cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12198264
title: rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments

description: We recently developed the rG4-seq method to detect and map <i>in vitro</i> RNA G-quadruplex (rG4s) structures on a transcriptome-wide scale. rG4-seq of purified human HeLa RNA has revealed many non-canonical rG4s and the effects adjacent sequences have on rG4 formation. In this study, we aimed to improve the outcomes and false-positive discrimination in rG4-seq experiments using a bioinformatic approach. By establishing connections between rG4-seq library preparation chemistry and the underlying properties of sequencing data, we identified how to mitigate indigenous sampling errors and background noise in rG4-seq. We applied these findings to develop a novel bioinformatics pipeline named rG4-seeker (https://github.com/TF-Chan-Lab/rG4-seeker), which uses tailored noise models to autonomously assess and optimize rG4 detections in a replicate-independent manner. Compared with previous methods, rG4-seeker exhibited better false-positive discrimination and improved sensitivity for non-canonical rG4s. Using rG4-seeker, we identified novel features in rG4 formation that were missed previously. rG4-seeker provides a reliable and sensitive approach for rG4-seq investigations, laying the foundations for further elucidation of rG4 biology.
DOI: 10.6084/m9.figshare.11948718
title: Multiple dengue virus serotypes resistant transgenic <i>Aedes aegypti</i> fitness evaluated under laboratory conditions

description: Dengue viruses (DENV) are the wildest transmitted arbovirus members of the family <i>Flaviviridae</i>, genus <i>Flavivirus</i>. Dengue viruses are composed of four serotypes, DENV1, 2, 3, and 4, and these viruses can cause dengue fever and dengue haemorrhagic fever or dengue shock syndrome, when infecting humans. RNA interference (RNAi) is a self-defence mechanism, which can be used to prevent invasions of RNA viruses to the host. Genetically engineering a host with an RNAi molecule that targets a single virus serotype may develop escape mutants, and can cause unusual dominance over other serotypes. Therefore, the simultaneous targeting of multiple serotypes is necessary to block DENV transmission. Here, we report the development of transgenic <i>Aedes aegypti</i> based on a bioinformatically designed multiple miRshRNA (microRNA-based shRNA) DNA sequence under the control of a blood-meal induced promoter, Carboxypeptidase A, to induce RNAi for DENV in <i>Aedes aegypti</i>, and demonstrate the expression of a synthetic multiple shRNA polycistronic cluster having RNA interference sequences to target DENV genomes. The transgenic mosquitoes have lower rates of infection, dissemination, and transmission for DENV2 and DENV4 compared to wild mosquitoes, with a significant reduction of dengue copy number and antigen levels in the midgut. These levels of DENV were low enough to make transgenic mosquitoes stop the DENV transmission from infected host to a susceptible host and refractory to DENV2 and DENV4 infection. Such multiple resistance in <i>Ae. aegypti</i> has not been documented previously. Laboratory fitness measurement of transgenic <i>Ae. aegypti</i> showed results comparable to other reported transgenic mosquitoes.
DOI: 10.6084/m9.figshare.12089016.v1
title: The large repertoire of 2ʹ-<i>O</i>-methylation guided by C/D snoRNAs on <i>Trypanosoma brucei</i> rRNA

description: The parasite <i>Trypanosoma brucei</i> cycles between insect and mammalian hosts, and is the causative agent of sleeping sickness. Here, we performed genome-wide mapping of 2ʹ-<i>O</i>-methylations (Nms) on trypanosome rRNA using three high-throughput sequencing methods; RibOxi-seq, RiboMeth-seq and 2ʹ-<i>O</i>Me-seq. This is the first study using three genome-wide mapping approaches on rRNA from the same species showing the discrepancy among the methods. RibOxi-seq detects all the sites, but RiboMeth-seq is the only method to evaluate the level of a single Nm site. The sequencing revealed at least ninety-nine Nms guided by eighty-five snoRNAs among these thirty-eight Nms are trypanosome specific sites. We present the sequence and target of the C/D snoRNAs guiding on rRNA. This is the highest number of Nms detected to date on rRNA of a single cell parasite. Based on RiboMeth-seq, several Nm sites were found to be differentially regulated at the two stages of the parasite life cycle, the insect procyclic form (PCF) versus the bloodstream form (BSF) in the mammalian host.
DOI: 10.6084/m9.figshare.12198264.v1
title: rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments

description: We recently developed the rG4-seq method to detect and map <i>in vitro</i> RNA G-quadruplex (rG4s) structures on a transcriptome-wide scale. rG4-seq of purified human HeLa RNA has revealed many non-canonical rG4s and the effects adjacent sequences have on rG4 formation. In this study, we aimed to improve the outcomes and false-positive discrimination in rG4-seq experiments using a bioinformatic approach. By establishing connections between rG4-seq library preparation chemistry and the underlying properties of sequencing data, we identified how to mitigate indigenous sampling errors and background noise in rG4-seq. We applied these findings to develop a novel bioinformatics pipeline named rG4-seeker (https://github.com/TF-Chan-Lab/rG4-seeker), which uses tailored noise models to autonomously assess and optimize rG4 detections in a replicate-independent manner. Compared with previous methods, rG4-seeker exhibited better false-positive discrimination and improved sensitivity for non-canonical rG4s. Using rG4-seeker, we identified novel features in rG4 formation that were missed previously. rG4-seeker provides a reliable and sensitive approach for rG4-seq investigations, laying the foundations for further elucidation of rG4 biology.
DOI: 10.6084/m9.figshare.12084861
title: miRNA target identification and prediction as a function of time in gene expression data

description: The understanding of miRNA target interactions is still limited due to conflicting data and the fact that high-quality validation of targets is a time-consuming process. Faster methods like high-throughput screens and bioinformatics predictions are employed but suffer from several problems. One of these, namely the potential occurrence of downstream (i.e. secondary) effects in high-throughput screens has been only little discussed so far. However, such effects limit usage for both the identification of interactions and for the training of bioinformatics tools. In order to analyse this problem more closely, we performed time-dependent microarray screening experiments overexpressing human miR-517a-3p, and, together with published time-dependent datasets of human miR-17-5p, miR-135b and miR-124 overexpression, we analysed the dynamics of deregulated genes. We show that the number of deregulated targets increases over time, whereas seed sequence content and performance of several miRNA target prediction algorithms actually decrease over time. Bioinformatics recognition success of validated miR-17 targets was comparable to that of data gained only 12 h post-transfection. We therefore argue that the timing of microarray experiments is of critical importance for detecting direct targets with high confidence and for the usability of these data for the training of bioinformatics prediction tools.
DOI: 10.6084/m9.figshare.12084861.v1
title: miRNA target identification and prediction as a function of time in gene expression data

description: The understanding of miRNA target interactions is still limited due to conflicting data and the fact that high-quality validation of targets is a time-consuming process. Faster methods like high-throughput screens and bioinformatics predictions are employed but suffer from several problems. One of these, namely the potential occurrence of downstream (i.e. secondary) effects in high-throughput screens has been only little discussed so far. However, such effects limit usage for both the identification of interactions and for the training of bioinformatics tools. In order to analyse this problem more closely, we performed time-dependent microarray screening experiments overexpressing human miR-517a-3p, and, together with published time-dependent datasets of human miR-17-5p, miR-135b and miR-124 overexpression, we analysed the dynamics of deregulated genes. We show that the number of deregulated targets increases over time, whereas seed sequence content and performance of several miRNA target prediction algorithms actually decrease over time. Bioinformatics recognition success of validated miR-17 targets was comparable to that of data gained only 12 h post-transfection. We therefore argue that the timing of microarray experiments is of critical importance for detecting direct targets with high confidence and for the usability of these data for the training of bioinformatics prediction tools.
DOI: 10.6084/m9.figshare.12123849
title: LARP1 isoform expression in human cancer cell lines

description: LARP1 is an oncogenic RNA-binding protein required for ribosome biogenesis and cancer cell survival. From published <i>in vitro</i> studies, there is disparity over which of two different LARP1 protein isoforms (termed the long LI-LARP1 and short SI-LARP1) is the canonical. Here, after conducting a series of biochemical and cellular assays, we conclude that LI-LARP1 (NM_033551.3 &gt; NP_056130.2) is the dominantly expressed form. We observe that SI-LARP1 (NM_015315.5&gt; NP_056130.2) is epigenetically repressed and that this repression is evolutionarily conserved in all but a small subclade of mammalian species. As with other LARP family members, there are multiple potential LARP1 mRNA isoforms that appear to be censored within the nucleus. The capacity of the cell to modulate splicing and expression of these apparently ‘redundant’ mRNAs hints at contextually specific mechanisms of LARP1 expression.
DOI: 10.6084/m9.figshare.12123849.v1
title: LARP1 isoform expression in human cancer cell lines

description: LARP1 is an oncogenic RNA-binding protein required for ribosome biogenesis and cancer cell survival. From published <i>in vitro</i> studies, there is disparity over which of two different LARP1 protein isoforms (termed the long LI-LARP1 and short SI-LARP1) is the canonical. Here, after conducting a series of biochemical and cellular assays, we conclude that LI-LARP1 (NM_033551.3 &gt; NP_056130.2) is the dominantly expressed form. We observe that SI-LARP1 (NM_015315.5&gt; NP_056130.2) is epigenetically repressed and that this repression is evolutionarily conserved in all but a small subclade of mammalian species. As with other LARP family members, there are multiple potential LARP1 mRNA isoforms that appear to be censored within the nucleus. The capacity of the cell to modulate splicing and expression of these apparently ‘redundant’ mRNAs hints at contextually specific mechanisms of LARP1 expression.
DOI: 10.6084/m9.figshare.9968510.v1
title: The LARP1 La-Module recognizes both ends of TOP mRNAs

description: La-Related Protein 1 (LARP1) is an RNA-binding protein that regulates the stability and translation of mRNAs encoding the translation machinery, including ribosomal proteins and translation factors. These mRNAs are characterized by a 5ʹ-terminal oligopyrimidine (TOP) motif that coordinates their temporal and stoichiometric expression. While LARP1 represses TOP mRNA translation <i>via</i> the C-terminal DM15 region, the role of the N-terminal La-Module in the recognition and translational regulation of TOP mRNAs remains elusive. Herein we show that the LARP1 La-Module also binds TOP motifs, although in a cap-independent manner. We also demonstrate that it recognizes poly(A) RNA. Further, our data reveal that the LARP1 La-Module can simultaneously engage TOP motifs and poly(A) RNA. These results evoke an intriguing molecular mechanism whereby LARP1 could regulate translation and stabilization of TOP transcripts.
DOI: 10.6084/m9.figshare.9968510
title: The LARP1 La-Module recognizes both ends of TOP mRNAs

description: La-Related Protein 1 (LARP1) is an RNA-binding protein that regulates the stability and translation of mRNAs encoding the translation machinery, including ribosomal proteins and translation factors. These mRNAs are characterized by a 5ʹ-terminal oligopyrimidine (TOP) motif that coordinates their temporal and stoichiometric expression. While LARP1 represses TOP mRNA translation <i>via</i> the C-terminal DM15 region, the role of the N-terminal La-Module in the recognition and translational regulation of TOP mRNAs remains elusive. Herein we show that the LARP1 La-Module also binds TOP motifs, although in a cap-independent manner. We also demonstrate that it recognizes poly(A) RNA. Further, our data reveal that the LARP1 La-Module can simultaneously engage TOP motifs and poly(A) RNA. These results evoke an intriguing molecular mechanism whereby LARP1 could regulate translation and stabilization of TOP transcripts.
DOI: 10.6084/m9.figshare.12010722
title: Distribution, organization an evolutionary history of La and LARPs in eukaryotes

description: The fate of any cellular RNA is largely influenced by the nature and diversity of its interactions with various RNA-binding proteins (RBPs) leading to the formation of a biologically significant ribonucleoprotein (RNP) complex. La motif-containing proteins (composed of genuine La and La-related proteins (LARPs)) represent an evolutionary conserved family of RBPs that encompass a large range of crucial functions, involving coding and non-coding RNAs. In this work, we provide data that extend our previous knowledge on the distribution, organization and evolutionary history of this important protein family. Using a repertoire of 345 La motif-containing proteins from 135 species representing all major eukaryotic lineages, we were able to pinpoint many lineage-specific variations in the structural organization of La and LARPs and propose new evolutive scenarios to explain their modern genomic distribution.
DOI: 10.6084/m9.figshare.12010722.v1
title: Distribution, organization an evolutionary history of La and LARPs in eukaryotes

description: The fate of any cellular RNA is largely influenced by the nature and diversity of its interactions with various RNA-binding proteins (RBPs) leading to the formation of a biologically significant ribonucleoprotein (RNP) complex. La motif-containing proteins (composed of genuine La and La-related proteins (LARPs)) represent an evolutionary conserved family of RBPs that encompass a large range of crucial functions, involving coding and non-coding RNAs. In this work, we provide data that extend our previous knowledge on the distribution, organization and evolutionary history of this important protein family. Using a repertoire of 345 La motif-containing proteins from 135 species representing all major eukaryotic lineages, we were able to pinpoint many lineage-specific variations in the structural organization of La and LARPs and propose new evolutive scenarios to explain their modern genomic distribution.
DOI: 10.5281/zenodo.4743866
title: TAMUoic2019 Database P42 Kernel Extension

description: The P42 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4743865
title: TAMUoic2019 Database P42 Kernel Extension

description: The P42 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4744479
title: Predictors of intergenerational PTSD in Rwanda after the 1994 genocide against the Tutsi.

description: Data set for the study on predictors of intergenerational PTSD in Rwanda
DOI: 10.5281/zenodo.4744478
title: Predictors of intergenerational PTSD in Rwanda after the 1994 genocide against the Tutsi.

description: Data set for the study on predictors of intergenerational PTSD in Rwanda
DOI: 10.5281/zenodo.4744026
title: IDSL.IPA results for the ST001154 study (HILIC POS)

description: HILIC ESI POS data files from the ST001154 study were processed using the IDSL.IPA pipeline. Individual peaklist, alignment results and the sample and compound centric annotation results are provided in this dataset.
DOI: 10.5281/zenodo.4744025
title: IDSL.IPA results for the ST001154 study (HILIC POS)

description: HILIC ESI POS data files from the ST001154 study were processed using the IDSL.IPA pipeline. Individual peaklist, alignment results and the sample and compound centric annotation results are provided in this dataset.
DOI: 10.5281/zenodo.4744029
title: IDSL.IPA results for the ST000923 study (RP NEG)

description: 604 LCMS data files (RP NEG) from the ST000923 study were re-processed using the IDSL.IPA software. The results include individual peaklists and alignment results.
DOI: 10.5281/zenodo.4744028
title: IDSL.IPA results for the ST000923 study (RP NEG)

description: 604 LCMS data files (RP NEG) from the ST000923 study were re-processed using the IDSL.IPA software. The results include individual peaklists and alignment results.
DOI: 10.12751/g-node.arf7ol
title: Dataset of cortical activity recorded with high spatial resolution from anesthetized rats

description: Publicly available neural recordings obtained with high spatial resolution are scarce. Here, we present an electrophysiological dataset recorded from the neocortex of twenty rats anesthetized with ketamine/xylazine. The wideband, spontaneous recordings were acquired with a single-shank silicon-based probe having 128 densely packed recording sites arranged in a 32x4 array. The dataset contains the activity of a total of 7126 sorted single units extracted from all layers of the cortex. Here, we share raw neural recordings, as well as spike times, extracellular spike waveforms and several properties of units packaged in a standardized electrophysiological data format. For technical validation of our dataset, we provide the distributions of derived single unit properties along with various spike sorting quality metrics.
description: IsDescribedBy: Fiáth, R., Raducanu, B. C., Musa, S., Andrei, A., Lopez, C. M., van Hoof, C., Ruther, P., Aarts, A., Horváth, D., Ulbert, I. (2018) A silicon-based neural probe with densely-packed low-impedance titanium nitride microelectrodes for ultrahigh-resolution in vivo recordings. Biosensors and Bioelectronics 106: 86-92. (https://doi.org/10.1016/j.bios.2018.01.060)
DOI: 10.6084/m9.figshare.14251130.v1
title: Do different activation patterns between the medial and the lateral gastrocnemius translate into different fascicle behavior during walking?

description: The file contains all the results analysed in the study in .mat format. For each measurement (i.e. EMG, muscle fascicle length, muscle fascicle pennation angle and muscle fascicle velocity), the individual and group mean patterns during level and incline walking are availables as well as the parameters extracted from these patterns (i.e. peak EMG amplitude, average EMG amplitude during stance, average EMG amplitude during the whole cycle, the amount of fascicle lengthening, the amount of fascicle shortening, the change in pennation angle during the fascicle lengthening period, the change in pennation angle during the fascicle shortening period and the peak shortening velocity). An example of EMG and ultrasound raw data accompagnied by an "user guide" document was also available. All methodological considerations are described in the scientific article linked to the data.
DOI: 10.34740/kaggle/dsv/2213789
title: Nepal ICU and Ventilators Occupancy for COVID
DOI: 10.5281/zenodo.4744495
title: IDSL.IPA results for the ST001237 study (HILIC-POS)

description: 1,382 HILIC ESI POS data files for the ST001237 study were re-processed with the IDSL.IPA software. The results contain the individual peaklist and the alignment results.
DOI: 10.5281/zenodo.4744494
title: IDSL.IPA results for the ST001237 study (HILIC-POS)

description: 1,382 HILIC ESI POS data files for the ST001237 study were re-processed with the IDSL.IPA software. The results contain the individual peaklist and the alignment results.
DOI: 10.6084/m9.figshare.14558802
title: Relative abundance of skin microbiome composition of tinea pedis

description: Relative abundances of taxas at phylum, genus and species levels in patients with tinea pedis (Pt), patients at remission stage (rem) and healthy controls (h.c.).
DOI: 10.6084/m9.figshare.14558802.v2
title: Relative abundance of skin microbiome composition of tinea pedis

description: Relative abundances of taxas at phylum, genus and species levels in patients with tinea pedis (Pt), patients at remission stage (rem) and healthy controls (h.c.).
DOI: 10.6084/m9.figshare.14558802.v1
title: relative abundance of skin microbiome composition of tinea pedis

description: Relative abundances of taxas at phylum, genus and species levels in patients with tinea pedis (Pt), patients at remission stage (rem) and healthy controls (h.c.).
DOI: 10.6084/m9.figshare.12971902
title: The Rab7 subfamily across <i>Paramecium aurelia</i> species; evidence of high conservation in sequence and function

description: We examined sequence conservation and signatures of selection in Rab7 proteins across 11 <i>Paramecium aurelia</i> species, and determined the localization patterns of two <i>P. tetraurelia</i> Rab7 paralogs when expressed as GFP fusions in live cells. We found that, while there is a variable number of Rab7 paralogs per genome, Rab7 genes are highly conserved in sequence and appear to be under strong purifying selection across <i>aurelias</i>. Additionally, and surprisingly based on earlier studies, we found that two <i>P. tetraurelia</i> Rab7 proteins have virtually identical localization patterns. Consistent with this, when we examined the gene family of a highly conserved Rab binding partner across <i>aurelias</i> (Rab-Interacting Lysosomal Protein, or RILP), we found that residues in key binding sites in RILPs were absolutely conserved in 13 of 21 proteins, representing genes from 9 of the 11 species examined. Of note, RILP gene number appears to be even more constrained than Rab7 gene number per genome. <b>Abbreviation</b>: WGD: Whole genome duplication