cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3840327
title: Role of interspecies interactions in dual-species biofilms developed <i>in vitro</i> by uropathogens isolated from polymicrobial urinary catheter-associated bacteriuria

description: Most catheter-associated urinary tract infections are polymicrobial. Here, uropathogen interactions in dual-species biofilms were studied. The dual-species associations selected based on their prevalence in clinical settings were <i>Klebsiella pneumoniae</i>–<i>Escherichia coli</i>, <i>E. coli</i>–<i>Enterococcus faecalis</i>, <i>K. pneumoniae</i>–<i>E. faecalis</i>, and <i>K. pneumoniae</i>–<i>Proteus mirabilis</i>. All species developed single-species biofilms in artificial urine. The ability of <i>K. pneumoniae</i> to form biofilms was not affected by <i>E. coli</i> or <i>E. faecalis</i> co-inoculation, but was impaired by <i>P. mirabilis</i>. Conversely, <i>P. mirabilis</i> established a biofilm when co-inoculated with <i>K. pneumoniae</i>. Additionally, <i>E. coli</i> persistence in biofilms was hampered by <i>K. pneumoniae</i> but not by <i>E. faecalis</i>. Interestingly, <i>E. coli</i>, but not <i>K. pneumoniae</i>, partially inhibited <i>E. faecalis</i> attachment to the surface and retarded biofilm development. The findings reveal bacterial interactions between uropathogens in dual-species biofilms ranged from affecting initial adhesion to outcompeting one bacterial species, depending on the identity of the partners involved.
DOI: 10.7910/dvn/v1rjpf/rb6n8a
title: mea20160211_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840327.v1
title: Role of interspecies interactions in dual-species biofilms developed <i>in vitro</i> by uropathogens isolated from polymicrobial urinary catheter-associated bacteriuria

description: Most catheter-associated urinary tract infections are polymicrobial. Here, uropathogen interactions in dual-species biofilms were studied. The dual-species associations selected based on their prevalence in clinical settings were <i>Klebsiella pneumoniae</i>–<i>Escherichia coli</i>, <i>E. coli</i>–<i>Enterococcus faecalis</i>, <i>K. pneumoniae</i>–<i>E. faecalis</i>, and <i>K. pneumoniae</i>–<i>Proteus mirabilis</i>. All species developed single-species biofilms in artificial urine. The ability of <i>K. pneumoniae</i> to form biofilms was not affected by <i>E. coli</i> or <i>E. faecalis</i> co-inoculation, but was impaired by <i>P. mirabilis</i>. Conversely, <i>P. mirabilis</i> established a biofilm when co-inoculated with <i>K. pneumoniae</i>. Additionally, <i>E. coli</i> persistence in biofilms was hampered by <i>K. pneumoniae</i> but not by <i>E. faecalis</i>. Interestingly, <i>E. coli</i>, but not <i>K. pneumoniae</i>, partially inhibited <i>E. faecalis</i> attachment to the surface and retarded biofilm development. The findings reveal bacterial interactions between uropathogens in dual-species biofilms ranged from affecting initial adhesion to outcompeting one bacterial species, depending on the identity of the partners involved.
DOI: 10.7910/dvn/v1rjpf/l5ypst
title: mea20161212_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ojqcpr
title: mea20161227_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ldp9cw
title: mea20160907_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840192
title: Permissions documents for reproduction of third party copyrighted works in Flow Synthesis of Silver Nanowires

description: This fileset includes PDFs of documents giving me permission to reproduce the third party copyrighted works in my PhD thesis <i>Flow Synthesis of Silver Nanowires</i>.
DOI: 10.7910/dvn/v1rjpf/jvz0de
title: mea20160511_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840153
title: Marine Microbial Eukaryotic Transcriptome Sequencing Project, re-assemblies

description: The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) data set contains cultured samples of pelagic and endosymbiotic marine eukaryotic species representing more than 40 phyla (Keeling et al. 2014).<br>Methods for the de novo transcriptome assembly are described in the Eel pond khmer protocols (Brown et al. 2015).<br>Scripts available on github: <br>https://github.com/dib-lab/dib-MMETSP<br><br>C. Titus Brown, Camille Scott, and Leigh Sheneman. 2015. The Eel Pond mRNAseq Protocol. https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/<br>Keeling et al. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing. http://dx.doi.org/10.1371/journal.pbio.1001889<br>
DOI: 10.7910/dvn/v1rjpf/rwypcb
title: mea20150929_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840144
title: Custom Chip Description Format files for Ensembl gene regions

description: Zip file of custom CDFs for human u133 plus 2.0, mouse genome 430 2.0, and rat genome 230 2.0 gene chips using ensembl annotations at the gene, transcript, and gene region (CDS, exon, UTR) level. <br>
DOI: 10.7910/dvn/v1rjpf/zln3ch
title: mea20160716_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840144.v1
title: Custom Chip Description Format files for Ensembl gene regions

description: Zip file of custom CDFs for human u133 plus 2.0, mouse genome 430 2.0, and rat genome 230 2.0 gene chips using ensembl annotations at the gene, transcript, and gene region (CDS, exon, UTR) level. <br>
DOI: 10.6084/m9.figshare.3840153.v1
title: Marine Microbial Eukaryotic Transcriptome Sequencing Project, re-assemblies

description: The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) data set contains cultured samples of pelagic and endosymbiotic marine eukaryotic species representing more than 40 phyla (Keeling et al. 2014).<br>Each of these files is a de novo transcriptome assembly of one individual sequencing sample, defined by a unique SRR id. Files are named as follows:<br><b>Genus_species_strain_SRR_MMETSP.Trinity.fasta</b><br>For those samples with different names between the metadata in NCBI-SRA and imicrobe, files were named as follows:<br><b>Genus_species(SRA)_strain_SRR_MMETSP_alt_Genus_species(imicrobe).Trinity.fasta</b><br>Methods for the de novo transcriptome assembly are described in the Eel pond khmer protocols (Brown et al. 2015). Authomated scripts are available on github: <br>https://github.com/ljcohen/MMETSP<br>C. Titus Brown, Camille Scott, and Leigh Sheneman. 2015. The Eel Pond mRNAseq Protocol. https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/
DOI: 10.7910/dvn/v1rjpf/sbywsc
title: mea20160622_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840153.v2
title: Marine Microbial Eukaryotic Transcriptome Sequencing Project, re-assemblies

description: The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) data set contains cultured samples of pelagic and endosymbiotic marine eukaryotic species representing more than 40 phyla (Keeling et al. 2014).<br>Each of these files is a de novo transcriptome assembly of one individual sequencing sample, defined by a unique SRR id. Files are named as follows:<br><b>Genus_species_strain_SRR_MMETSP.Trinity.fasta</b><br>For those samples with different names between the metadata in NCBI-SRA and imicrobe, files were named as follows:<br><b>Genus_species(SRA)_strain_SRR_MMETSP_alt_Genus_species(imicrobe).Trinity.fasta</b><br>Methods for the de novo transcriptome assembly are described in the Eel pond khmer protocols (Brown et al. 2015). Automated scripts are available on github: <br>https://github.com/ljcohen/MMETSP<br>C. Titus Brown, Camille Scott, and Leigh Sheneman. 2015. The Eel Pond mRNAseq Protocol. https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/
DOI: 10.7910/dvn/v1rjpf/y4tfiq
title: mea20160208_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rwcwyc
title: mea20161219_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/adzvdo
title: mea20150125_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840030.v1
title: Experimental Materials - Studies 1-3

description: Study Materials
DOI: 10.7910/dvn/v1rjpf/4purkm
title: mea20160413_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840153.v4
title: Marine Microbial Eukaryotic Transcriptome Sequencing Project, re-assemblies

description: The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) data set contains cultured samples of pelagic and endosymbiotic marine eukaryotic species representing more than 40 phyla (Keeling et al. 2014).<br>Each of these files is a de novo transcriptome assembly of one individual sequencing sample, defined by a unique SRR id. Files are named as follows:<br><b>Genus_species(SRA)_strain_SRR_MMETSP_alt_Genus_species(imicrobe).Trinity.fasta</b><br>Methods for the de novo transcriptome assembly are described in the Eel pond khmer protocols (Brown et al. 2015). Automated scripts are available on github: <br>https://github.com/ljcohen/MMETSP<br>C. Titus Brown, Camille Scott, and Leigh Sheneman. 2015. The Eel Pond mRNAseq Protocol. https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/
DOI: 10.7910/dvn/v1rjpf/i9styo
title: mea20151018_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840153.v5
title: Marine Microbial Eukaryotic Transcriptome Sequencing Project, re-assemblies

description: The Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) data set contains cultured samples of pelagic and endosymbiotic marine eukaryotic species representing more than 40 phyla (Keeling et al. 2014).<br>Methods for the de novo transcriptome assembly are described in the Eel pond khmer protocols (Brown et al. 2015). Automated scripts are available on github: <br>https://github.com/ljcohen/MMETSP<br>C. Titus Brown, Camille Scott, and Leigh Sheneman. 2015. The Eel Pond mRNAseq Protocol. https://khmer-protocols.readthedocs.io/en/ctb/mrnaseq/
DOI: 10.7910/dvn/v1rjpf/kp3ghe
title: mea20161118_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/fhlioq
title: mea20160414_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3840021
title: Individual images of Xenopus laevis tadpoles

description: <b>Methods</b><br><br>Pictures of animals were acquired during the course of experimental work in the laboratory of Hans Straka at the Ludwig-Maximilians-Universität Munich. Details on methods of these experiments are available in publications from the laboratory (see references). All pictures were taken under MS-222 anesthesia of the animal.<br> <br> <i>Images:</i> All images were acquired using a camera (Moticam 580) on an Olympus SHX16 dissection scope using both a white and a black background and from a ventral and a dorsal view (illumination by a ZLED CLS 6000). Due to the size of the animals, multiple overlapping images were collected and stitched in Adobe Photoshop using the File &gt; Automate &gt; Photomerge function. A scale bar was added in ImageJ. For all images with a white background and a dorsal view, a mask was created in Photoshop.<br> <br> The white dorsal views of the animals were assembled in an overview and are available in 'Xenopus laevis: overview over late tadpole stages' (see references). Schematics are available in 'Schemes of Xenopus laevis tadpoles' (see references)<br><br>Version 2: addition of stage 55 image.<br>
DOI: 10.6084/m9.figshare.3840024
title: Study 3 Image Rating Support for Welfare

description: Study 3 Image Rating Support for Welfare
DOI: 10.6084/m9.figshare.3840024.v1
title: Study 3 Image Rating Support for Welfare

description: Study 3 Image Rating Support for Welfare
DOI: 10.7910/dvn/v1rjpf/2udqvj
title: mea20161112_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/2x5aq0
title: mea20150416_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839991
title: Xenopus laevis: overview over late tadpole stages

description: Overview of the developmental stages of <i>Xenopus laevis</i> - i.e. composite of all the individual images with a dorsal view and a white background (the individual images are available in 'Individual images of Xenopus laevis tadpoles'; see references). 'WhiteDorsalCollection' is a composite of images with the background removed; the other files have been generated using different tracing options in Adobe Illustrator to convert the images to vector graphics (the filename indicates the tracing option).
DOI: 10.7910/dvn/v1rjpf/ek0bel
title: mea20160608_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839970
title: Study 2 Image Rating

description: Study 2 Image Rating
DOI: 10.6084/m9.figshare.3839958
title: Study 2 Image Generation - Welfare Condition

description: Study 2 Image Generation - Welfare Condition
DOI: 10.6084/m9.figshare.3839970.v1
title: Study 2 Image Rating

description: Study 2 Image Rating
DOI: 10.7910/dvn/v1rjpf/9nmz1p
title: mea20150615_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839958.v1
title: Study 2 Image Generation - Welfare Condition

description: Study 2 Image Generation - Welfare Condition
DOI: 10.6084/m9.figshare.3839946
title: Study 1 Image Generation Data

description: Study 1 Image generation data
DOI: 10.6084/m9.figshare.3839955
title: Study 2 Image Generation - NonRecipient Condition

description: Study 2 Image Generation - NonRecipient Condition
DOI: 10.6084/m9.figshare.3839955.v1
title: Study 2 Image Generation - NonRecipient Condition

description: Study 2 Image Generation - NonRecipient Condition
DOI: 10.6084/m9.figshare.3839946.v1
title: Study 1 Image Generation Data

description: Study 1 Image generation data
DOI: 10.7910/dvn/v1rjpf/b26i7y
title: mea20161228_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839934
title: Study 1 Image Rating.sav

description: These are the data for Study 1 image rating.
DOI: 10.7910/dvn/v1rjpf/alcvxe
title: mea20160605_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839934.v1
title: Study 1 Image Rating.sav

description: These are the data for Study 1 image rating.
DOI: 10.6084/m9.figshare.3839898
title: Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5,405 pneumococcal genomes

description: Supplementary figures and tables as published in <i>Microbial Genomics</i> in the following article: "Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5,405 pneumococcal genomes" [10.1099/mgen.0.000090]
DOI: 10.6084/m9.figshare.3839886
title: DTPM_Beige.pdf

description: <sub>Raw data for "Limited Accuracy of colour <i>Doppler</i> Ultrasound dynamic tissue perfusion Measurement in diabetic Adults"</sub><sub>Columns contain single Perfusion intensity measures</sub>
DOI: 10.7910/dvn/v1rjpf/foxtpq
title: mea20160718_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839886.v1
title: DTPM_Beige.pdf

description: <sub>Raw data for "Limited Accuracy of colour <i>Doppler</i> Ultrasound dynamic tissue perfusion Measurement in diabetic Adults"</sub><sub>Columns contain single Perfusion intensity measures</sub>
DOI: 10.6084/m9.figshare.3839898.v1
title: Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5,405 pneumococcal genomes

description: Supplementary figures and tables as published in <i>Microbial Genomics</i> in the following article: "Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5,405 pneumococcal genomes" [10.1099/mgen.0.000090]
DOI: 10.7910/dvn/v1rjpf/rcgca1
title: mea20150810_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839838
title: Airway microbial diversity

description: The sequence data and mapping file for all the samples included in the study have been deposited.
DOI: 10.7910/dvn/v1rjpf/cgknwn
title: mea20151008_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/9stqmm
title: mea20150502_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839805
title: The optical density measurements of S. aureus cultures in LB medium with the addition of serum or filtrated serum.

description: 96 well plate cultures of <i>S. aureus </i>in different media (either LB medium pH = 7, LB medium pH= 5, LB medium with 7% serum, or LB medium with 7% filtrated serum).
DOI: 10.7910/dvn/v1rjpf/kcsmgn
title: mea20150525_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839838.v3
title: Airway microbial diversity

description: The sequence data and mapping file for all the samples included in the study have been deposited.
DOI: 10.6084/m9.figshare.3839838.v2
title: Airway microbial diversity

description: The sequence data and mapping file for all the samples included in the study have been deposited.
DOI: 10.7910/dvn/v1rjpf/duoows
title: mea20151029_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839799
title: Optical density measurements of S. aureus growth in LB medium with presence or absence of serum from healthy and atopic dermatitis donors.

description: The growth of <i>S. aureus </i>in the presence of serum (7% in LB medium) evaluated by measuring the optical density at 600 nm wavelength. Data represent the effect of serum in 5 AD patients and 5 healthy individuals.
DOI: 10.6084/m9.figshare.3839793
title: Optical density measurements of S. aureus and S. epidermidis growth in LB medium with propionic acid.

description: The optical density measurements on a 96 well plates made with Dynex MRX, of <i>S. aureus</i> and <i>S. epidermidis</i> growth in various molar condensations of propionic acid.
DOI: 10.7910/dvn/v1rjpf/p6prmp
title: mea20150212_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839793.v1
title: Optical density measurements of S. aureus and S. epidermidis growth in LB medium with propionic acid.

description: The optical density measurements on a 96 well plates made with Dynex MRX, of <i>S. aureus</i> and <i>S. epidermidis</i> growth in various molar condensations of propionic acid.
DOI: 10.7910/dvn/v1rjpf/ixm3zq
title: mea20150425_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839781
title: Optical density measurements of the influence of P. acnes fermentation products on the growth of S. aureus.

description: Optical density of <i>S. aureus</i> samples incubated with the supernatant from <i>P. acnes </i>cultures. <i>P. acnes</i> was cultured in Luria broth medium in the absence ( n = 5) or in the presence ( n = 5) of glycerol for five days. Subsequently, the cultures were centrifuged at 5000 rpm for 30 minutes and the supernatant was used as the medium to culture <i>S. aureus</i> in various concentrations. Here either with 6.25 % supernatant or 100% supernatant.
DOI: 10.7910/dvn/v1rjpf/fyzrr8
title: mea20160912_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839760
title: Using data mining to identify new research avenues

description: Slides of the talk "Using data mining to identify new research avenues", given by Adam Stevenson at the NSF Ceramics Workshop on September 12, 2016.
DOI: 10.6084/m9.figshare.3839781.v1
title: Optical density measurements of the influence of P. acnes fermentation products on the growth of S. aureus.

description: Optical density of <i>S. aureus</i> samples incubated with the supernatant from <i>P. acnes </i>cultures. <i>P. acnes</i> was cultured in Luria broth medium in the absence ( n = 5) or in the presence ( n = 5) of glycerol for five days. Subsequently, the cultures were centrifuged at 5000 rpm for 30 minutes and the supernatant was used as the medium to culture <i>S. aureus</i> in various concentrations. Here either with 6.25 % supernatant or 100% supernatant.
DOI: 10.6084/m9.figshare.3839748
title: Skin microbiome in atopic dermatitis: OTU counts.

description: The datasets contain an OTU table, with sample names as column names, and OTU number as row names. The respective OTU number can be found in the "tax_table" data frame, and the respective sample description -- in the "sam_data" table.<br>Standard comma separated values, UTF-8 encoding.<br>
DOI: 10.6084/m9.figshare.3839760.v1
title: Using data mining to identify new research avenues

description: Slides of the talk "Using data mining to identify new research avenues", given by Adam Stevenson at the NSF Ceramics Workshop on September 12, 2016.
DOI: 10.7910/dvn/v1rjpf/v7nhyn
title: mea20150220_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/9aolfl
title: mea20150824_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839745.v1
title: 1200 prediction plots.xlsx

description: Data corresponding to the 1200 prediction plots.
DOI: 10.6084/m9.figshare.3839745.v2
title: Presence and abundance of Pectenia plumbea in the Iberian Peninsula

description: Data corresponding to the 400 modeled plots and the 1200 prediction plots.
DOI: 10.7910/dvn/v1rjpf/wostcs
title: mea20161024_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/uceqvv
title: mea20150404_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839745.v3
title: Presence and abundance of Pectenia plumbea in the Iberian Peninsula

description: Data corresponding to the 400 modeled plots and the 1200 prediction plots.
DOI: 10.7910/dvn/v1rjpf/izdpbz
title: mea20150806_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3839715
title: PowerPoint Slides for: Early Changes in Monocyte Adhesion Molecule Expression and Tumor Necrosis Factor-α Levels in Chronic Kidney Disease - A 5-Year Prospective Study

description: <i>Background:</i> Despite the absence of clinical symptoms, patients with chronic kidney disease (CKD) exhibit elevated levels of pro-inflammatory markers. To investigate whether it is possible to detect inflammatory activity and altered monocyte function at an early stage of renal disease, we studied patients with CKD stages 2-3 over 5 years. <i>Methods:</i> The expression of adhesion molecules on monocytes at resting state and after stimulation with formyl-methionyl-leucyl-phenylalanine (fMLP), as well as oxidative metabolism capacity was measured with flow cytometry in 108 CKD patients and healthy controls. Soluble markers of inflammation, such as cytokines, were analyzed using the Milliplex technique. <i>Results:</i> Patients showed significantly lower CD11b expression after stimulation during the 3rd (p = 0.002) and the 5th year (p &lt; 0.001), together with a lower oxidative burst in response to fMLP over time (p = 0.02). The expression of CD62L on resting monocytes was lower during the 3rd (p = 0.001) and the 5th (p = 0.001) year in patients. Levels of tumor necrosis factor-α and RANTES were significantly increased (p = 0.001, p = 0.006) and interleukin-12 levels were also higher in CKD patients during the 5th year (p = 0.007). <i>Conclusion:</i>Monocytes in CKD stages 2-3 show emerging functional abrasions, with altered adhesion molecule expression and impaired fMLP response. These findings suggest that a transformation of monocyte function occurs at an early phase of renal impairment and may together with increased plasma levels of pro-inflammatory cytokines contribute to the higher vulnerability of CKD patients to comorbidities, such as infections and cardiovascular disease.
DOI: 10.7910/dvn/v1rjpf/tcxch4
title: mea20150101_03.txt.gz

description: :unav