cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13092846.v1
title: Tissue-specific and transcription-dependent mechanisms regulate primary microRNA processing efficiency of the human Chromosome 19 MicroRNA Cluster

description: One of the longest human microRNA (miRNA) clusters is located on chromosome 19 (C19MC), containing 46 miRNA genes, which were considered to be expressed simultaneously and at similar levels from a common long noncoding transcript. Investigating the two tissue types where C19MC is exclusively expressed, we could show that there is a tissue-specific and chromosomal position-dependent decrease in mature miRNA levels towards the 3ʹ end of the cluster in embryonic stem cells but not in placenta. Although C19MC transcription level is significantly lower in stem cells, this gradual decrease is not present at the primary miRNA levels, indicating that difference in posttranscriptional processing could explain this observation. By depleting Drosha, the nuclease component of the Microprocessor complex, we could further enhance the positional decrease in stem cells, demonstrating that a tissue-specific, local availability of the Microprocessor complex could lie behind the phenomenon. Moreover, we could describe a tissue-specific promoter being exclusively active in placenta, and the epigenetic mark analysis suggested the presence of several putative enhancer sequences in this region. Performing specific chromatin immunoprecipitation followed by quantitative real-time PCR experiments we could show a strong association of Drosha with selected enhancer regions in placenta, but not in embryonic stem cells. These enhancers could provide explanation for a more efficient co-transcriptional recruitment of the Microprocessor, and therefore a more efficient processing of pri-miRNAs throughout the cluster in placenta. Our results point towards a new model where tissue-specific, posttranscriptional “fine-tuning” can differentiate among miRNAs that are expressed simultaneously from a common precursor.
DOI: 10.5281/zenodo.4732272
title: TAMUoic2019 Database P22 Kernel Extension

description: The P22 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.4732271
title: TAMUoic2019 Database P22 Kernel Extension

description: The P22 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: 10.18739/a2g15tc2k
title: Meteorological, Radiation, and Soil Temperature Data, Kuparuk River and Nearby Watersheds: Roche Moutonnée Creek (RMC), 2015-2018.

description: The data files in this data set contain climate information from sites on the North Slope of Alaska in or near the Kuparuk River basin. The data was collected for a hydrologic study of rivers in the North Slope region between 1985-present. Hydro-meteorological stations were established at various locations throughout the Kuparuk, but also in the Putuligayuk and Sagavanirktok watersheds. The variables collected at most stations were air temperature, humidity, wind speed and direction, soil temperature, snow temperature, precipitation, snow depth, and radiation. In the Roche Moutonnee Creek watershed (headwaters of the Sagavanirktok River), the Roche Moutonnee Creek (RMC) meteorological station operated from 2015-2018. IMPORTANT NOTE: Updates and corrections were made to the original datasets by the investigators, and all of the previously published data files should be replaced with this updated dataset. The following corrections were made to the datasets: 1) data from annual .csv files were merged into one .csv file (for each station) containing all years of data, 2) appended new data collected into the .csv file 3) standardized file headers, 4) standardized variable names, units, and sensor installation height above ground surface 5) reviewed all data for quality assurance and added qualifiers to erroneous data, 6) added a data qualifier to wind data during periods of extensive riming on wind sensors, 7) added a qualifier when air temperatures are below -39 degrees Celsius (C) (minimum reporting temperature of some air temperature sensors), and 8) removed duplicative data and fixed timestamp issues.
DOI: 10.6084/m9.figshare.14562045
title: Alignment topoisomerase amino acid sequences.docx

description: sequences of the staphylococcus aureus mutants<br>
DOI: 10.6084/m9.figshare.14562045.v1
title: Alignment topoisomerase amino acid sequences.docx

description: sequences of the staphylococcus aureus mutants<br>
DOI: 10.6084/m9.figshare.13312254.v1
title: Antisense RNA asPcrL regulates expression of photosynthesis genes in <i>Rhodobacter sphaeroides</i> by promoting RNase III-dependent turn-over of <i>puf</i> mRNA

description: Anoxygenic photosynthesis is an important pathway for <i>Rhodobacter sphaeroides</i> to produce ATP under oxygen-limiting conditions. The expression of its photosynthesis genes is tightly regulated at transcriptional and post-transcriptional levels in response to light and oxygen signals, to avoid photooxidative stress by the simultaneous presence of pigments, light and oxygen. The <i>puf</i> operon encodes pigment-binding proteins of the light-harvesting complex I (genes <i>pufB</i> and <i>pufA</i>), of the reaction center (genes <i>pufL</i> and <i>pufM</i>), a scaffold protein (gene <i>pufX</i>) and includes the gene for sRNA PcrX. Segmental differences in the stability of the <i>pufBALMX-pcrX</i> mRNA contribute to the stoichiometry of LHI to RC complexes. With asPcrL we identified the third sRNA and the first antisense RNA that is involved in balancing photosynthesis gene expression in <i>R. sphaeroides</i>. asPcrL influences the stability of the <i>pufBALMX-pcrX</i> mRNA but not of the <i>pufBA</i> mRNA and consequently the stoichiometry of photosynthetic complexes. By base pairing to the <i>pufL</i> region asPcrL promotes RNase III-dependent degradation of the <i>pufBALMX-prcX</i> mRNA. Since asPcrL is activated by the same protein regulators as the <i>puf</i> operon including PcrX it is part of an incoherent feed-forward loop that fine-tunes photosynthesis gene expression. Graphical Abstract Graphical Abstract
DOI: 10.6084/m9.figshare.13134928
title: Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast

description: Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.
DOI: 10.6084/m9.figshare.13134928.v2
title: Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast

description: Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.
DOI: 10.6084/m9.figshare.13134928.v1
title: Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.

description: Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, crosstalk in which mRNA decay machinery and transcription machinery respectively impact transcription and mRNA stability. Rpb4, and likely dimer Rpb4/7, seem the central components of the RNA pol II governing these processes. In this work we unravel the molecular mechanisms participated by Rpb4 that mediate the posttranscriptional events regulating mRNA imprinting and stability. By RIP-Seq, we analysed genome-wide the association of Rpb4 with mRNAs and demonstrated that it targeted a large population of more than 1400 transcripts. A group of these mRNAs was also the target of the RNA binding protein, Puf3. We demonstrated that Rpb4 and Puf3 physically, genetically, and functionally interact and also affect mRNA stability, and likely the imprinting, of a common group of mRNAs. Furthermore, the Rpb4 and Puf3 association with mRNAs depends on one another. We also demonstrated, for the first time, that Puf3 associates with chromatin in an Rpb4-dependent manner. Our data also suggest that Rpb4 could be a key element of the RNA pol II that coordinates mRNA synthesis, imprinting and stability in cooperation with RBPs.
DOI: 10.6084/m9.figshare.14562066.v1
title: alignement topoisomerase amino acid sequences

description: staphylococcus aureus quinolone resistant mutants<br>
DOI: 10.6084/m9.figshare.14562066
title: alignement topoisomerase amino acid sequences

description: staphylococcus aureus quinolone resistant mutants<br>
DOI: 10.6084/m9.figshare.14560530
title: SAM 40: Dataset of 40 Subject EEG Recordings to Monitor the Induced-Stress while performing Stroop Color-Word Test, Arithmetic Task, and Mirror Image Recognition Task

description: This dataset presents a collection of electroencephalographic (EEG) data recorded from 40 subjects (female: 14, male: 26, mean age: 21.5 years). The dataset was recorded from the subjects while performing various tasks such as: Stroop color-word test (SCWT), solving arithmetic questions, identification of symmetric mirror images, and a state of relaxation. Three trials were recorded for each of the individual tasks. The experiment was primarily conducted to monitor the short-term stress elicited in an individual while performing the aforementioned cognitive tasks. 32-channel EEG was recorded using the Emotiv Epoc Flex gel kit. The EEG data were further processed to remove the baseline drifts by subtracting the average trend obtained using the Savitzky-Golay filter. Furthermore, the artifacts were removed by applying wavelet thresholding. The processed data was then segmented into non-overlapping epochs of 25 seconds depending on the various tasks performed by the subjects.
DOI: 10.6084/m9.figshare.14562051
title: mplus data with further understanding the black sheep effect

description: This data includes sociological and research variables. We provide the definition of abbreviations at data file below. SEX= gender; MAR= marital status; AGE=age; EDU= education level; TEN= tenure; GROUP= department; MASC= masculine; FEMI= feminine; BEL= belonging; AUT= autonomy frustration at psychological need of frustration; REL= relatedness frustration at psychological need of frustration; COM= competence frustration at psychological need of frustration; STAY= stay intention; EST= esteem; THW= psychological need of frustration.
DOI: 10.6084/m9.figshare.14562051.v1
title: mplus data with further understanding the black sheep effect

description: This data includes sociological and research variables. We provide the definition of abbreviations at data file below. SEX= gender; MAR= marital status; AGE=age; EDU= education level; TEN= tenure; GROUP= department; MASC= masculine; FEMI= feminine; BEL= belonging; AUT= autonomy frustration at psychological need of frustration; REL= relatedness frustration at psychological need of frustration; COM= competence frustration at psychological need of frustration; STAY= stay intention; EST= esteem; THW= psychological need of frustration.
DOI: 10.5281/zenodo.4674505
title: List of publications examined in "Digital Humanities as a Cross-disciplinary Battleground: An Examination of Inscriptions in Journal Publications"

description: This is the list of publications examined in our paper entitled "Digital Humanities as a Cross-disciplinary Battleground: An Examination of Inscriptions in Journal Publications." The list contains 252 journal publications randomly selected from a list of digital humanities journals indexed in the Crossref database. More details of this dataset can be found: https://arxiv.org/abs/2103.15934.
DOI: 10.5281/zenodo.4674504
title: List of publications examined in "Digital Humanities as a Cross-disciplinary Battleground: An Examination of Inscriptions in Journal Publications"

description: This is the list of publications examined in our paper entitled "Digital Humanities as a Cross-disciplinary Battleground: An Examination of Inscriptions in Journal Publications." The list contains 252 journal publications randomly selected from a list of digital humanities journals indexed in the Crossref database. More details of this dataset can be found: https://arxiv.org/abs/2103.15934.
DOI: 10.6084/m9.figshare.12114543.v1
title: The rare lncRNA GOLLD is widespread and structurally conserved among <i>Mycobacterium</i> tRNA arrays

description: Noncoding RNA (ncRNA) genes produce transcripts involved in a wide range of functions, including catalytic and regulatory functions. Besides, some transcripts have highly complex structures that may impact their activities. Among the largest bacterial ncRNAs, there is the rare GOLLD RNA, which is associated with tRNA genes and supposed to be chromosome- and phage-encoded in specialized groups of bacteria, including those from <i>Lactobacillales</i> and <i>Actinomycetales</i> orders. The only GOLLD structure was inferred from a variety of sequences, including many marine metagenomes. To explore GOLLD RNA in bacterial genomes, we mined the GOLLD gene in thousands of <i>Mycobacterium</i> and virus genomes using Infernal software. We identified this gene in 350 mycobacteria, including megaplasmids, and 39 bacteriophages, mainly in the genomic context of tRNA arrays. <i>Mycobacterium</i> GOLLD genes presented a high diversity and were distributed in three phylogenetic groups: (i) <i>Mycobacterium</i> exclusive; (ii) <i>Mycobacterium</i> and mycobacteriophages; and (iii) mycobacteriophage exclusive. We also determined the GOLLD secondary structure of each group using R2 R software based on GOLLD alignments generated by Infernal software. All GOLLD groups displayed a 3ʹ half conserved structure, including utter E-loops pseudoknots substructures, also shared by non<i>-Mycobacterium</i> GOLLD while the 5ʹ half motif was different among the groups. Here, we showed that the lncRNA GOLLD is widespread in <i>Mycobacterium</i> within tRNA arrays and corroborated the previously predicted GOLLD secondary structure.
DOI: 10.6084/m9.figshare.12114543
title: The rare lncRNA GOLLD is widespread and structurally conserved among <i>Mycobacterium</i> tRNA arrays

description: Noncoding RNA (ncRNA) genes produce transcripts involved in a wide range of functions, including catalytic and regulatory functions. Besides, some transcripts have highly complex structures that may impact their activities. Among the largest bacterial ncRNAs, there is the rare GOLLD RNA, which is associated with tRNA genes and supposed to be chromosome- and phage-encoded in specialized groups of bacteria, including those from <i>Lactobacillales</i> and <i>Actinomycetales</i> orders. The only GOLLD structure was inferred from a variety of sequences, including many marine metagenomes. To explore GOLLD RNA in bacterial genomes, we mined the GOLLD gene in thousands of <i>Mycobacterium</i> and virus genomes using Infernal software. We identified this gene in 350 mycobacteria, including megaplasmids, and 39 bacteriophages, mainly in the genomic context of tRNA arrays. <i>Mycobacterium</i> GOLLD genes presented a high diversity and were distributed in three phylogenetic groups: (i) <i>Mycobacterium</i> exclusive; (ii) <i>Mycobacterium</i> and mycobacteriophages; and (iii) mycobacteriophage exclusive. We also determined the GOLLD secondary structure of each group using R2 R software based on GOLLD alignments generated by Infernal software. All GOLLD groups displayed a 3ʹ half conserved structure, including utter E-loops pseudoknots substructures, also shared by non<i>-Mycobacterium</i> GOLLD while the 5ʹ half motif was different among the groups. Here, we showed that the lncRNA GOLLD is widespread in <i>Mycobacterium</i> within tRNA arrays and corroborated the previously predicted GOLLD secondary structure.
DOI: 10.6084/m9.figshare.11948718.v1
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
title: The large repertoire of 2’-O-methylation guided by C/D snoRNAs on Trypanosoma brucei 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.12089016.v2
title: The large repertoire of 2’-O-methylation guided by C/D snoRNAs on Trypanosoma brucei 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.