cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21836281.v1
title: Ammonoids of the Oxynotum Zone and Raricostatum Zone (Densinodulum Subzone) of Sinemurian, Lower Jurassic, in the Asturian and Lusitanian basins

description: This research is focused on the ammonoids of Oxynotum Zone and Raricostatum Zone (Densinodulum Subzone) from Asturian (Spain) and Lusitanian (Portugal) basins. They come from expanded sections from where 216 specimens have been collected. These have been classified in eight genera and 15 species that belong to families Echioceratidae, Oxynoticeratidae and Eoderoceratidae. Most of the ammonoids are typical of the Northwest European Province. Echioceratidae is the most frequent in the Asturian Basin, whereas Oxynoticeratidae is the predominant in the Lusitanian Basin. Eoderoceratidae specimens are scarcer, and they are registered only between the middle part of Oxynotum Subzone and the lower part of Densinodulum Subzone. A new species is proposed for the upper part of Oxynotum Subzone of the Lusitanian Basin, <i>Plesechioceras rochai</i> sp. nov., which is relatively frequent. As well, also in Portugal, <i>Cheltonia</i> sp. is registered in Densinodulum Subzone, which is a form different from <i>Cheltonia accipitris</i>. This provides new evidence to support the hypothesis of the relation micro-macroconch between the genera <i>Oxynoticeras</i> (M) and <i>Cheltonia</i> (m). Remarkable differences in the studied area are the presence of <i>Paroxynoticeras salisburgense</i> and <i>Plesechioceras</i> cf. <i>delicatum</i> in the Asturias Basin, and <i>Crucilobiceras densinodulum</i>, associated to <i>Oxynoticeras lymense</i>, in the Lusitanian Basin. https://zoobank.org/NomenclaturalActs/FEF11B83-03CA-4BD6-BB15-F3E9926B7C4F
DOI: 10.6084/m9.figshare.24162621
title: A Novel Primary Porcine Retinal Pigment Epithelium Cell Model with Preserved Properties

description: To establish an ethical, reliable, and expandable retinal pigment epithelial (RPE) cell model with maintained RPE properties compatible with multifarious assays. RPE cells from abattoir-obtained porcine eyes were cultured under various conditions. Morphology, RPE cell-specific protein markers (RPE-65, CRALBP), and the tight junction marker ZO-1 were analyzed by phase-contrast microscopy, immunocytochemistry, and western blot, and transepithelial electrical resistance (TEER) was determined to assess barrier function. The porcine RPE cells (pRPE) were best established using TrypLE Express, 10% fetal bovine serum (FBS) supplemented high-glucose media, and subculturing at semi-confluency. The pRPE cells maintained epithelioid morphology with ZO-1 positive tight junctions at the cell-to-cell borders, the ability to establish proper barrier function (TEERmax: 346/375 Ω⋅cm<sup>2</sup> at passage I/passage VI), and expressed CRALBP and RPE-65 for several passages. The RPE characteristics decreased and disappeared with transdifferentiation. This work describes, for the first time, a pRPE cell model that exhibits preserved RPE properties for several passages on cell culture plastic plates. Though RPE characteristics were maintained for at least 6 passages, the reduced CRALBP and RPE-65 with passaging emphasize that lower passage cells are advantageous to utilize, and that morphology, barrier function, and ZO-1 localization cannot be solely employed as a quality measure of RPE identity. Pigs are phylogenetically similar to humans, including similar physiology, anatomy and immune system. Therefore, porcine RPE cells constitute a relevant model system for studying human eye diseases, such as AMD.
DOI: 10.6084/m9.figshare.24162621.v2
title: A Novel Primary Porcine Retinal Pigment Epithelium Cell Model with Preserved Properties

description: To establish an ethical, reliable, and expandable retinal pigment epithelial (RPE) cell model with maintained RPE properties compatible with multifarious assays. RPE cells from abattoir-obtained porcine eyes were cultured under various conditions. Morphology, RPE cell-specific protein markers (RPE-65, CRALBP), and the tight junction marker ZO-1 were analyzed by phase-contrast microscopy, immunocytochemistry, and western blot, and transepithelial electrical resistance (TEER) was determined to assess barrier function. The porcine RPE cells (pRPE) were best established using TrypLE Express, 10% fetal bovine serum (FBS) supplemented high-glucose media, and subculturing at semi-confluency. The pRPE cells maintained epithelioid morphology with ZO-1 positive tight junctions at the cell-to-cell borders, the ability to establish proper barrier function (TEERmax: 346/375 Ω⋅cm<sup>2</sup> at passage I/passage VI), and expressed CRALBP and RPE-65 for several passages. The RPE characteristics decreased and disappeared with transdifferentiation. This work describes, for the first time, a pRPE cell model that exhibits preserved RPE properties for several passages on cell culture plastic plates. Though RPE characteristics were maintained for at least 6 passages, the reduced CRALBP and RPE-65 with passaging emphasize that lower passage cells are advantageous to utilize, and that morphology, barrier function, and ZO-1 localization cannot be solely employed as a quality measure of RPE identity. Pigs are phylogenetically similar to humans, including similar physiology, anatomy and immune system. Therefore, porcine RPE cells constitute a relevant model system for studying human eye diseases, such as AMD.
DOI: 10.6084/m9.figshare.24230333
title: Association of Tear Cytokine Ratios with Symptoms and Signs of Dry Eye Disease: Biomarker Data from the Dry Eye Assessment and Management Study

description: To assess the relationship between tear inflammatory cytokine ratios (CRs) and signs and symptoms of dry eye disease (DED) to investigate the possible use of tear CRs, which may better address the complexity of cytokine interactions than absolute cytokine levels, as a DED biomarker. Tear concentrations of IL-1b, IL-6, IL-8, IL-10, IL-17A, IFN-g, and TNF-a were measured using standardized procedures, as were DED signs (corneal and conjunctival staining scores, tear break-up time, Schirmer test, Meibomian gland plugging, tear osmolarity, composite sign severity score) and symptoms [Ocular Surface Disease Index (OSDI)]. Ratios between pro-inflammatory (IL-1b, IL-8, IL-17A, IFN-g, and TNF-a) and anti-inflammatory (IL-10) cytokines were calculated. Given its opposing roles in inflammation, IL-6 was tested as both a pro- and anti-inflammatory cytokine. Correlations between CR and DED symptoms and signs were calculated using Spearman correlation coefficients (rho). At baseline, 131 patients, 80.2% female and mean age 54.2 years (SD 14.1, range 20–82), from 10 sites of the Dry Eye Assessment and Management study had sufficient tear volumes ≥4 μL for analysis. IL-6:IL-10, IL-8:IL-10, and TNF-a:IL-10 had some significant correlations, mostly with conjunctival or corneal staining or the composite sign severity score (IL-8:IL-10 and conjunctival staining: rho = 0.19, <i>p</i> = 0.03; IL-6:IL-10 and corneal staining: rho = 0.31, <i>p</i> &lt; 0.001; IL-8:IL-10 and corneal staining: rho = 0.21, <i>p</i> = 0.01; IL-6:IL-10 and composite sign severity score: rho = 0.26, <i>p</i> = 0.003; IL-8:IL-10 and composite sign severity score: rho = 0.26, <i>p</i> = 0.003; TNF-a:IL-10 and corneal staining: rho = 0.29, <i>p</i> &lt; 0.001; TNF-a:IL-10 and Schirmer test: rho = −0.23, <i>p</i> = 0.009). CRs had no significant correlation with DED symptoms. All significant correlations using IL-6 in the denominator (anti-inflammatory) produced counterintuitive results based on clinical understanding of the disease. Pro- to anti-inflammatory CR was weakly correlated with some DED signs and not with symptoms, as measured by OSDI. Future studies in different dry eye populations are needed and should address sampling biases and tear collection techniques.
DOI: 10.6084/m9.figshare.24230333.v1
title: Association of Tear Cytokine Ratios with Symptoms and Signs of Dry Eye Disease: Biomarker Data from the Dry Eye Assessment and Management Study

description: To assess the relationship between tear inflammatory cytokine ratios (CRs) and signs and symptoms of dry eye disease (DED) to investigate the possible use of tear CRs, which may better address the complexity of cytokine interactions than absolute cytokine levels, as a DED biomarker. Tear concentrations of IL-1b, IL-6, IL-8, IL-10, IL-17A, IFN-g, and TNF-a were measured using standardized procedures, as were DED signs (corneal and conjunctival staining scores, tear break-up time, Schirmer test, Meibomian gland plugging, tear osmolarity, composite sign severity score) and symptoms [Ocular Surface Disease Index (OSDI)]. Ratios between pro-inflammatory (IL-1b, IL-8, IL-17A, IFN-g, and TNF-a) and anti-inflammatory (IL-10) cytokines were calculated. Given its opposing roles in inflammation, IL-6 was tested as both a pro- and anti-inflammatory cytokine. Correlations between CR and DED symptoms and signs were calculated using Spearman correlation coefficients (rho). At baseline, 131 patients, 80.2% female and mean age 54.2 years (SD 14.1, range 20–82), from 10 sites of the Dry Eye Assessment and Management study had sufficient tear volumes ≥4 μL for analysis. IL-6:IL-10, IL-8:IL-10, and TNF-a:IL-10 had some significant correlations, mostly with conjunctival or corneal staining or the composite sign severity score (IL-8:IL-10 and conjunctival staining: rho = 0.19, <i>p</i> = 0.03; IL-6:IL-10 and corneal staining: rho = 0.31, <i>p</i> &lt; 0.001; IL-8:IL-10 and corneal staining: rho = 0.21, <i>p</i> = 0.01; IL-6:IL-10 and composite sign severity score: rho = 0.26, <i>p</i> = 0.003; IL-8:IL-10 and composite sign severity score: rho = 0.26, <i>p</i> = 0.003; TNF-a:IL-10 and corneal staining: rho = 0.29, <i>p</i> &lt; 0.001; TNF-a:IL-10 and Schirmer test: rho = −0.23, <i>p</i> = 0.009). CRs had no significant correlation with DED symptoms. All significant correlations using IL-6 in the denominator (anti-inflammatory) produced counterintuitive results based on clinical understanding of the disease. Pro- to anti-inflammatory CR was weakly correlated with some DED signs and not with symptoms, as measured by OSDI. Future studies in different dry eye populations are needed and should address sampling biases and tear collection techniques.
DOI: 10.6084/m9.figshare.24551820
title: A Comparison of Culture Results and Visual Acuity in Contact Lens Related Microbial Keratitis

description: Evaluate the effect of corneal and contact lens-related (CLR) culture results on visual acuity (VA) in patients with microbial keratitis (MK). MK patients with corneal and CLR cultures were identified in the University of Michigan electronic health record from August 2012 to April 2022. Test results were classified as laboratory-positive or laboratory-negative. Linear regression was used to examine trends of VA and associations between changes in VA (differences of VA at 90-day and baseline VA) and corneal and CLR culture results, after adjustment for baseline VA. One-sample t-tests were used to test if the slope estimates were different from zero. MK patients (<i>n</i> = 50) were on average 49 years old (standard deviation = 20.9), 56% female, and 90% White. Positive corneal and CLR cultures were reported in 60% and 64% of patients, respectively, and 38% reported both. The agreement rate between corneal and CLR culture results was 30% (<i>n</i> = 15/50). LogMAR VA improved over time in patients with positive corneal and CLR cultures (Estimate=-0.19 per 10-day increase, <i>p</i> = 0.002), and in those with negative corneal and positive CLR cultures (Estimate= −0.17 per 10-day increase, <i>p</i> = 0.004). Compared to patients with negative corneal and CLR cultures, there was a trend toward improvement in VA for patients with positive corneal and CLR cultures (Estimate=-0.68, <i>p</i> = 0.068), and those with negative corneal and positive CLR cultures (Estimate= −0.74, <i>p</i> = 0.059), after adjusting for baseline VA. Positive CLR cultures are associated with significant improvement in VA over time. These additional cultures can provide guidance on appropriate antimicrobial selection, especially when corneal cultures are negative.
DOI: 10.6084/m9.figshare.24551820.v1
title: A Comparison of Culture Results and Visual Acuity in Contact Lens Related Microbial Keratitis

description: Evaluate the effect of corneal and contact lens-related (CLR) culture results on visual acuity (VA) in patients with microbial keratitis (MK). MK patients with corneal and CLR cultures were identified in the University of Michigan electronic health record from August 2012 to April 2022. Test results were classified as laboratory-positive or laboratory-negative. Linear regression was used to examine trends of VA and associations between changes in VA (differences of VA at 90-day and baseline VA) and corneal and CLR culture results, after adjustment for baseline VA. One-sample t-tests were used to test if the slope estimates were different from zero. MK patients (<i>n</i> = 50) were on average 49 years old (standard deviation = 20.9), 56% female, and 90% White. Positive corneal and CLR cultures were reported in 60% and 64% of patients, respectively, and 38% reported both. The agreement rate between corneal and CLR culture results was 30% (<i>n</i> = 15/50). LogMAR VA improved over time in patients with positive corneal and CLR cultures (Estimate=-0.19 per 10-day increase, <i>p</i> = 0.002), and in those with negative corneal and positive CLR cultures (Estimate= −0.17 per 10-day increase, <i>p</i> = 0.004). Compared to patients with negative corneal and CLR cultures, there was a trend toward improvement in VA for patients with positive corneal and CLR cultures (Estimate=-0.68, <i>p</i> = 0.068), and those with negative corneal and positive CLR cultures (Estimate= −0.74, <i>p</i> = 0.059), after adjusting for baseline VA. Positive CLR cultures are associated with significant improvement in VA over time. These additional cultures can provide guidance on appropriate antimicrobial selection, especially when corneal cultures are negative.
DOI: 10.5281/zenodo.10453887
title: D-PLACE aggregated dataset

description: Cite the source of the dataset as:




Kathryn R. Kirby, Russell D. Gray, Simon J. Greenhill, Fiona M. Jordan, Stephanie Gomes-Ng, Hans-Jörg Bibiko, Damián E. Blasi, Carlos A. Botero, Claire Bowern, Carol R. Ember, Dan Leehr, Bobbi S. Low, Joe McCarter, William Divale, and Michael C. Gavin. (2016). D-PLACE: A Global Database of Cultural, Linguistic and Environmental Diversity. PLoS ONE, 11(7): e0158391. doi:10.1371/journal.pone.0158391.
DOI: 10.5281/zenodo.3935420
title: CLDF Dataset derived from D-PLACE

description: This dataset contains the data from D-PLACE, the Database of Places, Language, Culture and Environment, serialized as CLDF StructureDataset.
DOI: 10.5281/zenodo.3952518
title: CLDF Dataset derived from D-PLACE

description: This dataset contains the data from D-PLACE, the Database of Places, Language, Culture and Environment, serialized as CLDF StructureDataset.
DOI: 10.5281/zenodo.4087927
title: CLDF Dataset derived from D-PLACE

description: This dataset contains the data from D-PLACE, the Database of Places, Language, Culture and Environment, serialized as CLDF StructureDataset.
DOI: 10.5281/zenodo.5554412
title: CLDF Dataset derived from D-PLACE

description: This dataset contains the data from D-PLACE, the Database of Places, Language, Culture and Environment, serialized as CLDF StructureDataset.
DOI: 10.6084/m9.figshare.24851532
title: Maps and models: primed myosin, primed actomyosin, and PostPS actomyosinSupplemental VideosValidation Reports

description: CryoEM maps and models: primed myosin, primed actomyosin, and PostPS actomyosinSupplementary Videos 1-4Validation Reports
DOI: 10.6084/m9.figshare.24851532.v3
title: Maps and models: primed myosin, primed actomyosin, and PostPS actomyosinSupplemental VideosValidation Reports

description: CryoEM maps and models: primed myosin, primed actomyosin, and PostPS actomyosinSupplementary Videos 1-4Validation Reports
DOI: 10.6084/m9.figshare.24851532.v2
title: Maps and models: primed myosin, primed actomyosin, and PostPS actomyosinSupplemental Videos

description: CryoEM maps and models: primed myosin, primed actomyosin, and PostPS actomyosinSupplementary Videos 1-4
DOI: 10.6084/m9.figshare.21701377.v1
title: The smallest late Miocene phocine from the Southern Caucasus and the Eastern Paratethys seal community crisis

description: The Caucasus is one of the most important areas for the study of Paratethyan Neogene phocids, with a number of ‘paleorookery’ sites that are still poorly studied. In this study, the remains of a fossil phocine from the Late Miocene locality of Eldari I (late Vallesian/late Sarmatian s.l.) in the Southern Caucasus are described and compared with other Paratethyan phocines. The new materials obtained from the site consists of the right complete forelimb bones along with the carpal and metacarpal bones in natural anatomical articulation and a right innominate bone fragment. Additionally, published remains of ‘<i>Phoca’ procaspica</i> from Eldari I are analysed. Based on morphological and morphometric studies, the Eldari I phocine is assigned to the genus <i>Praepusa</i>. The skeletal material demonstrates a distinct combination of diagnostic traits that can be attributed to the smallest representative of the subfamily, <i>Praepusa procaspica</i>. During the early Late Miocene (10 Ma.), major palaeoecological and palaeogeographic changes took place in the Eastern Paratethyan basin, which significantly decreased the diversity of phocids and had a negative impact on the remnant taxa; this was expressed in the Eldari I and Küçükçekmece seals by the decrease in body size and a change in the feeding apparatus. urn:lsid:zoobank.org:pub:497DEEE9-8557-4136-8AD7-B8749A0285A2
DOI: 10.6084/m9.figshare.24935886
title: Supplemental Tables for HxonIR by Sizhe Huang

description: Supplemental Tables for the paper "Hypoxanthine Alleviates High-Fat Diet Induced Insulin Resistance and Glycolipid Disorder" by Sizhe Huang and Qingfeng Du, et al.
DOI: 10.6084/m9.figshare.24935886.v1
title: Supplemental Tables for HxonIR by Sizhe Huang

description: Supplemental Tables for the paper "Hypoxanthine Alleviates High-Fat Diet Induced Insulin Resistance and Glycolipid Disorder" by Sizhe Huang and Qingfeng Du, et al.
DOI: 10.6084/m9.figshare.24211428
title: Novel Colorimetric and Light Scatter Methods for Point-of-Care Diagnosis of Peritonitis in Peritoneal Dialysis Patients_Underlying data for Figure Panels and Tables..xlsx

description: Excel spreadsheet containing, in separate tabs/sheets, the underlying numerical data for Figure 1a, b, c, d, f, Figure 3e, Figure 4 a, b, c, d, e, f and Table 2
DOI: 10.6084/m9.figshare.24211428.v1
title: Novel Colorimetric and Light Scatter Methods for Point-of-Care Diagnosis of Peritonitis in Peritoneal Dialysis Patients_Underlying data for Figure Panels and Tables..xlsx

description: Excel spreadsheet containing, in separate tabs/sheets, the underlying numerical data for Figure 1a, b, c, d, f, Figure 3e, Figure 4 a, b, c, d, e, f and Table 2
DOI: 10.34808/8nns-eq95
title: Study of the influence of the presence of Dr fimbriae on the adherence of cells of the recombinant Escherichia coli strain: BL21(DE3)/pACYCpBAD to polystyrene in a dynamic system

description: The attachment of bacteria begins the process of surface colonization, called biofilm development, characterized by a number of physicochemical and molecular interactions. Adherence to inert surfaces typically involves nonspecific interactions, whereas adherence to biological surfaces is associated with specific ligand-receptor interactions. In this study, the adherence ability of four genetically modified Escherichia coli strains—BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra, AAEC191A/pCC90, and AAEC191A/pACYCpBAD—was examined on both glass and polystyrene surfaces. The aim was to investigate the effect of the presence of Dr fimbriae on the adherence of bacteria to various carriers. The experiments were performed under various flow conditions.
The catalog contains original video data that can be played using Olympus' CellSense software. The videos contain full layers of data characterizing the image recording process.
DOI: 10.34808/43fs-vq84
title: Detection of cellulose production capacity of recombinant Escherichia coli strains BL21(DE3) and AAEC191A

description: Bacteria that form biofilms generate an extracellular matrix (ECM), where cellulose stands out as a key constituent. An approach for assessing microorganisms' cellulose production involves using calcofluor white staining on colonies. In this method, a fluorescent dye (calcofluor-white) is introduced to a stable YESCA substrate composed of casamino acids, agar, and yeast extract. The fluorescent dye specifically attaches to cellulose, enabling bacterial colonies to be observed under ultraviolet light. The study employed YESCA medium supplemented with calcofluor-white, as well as YESCA + 0.2% glucose medium supplemented with calcofluor-white.
The dataset contains original photos of bacterial colonies of the following E. coli strains: BL21(DE3)/pCC90, BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra D-mut, BL21(DE3)/pCC90 D54-STOP AAEC191A/pCC90, AAEC191A/pACYCpBAD, AAEC191A/pCC90 Dra D-mut, AAEC191A/pCC90 D54-STOP, BL21(DE3), AAEC191A and CFT073. Bacteria were cultured in YESCA medium with the addition of calcofluor-white at a temperature of 25OC and 37OC  for 5 days. Photographs of the colony were taken at one-day intervals.
DOI: 10.34808/zgfw-7g12
title: Detection of cellulose production capacity of recombinant Escherichia coli strains BL21(DE3) and AAEC191A

description: Bacteria that form biofilms generate an extracellular matrix (ECM), where cellulose stands out as a key constituent. An approach for assessing microorganisms' cellulose production involves using calcofluor white staining on colonies. In this method, a fluorescent dye (calcofluor-white) is introduced to a stable YESCA substrate composed of casamino acids, agar, and yeast extract. The fluorescent dye specifically attaches to cellulose, enabling bacterial colonies to be observed under ultraviolet light. The study employed YESCA medium supplemented with calcofluor-white, as well as YESCA + 0.2% glucose medium supplemented with calcofluor-white.
The dataset contains original photos of bacterial colonies of the following E. coli strains: BL21(DE3)/pCC90, BL21(DE3)/pACYCpBAD, BL21(DE3)/pCC90 Dra D-mut, BL21(DE3)/pCC90 D54-STOP AAEC191A/pCC90, AAEC191A/pACYCpBAD, AAEC191A/pCC90 Dra D-mut, AAEC191A/pCC90 D54-STOP, BL21(DE3), AAEC191A and CFT073. Bacteria were cultured in YESCA medium with the addition of calcofluor-white at a temperature of 25OC and 37OC  for 5 days. Photographs of the colony were taken at one-day intervals.