cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1310468.v2
title: Adhesion properties of <i>Lactobacillus rhamnosus</i> mucus-binding factor to mucin and extracellular matrix proteins

description: We previously described potential probiotic <i>Lactobacillus rhamnosus</i> strains, isolated from fermented mare milk produced in Sumbawa Island, Indonesia, which showed high adhesion to porcine colonic mucin (PCM) and extracellular matrix (ECM) proteins. Recently, mucus-binding factor (MBF) was found in the GG strain of <i>L. rhamnosus</i> as a mucin-binding protein. In this study, we assessed the ability of recombinant MBF protein from the FSMM22 strain, one of the isolates of <i>L. rhamnosus</i> from fermented Sumbawa mare milk, to adhere to PCM and ECM proteins by overlay dot blot and Biacore assays. MBF bound to PCM, laminin, collagen IV, and fibronectin with submicromolar dissociation constants. Adhesion of the FSMM22 <i>mbf</i> mutant strain to PCM and ECM proteins was significantly less than that of the wild-type strain. Collectively, these results suggested that MBF contribute to <i>L. rhamnosus</i> host colonization via mucin and ECM protein binding.
DOI: 10.6084/m9.figshare.1310468.v4
title: Adhesion properties of <i>Lactobacillus rhamnosus</i> mucus-binding factor to mucin and extracellular matrix proteins

description: We previously described potential probiotic <i>Lactobacillus rhamnosus</i> strains, isolated from fermented mare milk produced in Sumbawa Island, Indonesia, which showed high adhesion to porcine colonic mucin (PCM) and extracellular matrix (ECM) proteins. Recently, mucus-binding factor (MBF) was found in the GG strain of <i>L. rhamnosus</i> as a mucin-binding protein. In this study, we assessed the ability of recombinant MBF protein from the FSMM22 strain, one of the isolates of <i>L. rhamnosus</i> from fermented Sumbawa mare milk, to adhere to PCM and ECM proteins by overlay dot blot and Biacore assays. MBF bound to PCM, laminin, collagen IV, and fibronectin with submicromolar dissociation constants. Adhesion of the FSMM22 <i>mbf</i> mutant strain to PCM and ECM proteins was significantly less than that of the wild-type strain. Collectively, these results suggested that MBF contribute to <i>L. rhamnosus</i> host colonization via mucin and ECM protein binding.
DOI: 10.6084/m9.figshare.1310469.v2
title: Association of heterotrophic bacteria with aggregated <i>Arthrospira platensis</i> exopolysaccharides: implications in the induction of axenic cultures

description: Inducing an axenic culture of the edible cyanobacterium <i>Arthrospira</i> (<i>Spirulina</i>) <i>platensis</i> using differential filtration alone is never successful; thus, it has been thought that, in non-axenic cultures, a portion of contaminating bacteria is strongly associated with <i>Arthrospira</i> cells. However, examination of the behavior of these bacteria during filtration revealed that they were not associated with <i>Arthrospira</i> cells but with aggregates of exopolysaccharides present in the medium away from the <i>Arthrospira</i> cells. Based on this finding, a rapid and reliable method for preparing axenic trichomes of <i>A. platensis</i> was established. After verifying the axenicity of the resulting trichomes on enriched agar plates, they were individually transferred to fresh sterile medium using a handmade tool, a microtrowel, to produce axenic cultures. With this technique, axenic cultures of various <i>A. platensis</i> strains were successfully produced. The technique described in this study is potentially applicable to a wider range of filamentous cyanobacteria.
DOI: 10.6084/m9.figshare.1310466.v2
title: Identification of genes encoding photoconvertible (Class I) water-soluble chlorophyll-binding proteins from <i>Chenopodium ficifolium</i>

description: Photoconvertible water-soluble chlorophyll-binding proteins, called Class I WSCPs, have been detected in Chenopodiaceae, Amaranthaceae and Polygonaceae plant species. To date, <i>Chenopodium album WSCP</i> (<i>CaWSCP</i>) is the only cloned gene encoding a Class I WSCP. In this study, we identified two cDNAs encoding <i>Chenopodium ficifolium</i> Class I WSCPs, <i>CfWSCP1</i>, and <i>CfWSCP2</i>. Sequence analyses revealed that the open reading frames of <i>CfWSCP1</i> and <i>CfWSCP2</i> were 585 and 588 bp, respectively. Furthermore, both CfWSCPs contain cystein2 and cystein30, which are essential for the chlorophyll-binding ability of CaWSCP. Recombinant CfWSCP1 and CfWSCP2, expressed in <i>Escherichia coli</i> as hexa-histidine fusion proteins (CfWSCP1-His and CfWSCP2-His), formed inclusion bodies; however, we were able to solubilize these using a buffer containing 8 M urea and then refold them by dialysis. The refolded CfWSCP1-His and CfWSCP2-His could bind chlorophylls and exhibited photoconvertibility, confirming that the cloned CfWSCPs are further examples of Class I WSCPs.
DOI: 10.6084/m9.figshare.1310467.v2
title: Protein kinase C regulates the expression of cell wall-related genes in RlmA-dependent and independent manners in <i>Aspergillus nidulans</i>

description: A protein kinase C of <i>Aspergillus nidulans</i>, PkcA, is required for cell wall integrity (CWI) and is considered a major component of the regulating pathway. To investigate whether PkcA regulates the transcription of cell wall-related genes, we constructed strains expressing <i>pkcA</i>(R429A) that encodes an activated form of PkcA. The mRNA levels of most chitin synthase genes and an α-glucan synthase gene, <i>agsB</i>, were increased when <i>pkcA</i>(R429A) expression was induced. These mRNA increases were not observed or were only partially observed, in a deletion mutant of <i>rlmA</i>, an ortholog of <i>RLM1</i> that encodes a transcription factor in the CWI pathway in <i>Saccharomyces cerevisiae</i>. In addition, in a <i>pkcA</i> temperature-sensitive mutant under heat stress, the mRNA levels of some chitin synthase genes and <i>agsB</i> did not increase. These results suggest that PkcA is involved in CWI maintenance through the transcriptional regulation of cell wall-related genes.
DOI: 10.6084/m9.figshare.1310468.v3
title: Adhesion properties of <i>Lactobacillus rhamnosus</i> mucus-binding factor to mucin and extracellular matrix proteins

description: We previously described potential probiotic <i>Lactobacillus rhamnosus</i> strains, isolated from fermented mare milk produced in Sumbawa Island, Indonesia, which showed high adhesion to porcine colonic mucin (PCM) and extracellular matrix (ECM) proteins. Recently, mucus-binding factor (MBF) was found in the GG strain of <i>L. rhamnosus</i> as a mucin-binding protein. In this study, we assessed the ability of recombinant MBF protein from the FSMM22 strain, one of the isolates of <i>L. rhamnosus</i> from fermented Sumbawa mare milk, to adhere to PCM and ECM proteins by overlay dot blot and Biacore assays. MBF bound to PCM, laminin, collagen IV, and fibronectin with submicromolar dissociation constants. Adhesion of the FSMM22 <i>mbf</i> mutant strain to PCM and ECM proteins was significantly less than that of the wild-type strain. Collectively, these results suggested that MBF contribute to <i>L. rhamnosus</i> host colonization via mucin and ECM protein binding.
DOI: 10.6084/m9.figshare.1310466.v4
title: Identification of genes encoding photoconvertible (Class I) water-soluble chlorophyll-binding proteins from <i>Chenopodium ficifolium</i>

description: Photoconvertible water-soluble chlorophyll-binding proteins, called Class I WSCPs, have been detected in Chenopodiaceae, Amaranthaceae and Polygonaceae plant species. To date, <i>Chenopodium album WSCP</i> (<i>CaWSCP</i>) is the only cloned gene encoding a Class I WSCP. In this study, we identified two cDNAs encoding <i>Chenopodium ficifolium</i> Class I WSCPs, <i>CfWSCP1</i>, and <i>CfWSCP2</i>. Sequence analyses revealed that the open reading frames of <i>CfWSCP1</i> and <i>CfWSCP2</i> were 585 and 588 bp, respectively. Furthermore, both CfWSCPs contain cystein2 and cystein30, which are essential for the chlorophyll-binding ability of CaWSCP. Recombinant CfWSCP1 and CfWSCP2, expressed in <i>Escherichia coli</i> as hexa-histidine fusion proteins (CfWSCP1-His and CfWSCP2-His), formed inclusion bodies; however, we were able to solubilize these using a buffer containing 8 M urea and then refold them by dialysis. The refolded CfWSCP1-His and CfWSCP2-His could bind chlorophylls and exhibited photoconvertibility, confirming that the cloned CfWSCPs are further examples of Class I WSCPs.
DOI: 10.6084/m9.figshare.1310466.v3
title: Identification of genes encoding photoconvertible (Class I) water-soluble chlorophyll-binding proteins from <i>Chenopodium ficifolium</i>

description: Photoconvertible water-soluble chlorophyll-binding proteins, called Class I WSCPs, have been detected in Chenopodiaceae, Amaranthaceae and Polygonaceae plant species. To date, <i>Chenopodium album WSCP</i> (<i>CaWSCP</i>) is the only cloned gene encoding a Class I WSCP. In this study, we identified two cDNAs encoding <i>Chenopodium ficifolium</i> Class I WSCPs, <i>CfWSCP1</i>, and <i>CfWSCP2</i>. Sequence analyses revealed that the open reading frames of <i>CfWSCP1</i> and <i>CfWSCP2</i> were 585 and 588 bp, respectively. Furthermore, both CfWSCPs contain cystein2 and cystein30, which are essential for the chlorophyll-binding ability of CaWSCP. Recombinant CfWSCP1 and CfWSCP2, expressed in <i>Escherichia coli</i> as hexa-histidine fusion proteins (CfWSCP1-His and CfWSCP2-His), formed inclusion bodies; however, we were able to solubilize these using a buffer containing 8 M urea and then refold them by dialysis. The refolded CfWSCP1-His and CfWSCP2-His could bind chlorophylls and exhibited photoconvertibility, confirming that the cloned CfWSCPs are further examples of Class I WSCPs.
DOI: 10.6084/m9.figshare.1310467.v4
title: Protein kinase C regulates the expression of cell wall-related genes in RlmA-dependent and independent manners in <i>Aspergillus nidulans</i>

description: A protein kinase C of <i>Aspergillus nidulans</i>, PkcA, is required for cell wall integrity (CWI) and is considered a major component of the regulating pathway. To investigate whether PkcA regulates the transcription of cell wall-related genes, we constructed strains expressing <i>pkcA</i>(R429A) that encodes an activated form of PkcA. The mRNA levels of most chitin synthase genes and an α-glucan synthase gene, <i>agsB</i>, were increased when <i>pkcA</i>(R429A) expression was induced. These mRNA increases were not observed or were only partially observed, in a deletion mutant of <i>rlmA</i>, an ortholog of <i>RLM1</i> that encodes a transcription factor in the CWI pathway in <i>Saccharomyces cerevisiae</i>. In addition, in a <i>pkcA</i> temperature-sensitive mutant under heat stress, the mRNA levels of some chitin synthase genes and <i>agsB</i> did not increase. These results suggest that PkcA is involved in CWI maintenance through the transcriptional regulation of cell wall-related genes.
DOI: 10.6084/m9.figshare.1310467.v3
title: Protein kinase C regulates the expression of cell wall-related genes in RlmA-dependent and independent manners in <i>Aspergillus nidulans</i>

description: A protein kinase C of <i>Aspergillus nidulans</i>, PkcA, is required for cell wall integrity (CWI) and is considered a major component of the regulating pathway. To investigate whether PkcA regulates the transcription of cell wall-related genes, we constructed strains expressing <i>pkcA</i>(R429A) that encodes an activated form of PkcA. The mRNA levels of most chitin synthase genes and an α-glucan synthase gene, <i>agsB</i>, were increased when <i>pkcA</i>(R429A) expression was induced. These mRNA increases were not observed or were only partially observed, in a deletion mutant of <i>rlmA</i>, an ortholog of <i>RLM1</i> that encodes a transcription factor in the CWI pathway in <i>Saccharomyces cerevisiae</i>. In addition, in a <i>pkcA</i> temperature-sensitive mutant under heat stress, the mRNA levels of some chitin synthase genes and <i>agsB</i> did not increase. These results suggest that PkcA is involved in CWI maintenance through the transcriptional regulation of cell wall-related genes.
DOI: 10.6084/m9.figshare.1310459
title: Selected catalog of RADseq loci used for phylogenetic and clustering analysis of wolf-like canids

description: Selection of RADsequencing loci matching at least 10 samples of wolf-like canids (Side-striped jackal, Golden jackal, Ethiopian wolf, African wolf, Holoarctic grey wolf, domestic dog). The format of the table is the same as that produced by export_sql.pl in the Stacks (Catchen et al 2013) package. These dataset has been used for clustering and phylogenetic analysis in the refereneced paper.
DOI: 10.6084/m9.figshare.1310448
title: Data of theoretical modelling of epigenetically modified DNA sequences

description: Data file 1<br>Local base pair parameters for the central GC in d(GCG) and d(ACA) modifications. The shear, stretch and stagger parameters are measured in Å, and the buckle, propeller and opening parameters are measured in ˚. Data file 2<br>Base pair step and local helical parameters for the central GC in d(GCG) and d(ACA) modifications. The slide and X-displacement parameters are measured in Å, and the roll, twist and inclination parameters are measured in ˚. Data file 3<br>Comparison between the obtained base pair parameters for the d(GCG) using different levels of theory (DFT and the QM/MM with 2bps or 6bps in the high level layer). The shear, stretch and stagger parameters are measured in Å, and the buckle, propeller and opening parameters are measured in ˚. Data file 4<br>Comparison between the obtained base step parameters for the d(GCG) using different levels of theory (DFT and the QM/MM with 2bps or 6bps in the high level layer). The slide, shift and rise parameters are measured in Å, and the tilt, roll and twist parameters are measured in ˚. Data file 5<br>Values of local base pair parameters of central GC pair of d(GCG) obtained after energy minimization. The shear, stretch and stagger parameters are measured in Å, and the buckle, propeller and opening parameters are measured in ˚. Data file 6<br>Values of base pair step parameters of d(GCG), obtained after energy minimization. The shift, slide and rise parameters are measured in Å, and the tilt, roll and twist parameters are measured in °. Data file 7<br>Cartesian coordinates of key species.
DOI: 10.6084/m9.figshare.1310448.v1
title: Data of theoretical modelling of epigenetically modified DNA sequences

description: Data file 1<br>Local base pair parameters for the central GC in d(GCG) and d(ACA) modifications. The shear, stretch and stagger parameters are measured in Å, and the buckle, propeller and opening parameters are measured in ˚. Data file 2<br>Base pair step and local helical parameters for the central GC in d(GCG) and d(ACA) modifications. The slide and X-displacement parameters are measured in Å, and the roll, twist and inclination parameters are measured in ˚. Data file 3<br>Comparison between the obtained base pair parameters for the d(GCG) using different levels of theory (DFT and the QM/MM with 2bps or 6bps in the high level layer). The shear, stretch and stagger parameters are measured in Å, and the buckle, propeller and opening parameters are measured in ˚. Data file 4<br>Comparison between the obtained base step parameters for the d(GCG) using different levels of theory (DFT and the QM/MM with 2bps or 6bps in the high level layer). The slide, shift and rise parameters are measured in Å, and the tilt, roll and twist parameters are measured in ˚. Data file 5<br>Values of local base pair parameters of central GC pair of d(GCG) obtained after energy minimization. The shear, stretch and stagger parameters are measured in Å, and the buckle, propeller and opening parameters are measured in ˚. Data file 6<br>Values of base pair step parameters of d(GCG), obtained after energy minimization. The shift, slide and rise parameters are measured in Å, and the tilt, roll and twist parameters are measured in °. Data file 7<br>Cartesian coordinates of key species.
DOI: 10.6084/m9.figshare.1310459.v1
title: Selected catalog of RADseq loci used for phylogenetic and clustering analysis of wolf-like canids

description: Selection of RADsequencing loci matching at least 10 samples of wolf-like canids (Side-striped jackal, Golden jackal, Ethiopian wolf, African wolf, Holoarctic grey wolf, domestic dog). The format of the table is the same as that produced by export_sql.pl in the Stacks (Catchen et al 2013) package. These dataset has been used for clustering and phylogenetic analysis in the refereneced paper.
DOI: 10.6084/m9.figshare.1310445
title: Dermatological Journals Indexed in MEDLINE/PubMed

description: Dermatological Journals Indexed in MEDLINE/PubMed
DOI: 10.6084/m9.figshare.1310446
title: ebola-cases.csv

description: data on cases from WHO
DOI: 10.6084/m9.figshare.1310438
title: Dust Haze AAS 225 dissertation talk

description: 20 min dissertation talk slides for 225th AAS meeting in Seattle. Preseted in Low-mass Stars and Brown Dwarfs session.
DOI: 10.6084/m9.figshare.1310442
title: crossmodal rate perception data

description: anonymized experimental data
DOI: 10.6084/m9.figshare.1310446.v1
title: ebola-cases.csv

description: data on cases from WHO
DOI: 10.6084/m9.figshare.1310442.v1
title: crossmodal rate perception data

description: anonymized experimental data
DOI: 10.6084/m9.figshare.1310438.v1
title: Dust Haze AAS 225 dissertation talk

description: 20 min dissertation talk slides for 225th AAS meeting in Seattle. Preseted in Low-mass Stars and Brown Dwarfs session.
DOI: 10.6084/m9.figshare.1309953
title: Main Dataset for "Evolution of Popular Music: USA 1960–2010"

description: This is a large file (~20MB) called EvolutionPopUSA_MainData.csv, in comma-separated data format with column headers. Each row corresponds to a recording. The file is viewable in any text editor, and can also be opened in Excel or imported to other data processing programs. Below is a list of the column headers, with annotations. <strong>public_id</strong><br>unique ID of the recording <strong>artist_name</strong><br>name of the recording artist <strong>artist_name_clean</strong><br>artist name all upper case, no spaces, with secondary artists ("featuring") removed. <strong>track_name</strong><br>name of the track, i.e. usually name of the song <strong>first_entry</strong><br>date of the first entry into the Billboard Hot 100 <strong>quarter, year, fiveyear, decade</strong><br>transformations of first_entry to coarser time periods <strong>era</strong><br>era the track belongs to (1,...,4), as determined by Foote segmentation on the PC data (see below) <strong>cluster</strong><br>cluster membership of the track, as derived by k-means clustering on the PC data (see below) <strong>hTopic_01, ... , hTopic_08</strong><br>harmonic Topic weights, see description in the paper <strong>tTopic_01, ... , tTopic_08</strong><br>timbral Topic weights, see description in the paper <strong>PC1, ... , PC14</strong><br>principal components of the harmonic and timbral Topics <strong>harm_…</strong><br>193 columns of chord change counts; the chord change is indicated in the column label (e.g. harm_M.2.M means major chord followed by another major chord 2 semitones up). <strong>timb_01, ... , timb_35</strong><br>35 columns of timbre class counts (see description in supplementary information)
DOI: 10.6084/m9.figshare.1310422.v1
title: 18 July 2014 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1310269.v1
title: 16 July 2014 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1310422.v2
title: 2014 07 18 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1309950
title: Secondary Dataset (tags) for "Evolution of Popular Music: USA 1960–2010"

description: We also provide this additional file with genre tags for every song, which we used for validation. Here, too, the rows correspond to recordings. The data sets can be joined via the recording_id field.
DOI: 10.6084/m9.figshare.1309944
title: Data from: Feeding ecology informs parasite epidemiology: prey selection modulates encounter rate with Echinococcus multilocularis in urban coyotes. Liccioli, Bialowas, Ruckstuhl and Massolo. PLOS ONE

description: Excel file for diet analysis of coyotes based on fecal samples. Contains information on presence/absence and relative volume of the different food items.
DOI: 10.6084/m9.figshare.1310269.v2
title: 2014 07 16 Field Notes

description: Field notes including image and/or video records.
DOI: 10.6084/m9.figshare.1309943
title: Data from: Feeding ecology informs parasite epidemiology: prey selection modulates encounter rate with Echinococcus multilocularis in urban coyotes. Liccioli, Bialowas, Ruckstuhl and Massolo. PLOS ONE

description: Raw data describing the weight (in grams) of small mammal undigested items (bones, teeth, hair) found in coyote feces.
DOI: 10.6084/m9.figshare.1310427.v3
title: 2014 07 21 Field Notes

description: Field notes including image and/or video records. Original versions of all videos are available as of 21 Jan 2016 following the increase in allowed file size by figshare.
DOI: 10.6084/m9.figshare.1309944.v2
title: Data from: Feeding ecology informs parasite epidemiology: prey selection modulates encounter rate with Echinococcus multilocularis in urban coyotes. Liccioli, Bialowas, Ruckstuhl and Massolo. PLOS ONE

description: Excel file for diet analysis of coyotes based on fecal samples. Contains information on presence/absence and relative volume of the different food items.
DOI: 10.6084/m9.figshare.1309943.v2
title: Data from: Feeding ecology informs parasite epidemiology: prey selection modulates encounter rate with Echinococcus multilocularis in urban coyotes. Liccioli, Bialowas, Ruckstuhl and Massolo. PLOS ONE

description: Raw data describing the weight (in grams) of small mammal undigested items (bones, teeth, hair) found in coyote feces.
DOI: 10.6084/m9.figshare.1309944.v1
title: Data from: Feeding ecology informs parasite epidemiology: prey selection modulates encounter rate with Echinococcus multilocularis in urban coyotes.

description: Excel file for diet analysis of coyotes based on fecal samples. Contains information on presence/absence and relative volume of the different food items.
DOI: 10.6084/m9.figshare.1309938
title: Using iNaturalist to leran more about echinoderms (dataset)

description: Dataset accompanying paper (http://dx.doi.org/10.6084/m9.figshare.1309937)
DOI: 10.6084/m9.figshare.1309938.v1
title: Using iNaturalist to leran more about echinoderms (dataset)

description: Dataset accompanying paper (http://dx.doi.org/10.6084/m9.figshare.1309937)
DOI: 10.6084/m9.figshare.1309943.v1
title: Data from: Feeding ecology informs parasite epidemiology: prey selection modulates encounter rate with Echinococcus multilocularis in urban coyotes. PLOS ONE

description: Raw data describing the weight (in grams) of small mammal undigested items (bones, teeth, hair) found in coyote feces.
DOI: 10.6084/m9.figshare.1309952.v3
title: 2015 07 15 Field Notes

description: Field notes including image and/or video records. Original versions of all videos are available as of 21Jan 2016 following the increase in allowed file size by figshare.