cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9771413.v1
title: Blocking late stages of splicing quickly limits pre-spliceosome assembly in vivo

description: Pre-messenger RNA splicing involves multi-step assembly of the large spliceosome complexes that catalyse the two consecutive trans-esterification reactions, resulting in intron removal. There is evidence that proof-reading mechanisms monitor the fidelity of this complex process. Transcripts that fail these fidelity tests are thought to be directed to degradation pathways, permitting the splicing factors to be recycled. While studying the roles of splicing factors in vivo, in budding yeast, we performed targeted depletion of individual proteins, and analysed the effect on co-transcriptional spliceosome assembly and splicing efficiency. Unexpectedly, depleting factors such as Prp16 or Prp22, that are known to function at the second catalytic step or later in the splicing pathway, resulted in a defect in the first step of splicing, and accumulation of arrested spliceosomes. Through a kinetic analysis of newly synthesized RNA, we observed that a second step splicing defect (the primary defect) was rapidly followed by the first step of splicing defect. Our results show that knocking down a splicing factor can quickly lead to a recycling defect with splicing factors sequestered in stalled complexes, thereby limiting new rounds of splicing. We demonstrate that this ‘feed-back’ effect can be minimized by depleting the target protein more gradually or only partially, allowing a better separation between primary and secondary effects. Our findings indicate that splicing surveillance mechanisms may not always cope with spliceosome assembly defects, and suggest that work involving knock-down of splicing factors or components of other large complexes should be carefully monitored to avoid potentially misleading conclusions.
DOI: 10.15468/dl.768mz3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chiloglanis niger Roberts, 1989",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-16.9807 11.2818,-16.9054 11.0599,-16.8618 11.0599,-16.8618 11.7189,-16.9807 11.2818))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057525-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.9699254
title: Identification of the Selenoprotein S Positive UGA Recoding (SPUR) element and its position-dependent activity

description: Selenoproteins are a unique class of proteins that contain the 21<sup>st</sup> amino acid, selenocysteine (Sec). Addition of Sec into a protein is achieved by recoding of the UGA stop codon. All 25 mammalian selenoprotein mRNAs possess a 3′ UTR stem-loop structure, the Selenocysteine Insertion Sequence (SECIS), which is required for Sec incorporation. It is widely believed that the SECIS is the major RNA element that controls Sec insertion, however recent findings in our lab suggest otherwise for Selenoprotein S (SelS). Here we report that the first 91 nucleotides of the SelS 3′ UTR contain a proximal stem loop (PSL) and a conserved sequence we have named the SelS Positive UGA Recoding (SPUR) element. We developed a SelS-V5/UGA surrogate assay for UGA recoding, which was validated by mass spectrometry to be an accurate measure of Sec incorporation in cells. Using this assay, we show that point mutations in the SPUR element greatly reduce recoding in the reporter; thus, the SPUR is required for readthrough of the UGA-Sec codon. In contrast, deletion of the PSL increased Sec incorporation. This effect was reversed when the PSL was replaced with other stem-loops or an unstructured sequence, suggesting that the PSL does not play an active role in Sec insertion. Additional studies revealed that the position of the SPUR relative to the UGA-Sec codon is important for optimal UGA recoding. Our identification of the SPUR element in the SelS 3′ UTR reveals a more complex regulation of Sec incorporation than previously realized.
DOI: 10.6084/m9.figshare.9699254.v1
title: Identification of the Selenoprotein S Positive UGA Recoding (SPUR) element and its position-dependent activity

description: Selenoproteins are a unique class of proteins that contain the 21<sup>st</sup> amino acid, selenocysteine (Sec). Addition of Sec into a protein is achieved by recoding of the UGA stop codon. All 25 mammalian selenoprotein mRNAs possess a 3′ UTR stem-loop structure, the Selenocysteine Insertion Sequence (SECIS), which is required for Sec incorporation. It is widely believed that the SECIS is the major RNA element that controls Sec insertion, however recent findings in our lab suggest otherwise for Selenoprotein S (SelS). Here we report that the first 91 nucleotides of the SelS 3′ UTR contain a proximal stem loop (PSL) and a conserved sequence we have named the SelS Positive UGA Recoding (SPUR) element. We developed a SelS-V5/UGA surrogate assay for UGA recoding, which was validated by mass spectrometry to be an accurate measure of Sec incorporation in cells. Using this assay, we show that point mutations in the SPUR element greatly reduce recoding in the reporter; thus, the SPUR is required for readthrough of the UGA-Sec codon. In contrast, deletion of the PSL increased Sec incorporation. This effect was reversed when the PSL was replaced with other stem-loops or an unstructured sequence, suggesting that the PSL does not play an active role in Sec insertion. Additional studies revealed that the position of the SPUR relative to the UGA-Sec codon is important for optimal UGA recoding. Our identification of the SPUR element in the SelS 3′ UTR reveals a more complex regulation of Sec incorporation than previously realized.
DOI: 10.6084/m9.figshare.9755858
title: From reporters to endogenous genes: the impact of the first five codons on translation efficiency in <i>Escherichia coli</i>

description: Translation initiation is a critical step in the regulation of protein synthesis, and it is subjected to different control mechanisms, such as 5ʹ UTR secondary structure and initiation codon context, that can influence the rates at which initiation and consequentially translation occur. For some genes, translation elongation also affects the rate of protein synthesis. With a GFP library containing nearly all possible combinations of nucleotides from the 3<sup>rd</sup> to the 5<sup>th</sup> codon positions in the protein coding region of the mRNA, it was previously demonstrated that some nucleotide combinations increased GFP expression up to four orders of magnitude. While it is clear that the codon region from positions 3 to 5 can influence protein expression levels of artificial constructs, its impact on endogenous proteins is still unknown. Through bioinformatics analysis, we identified the nucleotide combinations of the GFP library in <i>Escherichia coli</i> genes and examined the correlation between the expected levels of translation according to the GFP data with the experimental measures of protein expression. We observed that <i>E. coli</i> genes were enriched with the nucleotide compositions that enhanced protein expression in the GFP library, but surprisingly, it seemed to affect the translation efficiency only marginally. Nevertheless, our data indicate that different enterobacteria present similar nucleotide composition enrichment as <i>E. coli</i>, suggesting an evolutionary pressure towards the conservation of short translational enhancer sequences.
DOI: 10.6084/m9.figshare.9755858.v2
title: From reporters to endogenous genes: the impact of the first five codons on translation efficiency in <i>Escherichia coli</i>

description: Translation initiation is a critical step in the regulation of protein synthesis, and it is subjected to different control mechanisms, such as 5ʹ UTR secondary structure and initiation codon context, that can influence the rates at which initiation and consequentially translation occur. For some genes, translation elongation also affects the rate of protein synthesis. With a GFP library containing nearly all possible combinations of nucleotides from the 3<sup>rd</sup> to the 5<sup>th</sup> codon positions in the protein coding region of the mRNA, it was previously demonstrated that some nucleotide combinations increased GFP expression up to four orders of magnitude. While it is clear that the codon region from positions 3 to 5 can influence protein expression levels of artificial constructs, its impact on endogenous proteins is still unknown. Through bioinformatics analysis, we identified the nucleotide combinations of the GFP library in <i>Escherichia coli</i> genes and examined the correlation between the expected levels of translation according to the GFP data with the experimental measures of protein expression. We observed that <i>E. coli</i> genes were enriched with the nucleotide compositions that enhanced protein expression in the GFP library, but surprisingly, it seemed to affect the translation efficiency only marginally. Nevertheless, our data indicate that different enterobacteria present similar nucleotide composition enrichment as <i>E. coli</i>, suggesting an evolutionary pressure towards the conservation of short translational enhancer sequences.
DOI: 10.6084/m9.figshare.9755858.v1
title: From reporters to endogenous genes: the impact of the first five codons on translation efficiency in <i>Escherichia coli</i>.

description: Translation initiation is a critical step in the regulation of protein synthesis, and it is subjected to different control mechanisms, such as 5ʹ UTR secondary structure and initiation codon context, that can influence the rates at which initiation and consequentially translation occur. For some genes, translation elongation also affects the rate of protein synthesis. With a GFP library containing nearly all possible combinations of nucleotides from the 3<sup>rd</sup> to the 5<sup>th</sup> codon positions in the protein coding region of the mRNA, it was previously demonstrated that some nucleotide combinations increased GFP expression up to four orders of magnitude. While it is clear that the codon region from positions 3 to 5 can influence protein expression levels of artificial constructs, its impact on endogenous proteins is still unknown. Through bioinformatics analysis, we identified the nucleotide combinations of the GFP library in <i>Escherichia coli</i> genes and examined the correlation between the expected levels of translation according to the GFP data with the experimental measures of protein expression. We observed that <i>E. coli</i> genes were enriched with the nucleotide compositions that enhanced protein expression in the GFP library, but surprisingly, it seemed to affect the translation efficiency only marginally. Nevertheless, our data indicate that different enterobacteria present similar nucleotide composition enrichment as <i>E. coli</i>, suggesting an evolutionary pressure towards the conservation of short translational enhancer sequences.
DOI: 10.6084/m9.figshare.29366384
title: Model of GHRM practices impact on the employees.docx

description: Green human resource model, impacts on the employees
DOI: 10.6084/m9.figshare.29366384.v1
title: Model of GHRM practices impact on the employees.docx

description: Green human resource model, impacts on the employees
DOI: 10.18112/openneuro.ds005700.v1.0.3
title: NeuroEmo: An fMRI Dataset for Emotion Recognition
DOI: 10.15468/dl.2duag6
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is New Caledonia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Phyllanthus deplanchei Müll.Arg."
 ]
}

 The dataset includes 39 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057526-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sr2na9
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "TaxonKey is Bitis inornata (Smith, 1838)"
 ]
}

 The dataset includes 23 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057527-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15699034
title: Data for figures in the Publication "Unveiling aerosol–cloud interactions – Part 2: Minimising the effects of aerosol swelling and wet scavenging in ECHAM6-HAM2 for comparison to satellite data"

description: This repository contains data to produce figures for the paper:

"Neubauer, D., Christensen, M. W., Poulsen, C. A., and Lohmann, U.: Unveiling aerosol–cloud interactions – Part 2: Minimising the effects of aerosol swelling and wet scavenging in ECHAM6-HAM2 for comparison to satellite data, Atmos. Chem. Phys., 17, 13165–13185, https://doi.org/10.5194/acp-17-13165-2017, 2017. "

Note that scritps are to be found in the accompanying package (https://doi.org/10.5281/zenodo.15698754)
DOI: 10.5281/zenodo.15699033
title: Data for figures in the Publication "Unveiling aerosol–cloud interactions – Part 2: Minimising the effects of aerosol swelling and wet scavenging in ECHAM6-HAM2 for comparison to satellite data"

description: This repository contains data to produce figures for the paper:

"Neubauer, D., Christensen, M. W., Poulsen, C. A., and Lohmann, U.: Unveiling aerosol–cloud interactions – Part 2: Minimising the effects of aerosol swelling and wet scavenging in ECHAM6-HAM2 for comparison to satellite data, Atmos. Chem. Phys., 17, 13165–13185, https://doi.org/10.5194/acp-17-13165-2017, 2017. "

Note that scritps are to be found in the accompanying package (https://doi.org/10.5281/zenodo.15698754)
DOI: 10.15468/dl.uxezmt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coelastrum Naegeli",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.5808 -24.13,35.5909 -24.0715,30.5701 -24.0715,30.5701 -28.5786,32.4847 -28.5786,32.55 -28.5222,33.0346 -26.8668,32.9741 -26.7838,33.0415 -26.059,32.9304 -26.0011,32.7994 -26.1281,32.6834 -26.0015,32.813 -25.8728,32.8513 -25.7166,33.3048 -25.3731,35.1489 -24.6699,35.5808 -24.13))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057528-250525065834625/datasets/export for details.
DOI: 10.15468/dl.xjvqdf
title: Occurrence Download

description: A dataset containing 3540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "TaxonKey is Piliostigma thonningii (Schumach.) Milne-Redh."
 ]
}

 The dataset includes 3540 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057529-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pvxu76
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chiloglanis niger Roberts, 1989",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-17.18 12.1194,-16.8618 11.8636,-16.8618 16.9131,-16.9262 16.7412,-17.0293 15.9092,-17.4711 15.2969,-17.9089 15.085,-18.0432 14.7429,-17.8486 14.3198,-17.2612 13.8841,-17.2879 12.4225,-17.18 12.1194))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057530-250525065834625/datasets/export for details.
DOI: 10.15468/dl.h53kgz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coelastrum Naegeli",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((31.8862 -21.3285,30.5701 -20.3186,30.5701 -24.0715,35.5909 -24.0715,35.6007 -24.0157,35.6007 -23.8125,35.4969 -23.7035,35.6007 -23.165,35.6007 -22.9702,35.227 -22.2482,34.6862 -21.6944,34.013 -21.3095,33.5 -21.1593,32.9675 -21.1092,32.4352 -21.1612,31.8862 -21.3285))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057531-250525065834625/datasets/export for details.
DOI: 10.15468/dl.5ppcg2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chiloglanis niger Roberts, 1989",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-17.0425 19.3358,-16.8618 19.0648,-16.8618 20.0599,-16.9237 20.0599,-17.0425 19.3358))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057532-250525065834625/datasets/export for details.
DOI: 10.15468/dl.tt4n6z
title: Occurrence Download

description: A dataset containing 8885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Estrilda troglodytes (Lichtenstein, 1823)"
 ]
}

 The dataset includes 8885 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057535-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15125/bath-01370
title: Dataset for "The influence of occupant behaviour on indoor air quality and COVID-19 risk in refugee shelters and temporary houses"

description: The dataset contains the monitored data in six temporary houses in Japan. The dataset contains the outdoor temperature of the location and the indoor parameters of the temporary houses: indoor concentration of carbon dioxide, indoor temperature and relative humidity. The dataset also contains monitored occupant behaviour: occupancy, window and door operation, use of kitchen.
description: The continuous measurement of CO2, indoor and outdoor air temperature and relative humidity was performed from the 1st of December 2022 to the 8th of December 2022. The indoor parameters were measured at 2 minutely intervals in all the rooms of the temporary houses for seven consecutive days (168 hours). Measurements were performed by placing one sensor in each room of the temporary house. Sensors were placed in every room as follow, away from windows and heat sources and at a height of 1.1 m to minimise the influence of the households nearby. Outdoor CO2 has been recorded through spot measurements. The adopted CO2 sensor has a calibration function (auto/manual calibration) to compensate for sensor drift that can occur over time.
description: Sensor used for outdoor temperature: TANDD, model TR-52i
Sensor used for indoor CO2 and relative humidity: TANDD, model TR-76Ui
description: The data have been organised in six csv files, one for each temporary house.
DOI: 10.15468/dl.zdn8uy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coelastrum Naegeli",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((27.1586 -33.5889,28.2048 -32.9007,25.5395 -32.9007,25.5395 -34.1098,25.6468 -34.1222,25.7787 -34.0734,25.7098 -33.9109,25.8639 -33.797,26.4806 -33.8473,27.1586 -33.5889))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057536-250525065834625/datasets/export for details.
DOI: 10.15468/dl.76u5q4
title: Occurrence Download

description: A dataset containing 3574 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Mayaca fluviatilis Aubl."
 ]
}

 The dataset includes 3574 records from 258 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057534-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v4v5h9
title: Occurrence Download

description: A dataset containing 3540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "OccurrenceStatus is Present",
 "TaxonKey is Piliostigma thonningii (Schumach.) Milne-Redh."
 ]
}

 The dataset includes 3540 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057538-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t4zca2
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Angola",
 "TaxonKey is Francolinus afer (P.L.S.Müller, 1776)"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057537-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8sxqbr
title: Occurrence Download

description: A dataset containing 3540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Benin",
 "OccurrenceStatus is Present",
 "TaxonKey is Piliostigma thonningii (Schumach.) Milne-Redh."
 ]
}

 The dataset includes 3540 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057539-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hnhyb2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chiloglanis niger Roberts, 1989",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-23.2862 17.2255,-23.4937 16.8096,-23.4003 15.7935,-23.8743 15.8233,-24.2178 15.531,-24.9647 15.3946,-25.2488 14.8377,-25.0969 14.4751,-24.7024 14.3018,-23.9298 14.5093,-23.3237 14.4311,-22.7909 14.7585,-22.613 15.0206,-22.6491 15.5015,-22.293 15.7351,-22.1649 16.0843,-22.476 17.116,-22.919 17.3554,-23.2862 17.2255))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057540-250525065834625/datasets/export for details.