cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1353971.v3
title: Sense overlapping transcripts in IS<i>1341</i>-type transposase genes are functional non-coding RNAs in archaea

description: The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS<i>1341</i>-type transposase (<i>tnpB</i>) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon <i>Halobacterium salinarum</i> NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS<i>1341</i>-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a <i>H. salinarum</i> intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved <i>H. salinarum</i> growth, indicating that these ncRNAs are functional.
DOI: 10.5517/ccdc.csd.cc25vkh3
title: CCDC 2021525: Experimental Crystal Structure Determination

description: Related Article: D. Rodríguez, S.A. Guerrero, A. Palma, J. Cobo, C. Glidewell|2020|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|76|883|doi:10.1107/S2053229620010803
DOI: 10.5517/ccdc.csd.cc25vkj4
title: CCDC 2021526: Experimental Crystal Structure Determination

description: Related Article: D. Rodríguez, S.A. Guerrero, A. Palma, J. Cobo, C. Glidewell|2020|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|76|883|doi:10.1107/S2053229620010803
DOI: 10.6084/m9.figshare.1353971.v5
title: Sense overlapping transcripts in IS<i>1341</i>-type transposase genes are functional non-coding RNAs in archaea

description: The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS<i>1341</i>-type transposase (<i>tnpB</i>) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon <i>Halobacterium salinarum</i> NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS<i>1341</i>-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a <i>H. salinarum</i> intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved <i>H. salinarum</i> growth, indicating that these ncRNAs are functional.
DOI: 10.5517/ccdc.csd.cc25vkk5
title: CCDC 2021527: Experimental Crystal Structure Determination

description: Related Article: D. Rodríguez, S.A. Guerrero, A. Palma, J. Cobo, C. Glidewell|2020|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|76|883|doi:10.1107/S2053229620010803
DOI: 10.5517/ccdc.csd.cc25vkl6
title: CCDC 2021528: Experimental Crystal Structure Determination

description: Related Article: D. Rodríguez, S.A. Guerrero, A. Palma, J. Cobo, C. Glidewell|2020|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|76|883|doi:10.1107/S2053229620010803
DOI: 10.6084/m9.figshare.1353971.v4
title: Sense overlapping transcripts in IS<i>1341</i>-type transposase genes are functional non-coding RNAs in archaea

description: The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS<i>1341</i>-type transposase (<i>tnpB</i>) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon <i>Halobacterium salinarum</i> NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS<i>1341</i>-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a <i>H. salinarum</i> intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved <i>H. salinarum</i> growth, indicating that these ncRNAs are functional.
DOI: 10.6084/m9.figshare.1353913
title: Individual-area relationship best explains goose species density in wetlands

description: Use MCMCglmm to analysis the effect of ecological and human disturbance on two goose species densities in wetland.
DOI: 10.6084/m9.figshare.1353913.v1
title: Individual-area relationship best explains goose species density in wetlands

description: Use MCMCglmm to analysis the effect of ecological and human disturbance on two goose species densities in wetland.
DOI: 10.6084/m9.figshare.1353770
title: Seattle Street Clocks in 1924, 1927, 1928

description: Three inventories of every clock in downtown Seattle. They were made in 1924, 1927, and 1928. I stumbled upon them a few years ago at the Seattle Department of Transportation while I was trying to look up street use permits. I never discovered how to see old permits, but after I left a city employee emailed me saying she had found a folder of old records. Pure gold. Only the 1927 inventory included clocks outside of downtown. They all included a clock at the Japanese Commercial Bank that hung off the side of the building, and ’27 and ’28 included a similar clock at People’s Bank. Possibly those two clocks required a permit to hang out over the public right-of-way, as did the street clocks in the sidewalk. Other clocks downtown (for example on Colman ferry dock; King Street Station; Union Station) were not included, hinting at restrictive criteria.
DOI: 10.6084/m9.figshare.1352093
title: Alignment for the 5' UTR

description: Alignment for the 5' UTR region for the 4 Jalisco populations
DOI: 10.6084/m9.figshare.1352094
title: Alignment for the 66kb upstream region

description: Alignment for the 66kb upstream region for the 4 Jalisco populations
DOI: 10.5517/ccdc.csd.cc25wqyr
title: CCDC 2022655: Experimental Crystal Structure Determination

description: Related Article: N.T. Cong, H.T.X. Trang, P.D. Dung, T.H. Phuong, V.Q. Trung, N.D. Dat, D.T.T. Anh, N.V. Tuyen, L. Van Meervelt|2020|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|76|874|doi:10.1107/S2053229620011018
DOI: 10.6084/m9.figshare.1352093.v1
title: Alignment for the 5' UTR

description: Alignment for the 5' UTR region for the 4 Jalisco populations
DOI: 10.5517/ccdc.csd.cc25wqzs
title: CCDC 2022656: Experimental Crystal Structure Determination

description: Related Article: N.T. Cong, H.T.X. Trang, P.D. Dung, T.H. Phuong, V.Q. Trung, N.D. Dat, D.T.T. Anh, N.V. Tuyen, L. Van Meervelt|2020|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|76|874|doi:10.1107/S2053229620011018
DOI: 10.6084/m9.figshare.1352076
title: Long-term trends in Lake Ontario's benthic macroinvertebrate community from 1994–2008

description: The benthic macroinvertebrate community of Lake Ontario was assessed through a lakewide survey in 2008. <i>Diporeia</i> was very rare throughout the lake at all depths in 2008, and only four of 52 locations had densities &gt;100 m<sup>−2</sup>, all of them at depths &gt;90 m. The maximum density of <i>Diporeia</i> found at any location was at 257 m<sup>−2</sup> in 2008, which can be compared to maximum densities of 13,280 m<sup>−2</sup> observed in 1994. Lakewide <i>Diporeia</i> abundance declined with an additional order of magnitude from an average of 342 m<sup>−2</sup> in 2003 to 21 m<sup>−2</sup> in 2008. The Quagga Mussel (<i>D. rostriformis bugensis</i>) dominated the benthic macroinvertebrate community in 2008, comprising over 70% of the density and 98% of the biomass. No Zebra Mussels were identified in the 2008 samples. Quagga Mussels, Oligochaetes and Chironomids were most abundant between 31 and 90 m. Sphaeriids were rare at all depths, but were more abundant at sites deeper than 90 m. Between 2003 and 2008, lakewide <i>Dreissena</i> abundance declined by 43% primarily due to significant declines in the 10–30 m depth region (from 6500 m<sup>−2</sup> to 900 m<sup>−2</sup>). <i>Dreissena</i> did not decline significantly in the 30–90 m or over 90 m depth regions. The 2008 survey revealed a continued decline in <i>Diporeia</i> and Sphaeriid Clams, a replacement of Zebra Mussels by Quagga Mussels, and a decline in Quagga Mussels at depths shallower than 30 m. Oligochaetes and chironomids showed no significant changes since the 1990s.
DOI: 10.6084/m9.figshare.1352076.v1
title: Long-term trends in Lake Ontario's benthic macroinvertebrate community from 1994–2008

description: The benthic macroinvertebrate community of Lake Ontario was assessed through a lakewide survey in 2008. <i>Diporeia</i> was very rare throughout the lake at all depths in 2008, and only four of 52 locations had densities &gt;100 m<sup>−2</sup>, all of them at depths &gt;90 m. The maximum density of <i>Diporeia</i> found at any location was at 257 m<sup>−2</sup> in 2008, which can be compared to maximum densities of 13,280 m<sup>−2</sup> observed in 1994. Lakewide <i>Diporeia</i> abundance declined with an additional order of magnitude from an average of 342 m<sup>−2</sup> in 2003 to 21 m<sup>−2</sup> in 2008. The Quagga Mussel (<i>D. rostriformis bugensis</i>) dominated the benthic macroinvertebrate community in 2008, comprising over 70% of the density and 98% of the biomass. No Zebra Mussels were identified in the 2008 samples. Quagga Mussels, Oligochaetes and Chironomids were most abundant between 31 and 90 m. Sphaeriids were rare at all depths, but were more abundant at sites deeper than 90 m. Between 2003 and 2008, lakewide <i>Dreissena</i> abundance declined by 43% primarily due to significant declines in the 10–30 m depth region (from 6500 m<sup>−2</sup> to 900 m<sup>−2</sup>). <i>Dreissena</i> did not decline significantly in the 30–90 m or over 90 m depth regions. The 2008 survey revealed a continued decline in <i>Diporeia</i> and Sphaeriid Clams, a replacement of Zebra Mussels by Quagga Mussels, and a decline in Quagga Mussels at depths shallower than 30 m. Oligochaetes and chironomids showed no significant changes since the 1990s.
DOI: 10.6084/m9.figshare.1352094.v1
title: Alignment for the 66kb upstream region

description: Alignment for the 66kb upstream region for the 4 Jalisco populations
DOI: 10.6084/m9.figshare.1352072
title: PAWR-mediated suppression of BCL2 promotes switching of 3-azido withaferin A (3-AWA)-induced autophagy to apoptosis in prostate cancer cells

description: An active medicinal component of plant origin with an ability to overcome autophagy by inducing apoptosis should be considered a therapeutically active lead pharmacophore to control malignancies. In this report, we studied the effect of concentration-dependent 3-AWA (3-azido withaferin A) sensitization to androgen-independent prostate cancer (CaP) cells which resulted in a distinct switching of 2 interrelated conserved biological processes, i.e. autophagy and apoptosis. We have observed 3 distinct parameters which are hallmarks of autophagy in our studies. First, a subtoxic concentration of 3-AWA resulted in an autophagic phenotype with an elevation of autophagy markers in prostate cancer cells. This led to a massive accumulation of MAP1LC3B and EGFP-LC3B puncta coupled with gradual degradation of SQSTM1. Second, higher toxic concentrations of 3-AWA stimulated ER stress in CaP cells to turn on apoptosis within 12 h by elevating the expression of the proapoptotic protein PAWR, which in turn suppressed the autophagy-related proteins BCL2 and BECN1. This inhibition of BECN1 in CaP cells, leading to the disruption of the BCL2-BECN1 interaction by overexpressed PAWR has not been reported so far. Third, we provide evidence that <i>pawr-</i>KO MEFs exhibited abundant autophagy signs even at toxic concentrations of 3-AWA underscoring the relevance of PAWR in switching of autophagy to apoptosis. Last but not least, overexpression of EGFP-LC3B and DS-Red-BECN1 revealed a delayed apoptosis turnover at a higher concentration of 3-AWA in CaP cells. In summary, this study provides evidence that 3-AWA is a strong anticancer candidate to abrogate protective autophagy. It also enhanced chemosensitivity by sensitizing prostate cancer cells to apoptosis through induction of PAWR endorsing its therapeutic potential.
DOI: 10.6084/m9.figshare.1353770.v1
title: Seattle Street Clocks in 1924, 1927, 1928

description: Three inventories of every clock in downtown Seattle. They were made in 1924, 1927, and 1928. I stumbled upon them a few years ago at the Seattle Department of Transportation while I was trying to look up street use permits. I never discovered how to see old permits, but after I left a city employee emailed me saying she had found a folder of old records. Pure gold. Only the 1927 inventory included clocks outside of downtown. They all included a clock at the Japanese Commercial Bank that hung off the side of the building, and ’27 and ’28 included a similar clock at People’s Bank. Possibly those two clocks required a permit to hang out over the public right-of-way, as did the street clocks in the sidewalk. Other clocks downtown (for example on Colman ferry dock; King Street Station; Union Station) were not included, hinting at restrictive criteria.
DOI: 10.6084/m9.figshare.1352071
title: Soil aggregation data from Tabi et al. (1990)

description: <strong>Note<br></strong>The description is yet incomplete. <strong>Columns</strong><br>SOL: Pedologic class<br>SABLE: Sand proportion on mineral basis<br> LIMON: Silt proportion on mineral basis<br> ARGILE: Clay proportion on mineral basis<br> CO: Organic carbon proportion on dry basis<br>W1: 5.0-8.0 mm<br>W2: 2.0-5.0 mm<br>W3: 1.0-2.0mm<br>W4: &lt; 1.0 mm <strong>Reference</strong><br>Tabi M, Tardif L, Carrier D, Laflamme G, Rompré M. Inventaire des problèmes<br>de dégradation des sols agricoles du Québec. Rapport synthèse. Québec:<br>MAPAQ; 1990. url: http://huit.re/Welm8zYP
DOI: 10.6084/m9.figshare.1352069
title: Supplemental Data for article "Oral microbiota shift after 12-week supplementation with Lactobacillus reuteri DSM 17938 and PTA 5289"

description: Supplemental data for the publication entitled "Oral microbiota shift after 12-week supplementation with Lactobacillus reuteri DSM 17938 and PTA 5289; a randomized control trial" PLOS ONE PONE-D-14-49858. Nelly Romani Vestman 1, Tsute Chen 2, Pernilla Lif Holgerson 3, Carina Öhman 1, and<br>Ingegerd Johansson 1* 1,3 Department of Odontology/ 1 Cariology and 3 Pedodontics Section, Umeå University, Umeå, Sweden<br>2 Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA *Corresponding author:<br>Ingegerd Johansson<br>Department of Odontology/Cariology<br>Umeå universitet<br>SE-901 85 Umeå<br>Sweden<br>E-mail: ingegerd.johansson@odont.umu.se
DOI: 10.6084/m9.figshare.1353770.v2
title: Seattle Street Clocks in 1924, 1927, 1928

description: Three inventories of every clock in downtown Seattle. They were made in 1924, 1927, and 1928. I stumbled upon them a few years ago at the Seattle Department of Transportation while I was trying to look up street use permits. I never discovered how to see old permits, but after I left a city employee emailed me saying she had found a folder of old records. Pure gold. Only the 1927 inventory included clocks outside of downtown. They all included a clock at the Japanese Commercial Bank that hung off the side of the building, and ’27 and ’28 included a similar clock at People’s Bank. Possibly those two clocks required a permit to hang out over the public right-of-way, as did the street clocks in the sidewalk. Other clocks downtown (for example on Colman ferry dock; King Street Station; Union Station) were not included, hinting at restrictive criteria.
DOI: 10.6084/m9.figshare.1352072.v2
title: PAWR-mediated suppression of BCL2 promotes switching of 3-azido withaferin A (3-AWA)-induced autophagy to apoptosis in prostate cancer cells

description: An active medicinal component of plant origin with an ability to overcome autophagy by inducing apoptosis should be considered a therapeutically active lead pharmacophore to control malignancies. In this report, we studied the effect of concentration-dependent 3-AWA (3-azido withaferin A) sensitization to androgen-independent prostate cancer (CaP) cells which resulted in a distinct switching of 2 interrelated conserved biological processes, i.e. autophagy and apoptosis. We have observed 3 distinct parameters which are hallmarks of autophagy in our studies. First, a subtoxic concentration of 3-AWA resulted in an autophagic phenotype with an elevation of autophagy markers in prostate cancer cells. This led to a massive accumulation of MAP1LC3B and EGFP-LC3B puncta coupled with gradual degradation of SQSTM1. Second, higher toxic concentrations of 3-AWA stimulated ER stress in CaP cells to turn on apoptosis within 12 h by elevating the expression of the proapoptotic protein PAWR, which in turn suppressed the autophagy-related proteins BCL2 and BECN1. This inhibition of BECN1 in CaP cells, leading to the disruption of the BCL2-BECN1 interaction by overexpressed PAWR has not been reported so far. Third, we provide evidence that <i>pawr-</i>KO MEFs exhibited abundant autophagy signs even at toxic concentrations of 3-AWA underscoring the relevance of PAWR in switching of autophagy to apoptosis. Last but not least, overexpression of EGFP-LC3B and DS-Red-BECN1 revealed a delayed apoptosis turnover at a higher concentration of 3-AWA in CaP cells. In summary, this study provides evidence that 3-AWA is a strong anticancer candidate to abrogate protective autophagy. It also enhanced chemosensitivity by sensitizing prostate cancer cells to apoptosis through induction of PAWR endorsing its therapeutic potential.
DOI: 10.6084/m9.figshare.1352066
title: Apertium RDF Example Queries

description: Some example queries, to be run on the Apertum RDF SPARQL endpoint (http://linguistic.linkeddata.es/apertium/sparql-editor/), which illustrate how to obtain direct and indirect translations across languages, as well as links to external resources such as BabelNet. The query results are also provided, in html and csv formats.
DOI: 10.6084/m9.figshare.1352072.v1
title: PAWR-mediated suppression of BCL2 promotes switching of 3-azido withaferin A (3-AWA)-induced autophagy to apoptosis in prostate cancer cells

description: An active medicinal component of plant origin with an ability to overcome autophagy by inducing apoptosis should be considered a therapeutically active lead pharmacophore to control malignancies. In this report, we studied the effect of concentration-dependent 3-AWA (3-azido withaferin A) sensitization to androgen-independent prostate cancer (CaP) cells which resulted in a distinct switching of 2 interrelated conserved biological processes, i.e. autophagy and apoptosis. We have observed 3 distinct parameters which are hallmarks of autophagy in our studies. First, a subtoxic concentration of 3-AWA resulted in an autophagic phenotype with an elevation of autophagy markers in prostate cancer cells. This led to a massive accumulation of MAP1LC3B and EGFP-LC3B puncta coupled with gradual degradation of SQSTM1. Second, higher toxic concentrations of 3-AWA stimulated ER stress in CaP cells to turn on apoptosis within 12 h by elevating the expression of the proapoptotic protein PAWR, which in turn suppressed the autophagy-related proteins BCL2 and BECN1. This inhibition of BECN1 in CaP cells, leading to the disruption of the BCL2-BECN1 interaction by overexpressed PAWR has not been reported so far. Third, we provide evidence that <i>pawr-</i>KO MEFs exhibited abundant autophagy signs even at toxic concentrations of 3-AWA underscoring the relevance of PAWR in switching of autophagy to apoptosis. Last but not least, overexpression of EGFP-LC3B and DS-Red-BECN1 revealed a delayed apoptosis turnover at a higher concentration of 3-AWA in CaP cells. In summary, this study provides evidence that 3-AWA is a strong anticancer candidate to abrogate protective autophagy. It also enhanced chemosensitivity by sensitizing prostate cancer cells to apoptosis through induction of PAWR endorsing its therapeutic potential.
DOI: 10.6084/m9.figshare.1353770.v3
title: Seattle Street Clocks in 1924, 1927, 1928

description: Three inventories of every clock in downtown Seattle. They were made in 1924, 1927, and 1928. I stumbled upon them a few years ago at the Seattle Department of Transportation while I was trying to look up street use permits. I never discovered how to see old permits, but after I left a city employee emailed me saying she had found a folder of old records. Pure gold. Only the 1927 inventory included clocks outside of downtown. They all included a clock at the Japanese Commercial Bank that hung off the side of the building, and ’27 and ’28 included a similar clock at People’s Bank. Possibly those two clocks required a permit to hang out over the public right-of-way, as did the street clocks in the sidewalk. Other clocks downtown (for example on Colman ferry dock; King Street Station; Union Station) were not included, hinting at restrictive criteria.
DOI: 10.6084/m9.figshare.1352065
title: Original results generated by the QIIME software

description: For more information please refer to the publication. PONE-D-14-49858R1 Oral microbiota shift after 12-week supplementation with Lactobacillus reuteri DSM 17938 and PTA 5289; a randomized control trial.
DOI: 10.6084/m9.figshare.1352069.v1
title: Oral microbiota shift after 12-week supplementation with Lactobacillus reuteri DSM 17938 and PTA 5289

description: Supplemental data for the publication entitled "Oral microbiota shift after 12-week supplementation with Lactobacillus reuteri DSM 17938 and PTA 5289; a randomized control trial" PLOS ONE PONE-D-14-49858. Nelly Romani Vestman 1, Tsute Chen 2, Pernilla Lif Holgerson 3, Carina Öhman 1, and<br>Ingegerd Johansson 1* 1,3 Department of Odontology/ 1 Cariology and 3 Pedodontics Section, Umeå University, Umeå, Sweden<br>2 Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA *Corresponding author:<br>Ingegerd Johansson<br>Department of Odontology/Cariology<br>Umeå universitet<br>SE-901 85 Umeå<br>Sweden<br>E-mail: ingegerd.johansson@odont.umu.se
DOI: 10.6084/m9.figshare.1352064
title: Biology lessons for schools using the fruit fly Drosophila

description: OVERVIEW: An overview of resources given here is listen under this link: https://droso4schools.wordpress.com/learning-resources/<br>RATIONALE: For more than 100 years the fruit fly <em>Drosophila</em> <em>melanogaster</em> has been at the forefront of biological research and thus provides highly refined conceptual understanding of biology. Accordingly, much of the core biology curriculum can be explained extremely well using flies, spiced up with exciting, simple and inexpensive experiments that are memorable, reflect contemporary research and provide students with clear comprehension. Here we provide readily tested school biology lessons in form of PowerPoint files which are supported by explanatory background information, risk assessments, lesson plans, instructions and any other additional information that may save teachers time and effort to set up these lessons in their own classes. Furthermore, we set up the droso4schools website (link below) which provides further support materials suitable for revision or homework tasks, or simply to enhance the learning experience. Further <em>Drosophila</em>-specific information and resources can be found under the second link given below. If you find our resources helpful for your teaching, please, help us by sending an informal email to Andreas.Prokop@manchester.ac.uk<br>