moreover, the RsmA/N-titrating RNAs RsmY/RsmZ may be positively regulated by the RsmA/N-mediated translational repression of their upstream regulators, thus providing a possible mechanistic explanation for homoeostasis of the Rsm system. Thus, our study provides a detailed view of RsmA/N-RNA interactions and a resource for further investigation of the pleiotropic effects of RsmA/N on gene expression in <i>P. aeruginosa</i>.
DOI: 10.6084/m9.figshare.14446345.v2
title: Global identification of RsmA/N binding sites in <i>Pseudomonas aeruginosa</i> by <i>in vivo</i> UV CLIP-seq

description: <i>Pseudomonas aeruginosa</i> harbours two redundant RNA-binding proteins RsmA/RsmN (RsmA/N), which play a critical role in balancing acute and chronic infections. However, <i>in vivo</i> binding sites on target transcripts and the overall impact on the physiology remains unclear. In this study, we applied <i>in vivo</i> UV crosslinking immunoprecipitation followed by RNA-sequencing (UV CLIP-seq) to detect RsmA/N-binding sites at single-nucleotide resolution and mapped more than 500 binding sites to approximately 400 genes directly bound by RsmA/N in <i>P. aeruginosa</i>. This also verified the ANGGA sequence in apical loops skewed towards 5ʹUTRs as a consensus motif for RsmA/N binding. Genetic analysis combined with CLIP-seq results suggested previously unrecognized RsmA/N targets involved in LPS modification. Moreover, the RsmA/N-titrating RNAs RsmY/RsmZ may be positively regulated by the RsmA/N-mediated translational repression of their upstream regulators, thus providing a possible mechanistic explanation for homoeostasis of the Rsm system. Thus, our study provides a detailed view of RsmA/N-RNA interactions and a resource for further investigation of the pleiotropic effects of RsmA/N on gene expression in <i>P. aeruginosa</i>.
DOI: 10.6084/m9.figshare.14616895.v1
title: Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA

description: TrmB belongs to the class I S-adenosylmethionine (SAM)-dependent methyltransferases (MTases) and introduces a methyl group to guanine at position 7 (m<sup>7</sup>G) in tRNA. In tRNAs m<sup>7</sup>G is most frequently found at position 46 in the variable loop and forms a tertiary base pair with C13 and U22, introducing a positive charge at G46. The TrmB/Trm8 enzyme family is structurally diverse, as TrmB proteins exist in a monomeric, homodimeric, and heterodimeric form. So far, the exact enzymatic mechanism, as well as the tRNA-TrmB crystal structure is not known. Here we present the first crystal structures of <i>B. subtilis</i> TrmB in complex with SAM and SAH. The crystal structures of TrmB apo and in complex with SAM and SAH have been determined by X-ray crystallography to 1.9 Å (apo), 2.5 Å (SAM), and 3.1 Å (SAH). The obtained crystal structures revealed Tyr193 to be important during SAM binding and MTase activity. Applying fluorescence polarization, the dissociation constant K<sub>d</sub> of TrmB and tRNA<sup>Phe</sup> was determined to be 0.12 µM ± 0.002 µM. Luminescence-based methyltransferase activity assays revealed cooperative effects during TrmB catalysis with half-of-the-site reactivity at physiological SAM concentrations. Structural data retrieved from small-angle x-ray scattering (SAXS), mass-spectrometry of cross-linked complexes, and molecular docking experiments led to the determination of the TrmB-tRNA<sup>Phe</sup> complex structure.
DOI: 10.6084/m9.figshare.14829313
title: M6A-BiNP: predicting N<sup>6</sup>-methyladenosine sites based on bidirectional position-specific propensities of polynucleotides and pointwise joint mutual information

description: N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) plays an important role in various biological processes. Identifying m<sup>6</sup>A site is a key step in exploring its biological functions. One of the biggest challenges in identifying m<sup>6</sup>A sites is how to extract features comprising rich categorical information to distinguish m<sup>6</sup>A and non-m<sup>6</sup>A sites. To address this challenge, we propose bidirectional dinucleotide and trinucleotide position-specific propensities, respectively, in this paper. Based on this, we propose two feature-encoding algorithms: Position-Specific Propensities and Pointwise Mutual Information (PSP-PMI) and Position-Specific Propensities and Pointwise Joint Mutual Information (PSP-PJMI). PSP-PMI is based on the bidirectional dinucleotide propensity and the pointwise mutual information, while PSP-PJMI is based on the bidirectional trinucleotide position-specific propensity and the proposed pointwise joint mutual information in this paper. We introduce parameters α and β in PSP-PMI and PSP-PJMI, respectively, to represent the distance from the nucleotide to its forward or backward adjacent nucleotide or dinucleotide, so as to extract features containing local and global classification information. Finally, we propose the M6A-BiNP predictor based on PSP-PMI or PSP-PJMI and SVM classifier. The 10-fold cross-validation experimental results on the benchmark datasets of non-single-base resolution and single-base resolution demonstrate that PSP-PMI and PSP-PJMI can extract features with strong capabilities to identify m<sup>6</sup>A and non-m<sup>6</sup>A sites. The M6A-BiNP predictor based on our proposed feature encoding algorithm PSP-PJMI is better than the state-of-the-art predictors, and it is so far the best model to identify m<sup>6</sup>A and non-m<sup>6</sup>A sites.
DOI: 10.6084/m9.figshare.14829313.v1
title: M6A-BiNP: predicting N<sup>6</sup>-methyladenosine sites based on bidirectional position-specific propensities of polynucleotides and pointwise joint mutual information

description: N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) plays an important role in various biological processes. Identifying m<sup>6</sup>A site is a key step in exploring its biological functions. One of the biggest challenges in identifying m<sup>6</sup>A sites is how to extract features comprising rich categorical information to distinguish m<sup>6</sup>A and non-m<sup>6</sup>A sites. To address this challenge, we propose bidirectional dinucleotide and trinucleotide position-specific propensities, respectively, in this paper. Based on this, we propose two feature-encoding algorithms: Position-Specific Propensities and Pointwise Mutual Information (PSP-PMI) and Position-Specific Propensities and Pointwise Joint Mutual Information (PSP-PJMI). PSP-PMI is based on the bidirectional dinucleotide propensity and the pointwise mutual information, while PSP-PJMI is based on the bidirectional trinucleotide position-specific propensity and the proposed pointwise joint mutual information in this paper. We introduce parameters α and β in PSP-PMI and PSP-PJMI, respectively, to represent the distance from the nucleotide to its forward or backward adjacent nucleotide or dinucleotide, so as to extract features containing local and global classification information. Finally, we propose the M6A-BiNP predictor based on PSP-PMI or PSP-PJMI and SVM classifier. The 10-fold cross-validation experimental results on the benchmark datasets of non-single-base resolution and single-base resolution demonstrate that PSP-PMI and PSP-PJMI can extract features with strong capabilities to identify m<sup>6</sup>A and non-m<sup>6</sup>A sites. The M6A-BiNP predictor based on our proposed feature encoding algorithm PSP-PJMI is better than the state-of-the-art predictors, and it is so far the best model to identify m<sup>6</sup>A and non-m<sup>6</sup>A sites.
DOI: 10.6084/m9.figshare.14494569
title: Optimal RNA binding by Egalitarian, a Dynein cargo adaptor, is critical for maintaining oocyte fate in <i>Drosophila</i>

description: The Dynein motor is responsible for the localization of numerous mRNAs within <i>Drosophila</i> oocytes and embryos. The RNA binding protein, Egalitarian (Egl), is thought to link these various RNA cargoes with Dynein. Although numerous studies have shown that Egl is able to specifically associate with these RNAs, the nature of these interactions has remained elusive. Egl contains a central RNA binding domain that shares limited homology with an exonuclease, yet Egl binds to RNA without degrading it. Mutations have been identified within Egl that disrupt its association with its protein interaction partners, BicaudalD (BicD) and Dynein light chain (Dlc), but no mutants have been described that are specifically defective for RNA binding. In this report, we identified a series of positively charged residues within Egl that are required for RNA binding. Using corresponding RNA binding mutants, we demonstrate that specific RNA cargoes are more reliant on maximal Egl RNA biding activity for their correct localization in comparison to others. We also demonstrate that specification and maintenance of oocyte fate requires maximal Egl RNA binding activity. Even a subtle reduction in Egl’s RNA binding activity completely disrupts this process. Our results show that efficient RNA localization at the earliest stages of oogenesis is required for specification of the oocyte and restriction of meiosis to a single cell.
DOI: 10.6084/m9.figshare.14446345.v1
title: Global identification of RsmA/N binding sites in <i>Pseudomonas aeruginosa</i> by <i>in vivo</i> UV CLIP-seq

description: <i>Pseudomonas aeruginosa</i> harbors two redundant RNA-binding proteins RsmA/RsmN (RsmA/N), which play a critical role in balancing acute and chronic infections. However, <i>in vivo</i> binding sites on target transcripts and the overall impact on the physiology remains unclear. In this study, we applied <i>in vivo</i> UV crosslinking immunoprecipitation followed by RNA-sequencing (UV CLIP-seq) to detect RsmA/N binding sites at single-nucleotide resolution and mapped more than 500 binding sites to approximately 400 genes directly bound by RsmA/N in <i>P. aeruginosa</i>. This also verified the ANGGA sequence in apical loops skewed towards 5ʹUTRs as a consensus motif for RsmA/N binding. Genetic analysis combined with CLIP-seq results suggested previously unrecognized RsmA/N targets involved in LPS modification. Moreover, the RsmA/N-titrating RNAs RsmY/RsmZ may be positively regulated by the RsmA/N-mediated translational repression of their upstream regulators, thus providing a possible mechanistic explanation for homeostasis of the Rsm system. Thus, our study provides a detailed view of RsmA/N-RNA interactions and a resource for further investigation of the pleiotropic effects of RsmA/N on gene expression in <i>P. aeruginosa</i>.
DOI: 10.6084/m9.figshare.14494569.v1
title: Optimal RNA binding by Egalitarian, a Dynein cargo adaptor, is critical for maintaining oocyte fate in <i>Drosophila</i>

description: The Dynein motor is responsible for the localization of numerous mRNAs within <i>Drosophila</i> oocytes and embryos. The RNA binding protein, Egalitarian (Egl), is thought to link these various RNA cargoes with Dynein. Although numerous studies have shown that Egl is able to specifically associate with these RNAs, the nature of these interactions has remained elusive. Egl contains a central RNA binding domain that shares limited homology with an exonuclease, yet Egl binds to RNA without degrading it. Mutations have been identified within Egl that disrupt its association with its protein interaction partners, BicaudalD (BicD) and Dynein light chain (Dlc), but no mutants have been described that are specifically defective for RNA binding. In this report, we identified a series of positively charged residues within Egl that are required for RNA binding. Using corresponding RNA binding mutants, we demonstrate that specific RNA cargoes are more reliant on maximal Egl RNA biding activity for their correct localization in comparison to others. We also demonstrate that specification and maintenance of oocyte fate requires maximal Egl RNA binding activity. Even a subtle reduction in Egl’s RNA binding activity completely disrupts this process. Our results show that efficient RNA localization at the earliest stages of oogenesis is required for specification of the oocyte and restriction of meiosis to a single cell.
DOI: 10.5281/zenodo.6874926
title: Neuroanatomical correlates of Screening for Aphasia in NeuroDegeneration (SAND) battery in non-fluent/agrammatic variant of Primary Progressive Aphasia.

description: In this dataset we provide data from language assessments and MRI in a sample of avPPA patients.
DOI: 10.5281/zenodo.6874925
title: Neuroanatomical correlates of Screening for Aphasia in NeuroDegeneration (SAND) battery in non-fluent/agrammatic variant of Primary Progressive Aphasia.

description: In this dataset we provide data from language assessments and MRI in a sample of avPPA patients.
DOI: 10.5281/zenodo.6957443
title: A multicenter randomized phase 4 trial comparing Sodium Picosulphate plus Magnesium Citrate vs Polyethylene Glycol plus Ascorbic Acid for bowel PREparation before COLonoscopy. The PRECOL trial.

description: This is the database for final analysis of the PRECOL clinical trial, whose abstract follows Background<strong>.</strong> Adequate bowel preparation before colonoscopy is crucial. Unfortunately, up to 25% of all colonoscopies have inadequate bowel cleansing. From a patient perspective, bowel preparation is a main obstacle for colonoscopy. Several low-volume bowel preparations have been formulated to provide more tolerable purgative solutions without loss of efficacy. Methods: In this phase 4, randomized, multicenter, two-arm trial, adult outpatients undergoing colonoscopy received either Sodium Picosulphate plus Magnesium Citrate (SPMC) or Polyethylene Glycol plus Ascorbic Acid (PEG-ASC) for bowel preparation. The primary aims were to test quality of bowel cleansing (primary endpoint, scored according the Boston Bowel Preparation Scale) and patient’s acceptance (measured with 6 visual analogue scales). The study was open as for treatment assignment, and blinded for primary endpoint assessment that was done independently on videotaped colonoscopies by 2 endoscopists not aware of study arm. A sample size of 525 patients was calculated to recognize a difference of 10% in the proportion of successes between the arms with a two-sided alpha error of 0·05 and 90% statistical power. Findings: overall 550 subjects (279 assigned to PEG-ASC and 271 assigned to SPMC) represented the analysis population. There was no statistically significant difference in the success rate according to BBPS: 94·4% with PEG-ASC and 95·7% with SPMC (P=0·49). Acceptance and willing to repeat were significantly better for SPMC with all the scales. Compliance was less than full in 6·6% and 9·9% of cases with PEG-ASC and SPMC, respectively (P=0·17). Nausea and meteorism were significantly more bothersome with PEG-ASC than SPMC. There were no serious adverse events in either group. Interpretation. SPMC and PEG-ASC are not different in terms of efficacy, but SPMC is better tolerated than PEG-ASC. SPMC could be used as alternative to low-volume PEG based purgative solutions for bowel preparation. Funding. This research had no financial support. ClinicalTrials.gov NCT01649674; EudraCT 2011—000587—10.
DOI: 10.5281/zenodo.6957442
title: A multicenter randomized phase 4 trial comparing Sodium Picosulphate plus Magnesium Citrate vs Polyethylene Glycol plus Ascorbic Acid for bowel PREparation before COLonoscopy. The PRECOL trial.

description: This is the database for final analysis of the PRECOL clinical trial, whose abstract follows Background<strong>.</strong> Adequate bowel preparation before colonoscopy is crucial. Unfortunately, up to 25% of all colonoscopies have inadequate bowel cleansing. From a patient perspective, bowel preparation is a main obstacle for colonoscopy. Several low-volume bowel preparations have been formulated to provide more tolerable purgative solutions without loss of efficacy. Methods: In this phase 4, randomized, multicenter, two-arm trial, adult outpatients undergoing colonoscopy received either Sodium Picosulphate plus Magnesium Citrate (SPMC) or Polyethylene Glycol plus Ascorbic Acid (PEG-ASC) for bowel preparation. The primary aims were to test quality of bowel cleansing (primary endpoint, scored according the Boston Bowel Preparation Scale) and patient’s acceptance (measured with 6 visual analogue scales). The study was open as for treatment assignment, and blinded for primary endpoint assessment that was done independently on videotaped colonoscopies by 2 endoscopists not aware of study arm. A sample size of 525 patients was calculated to recognize a difference of 10% in the proportion of successes between the arms with a two-sided alpha error of 0·05 and 90% statistical power. Findings: overall 550 subjects (279 assigned to PEG-ASC and 271 assigned to SPMC) represented the analysis population. There was no statistically significant difference in the success rate according to BBPS: 94·4% with PEG-ASC and 95·7% with SPMC (P=0·49). Acceptance and willing to repeat were significantly better for SPMC with all the scales. Compliance was less than full in 6·6% and 9·9% of cases with PEG-ASC and SPMC, respectively (P=0·17). Nausea and meteorism were significantly more bothersome with PEG-ASC than SPMC. There were no serious adverse events in either group. Interpretation. SPMC and PEG-ASC are not different in terms of efficacy, but SPMC is better tolerated than PEG-ASC. SPMC could be used as alternative to low-volume PEG based purgative solutions for bowel preparation. Funding. This research had no financial support. ClinicalTrials.gov NCT01649674; EudraCT 2011—000587—10.
DOI: 10.6084/m9.figshare.14417129
title: Infrastructure-driven_development_Belo_Monte

description: Dataset compiled from different official statistical offices in Brazil to analyzed the impact of the Belo Monte hydropower plant on the region. The data was used in the paper <em>Infrastructure-driven development: the local social impact of a large hydropower plant in the Amazon</em>
DOI: 10.6084/m9.figshare.14417129.v3
title: Infrastructure-driven_development_Belo_Monte

description: Dataset compiled from different official statistical offices in Brazil to analyzed the impact of the Belo Monte hydropower plant on the region. The data was used in the paper <em>Infrastructure-driven development: the local social impact of a large hydropower plant in the Amazon</em>
DOI: 10.6084/m9.figshare.14417129.v2
title: Infrastructure-driven_development_Belo_Monte

description: Dataset compiled from different official statistical offices in Brazil to analyzed the impact of the Belo Monte hydropower plant on the region. The data was used in the paper <i>Infrastructure-driven development: the local social impact of a large hydropower plant in the Amazon </i>
DOI: 10.17045/sthlmuni.20418804
title: PenandPaper_Computerized_Notetaking_Data_2Aug22.csv

description: This data set includes student survey responses to three online questionnaire items. Data are separated into four regional groups (Indonesia, Sweden, Spain, and the US) as well as into groups that prefer pen and paper notetaking and who prefer computerized notetaking. Abbreviations for the data set are listed at the top of the document.
DOI: 10.17045/sthlmuni.20418804.v1
title: PenandPaper_Computerized_Notetaking_Data_2Aug22.csv

description: This data set includes student survey responses to three online questionnaire items. Data are separated into four regional groups (Indonesia, Sweden, Spain, and the US) as well as into groups that prefer pen and paper notetaking and who prefer computerized notetaking. Abbreviations for the data set are listed at the top of the document.
DOI: 10.5281/zenodo.4704872
title: Snowmelt observations: Understanding wind-driven melt of patchy snow cover

description: These are the images and a brief description of the applied workflow for the snowmelt observations used in the manuscript <strong><em>Understanding wind-driven snowmelt of patchy snow cover </em></strong>by Luuk van der Valk, Adriaan J. Teuling, Luc Girod, Norbert Pirk, Robin Stoffer and Chiel van Heerwaarden, The Cryosphere, submitted The images are taken from 11 June to 15 June 2019 in the Finseelvi catchment, Norway. The images are organized in separate folders for the upwind and downwind edge of the snow patch. For more specific information, see the manuscript.