cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12248033
title: Surgical and Immunohistochemical Outcomes of Scleral Reconstruction with Autogenic, Allogenic and Xenogenic Grafts: An Experimental Rabbit Model

description: <b>Purpose</b>: Choukroun’s platelet-rich fibrin (PRF), a second-generation platelet concentrate, has unique morphological and chemical features and may be considered as a scaffold for scleral reinforcement and regeneration. The purpose of this study was to compare the use of xenogenic human-derived amniotic membrane (HAM), allogenic sclera, and autogenic PRF in rabbit lamellar scleral defect model with respect to both anatomical and immunohistochemical improvement. <b>Methods</b>: A total of 45 adult New Zealand rabbits were randomized into five groups: normal control; without surgical procedure, negative control; scleral defect model (SDM), xenogenic HAM; SDM+HAM graft, allogenic sclera; SDM+allogenic sclera graft, autogenic PRF; SDM+autogenic PRF graft. Clinical findings, Hematoxylin&Eozin (HE), Masson Trichrome, Verhoeff Acid Fuchsin, Transforming Growth Factor β Receptor 1, Fibroblast Growth Factor, Bone Morphogenetic Protein 2, collagen type 1, aggrecan, and Matrix Metalloproteinase 2 were evaluated. <b>Results</b>: Ocular surface inflammation was significantly lower in normal control and autogenic PRF groups (<i>p</i> p = .02), was out of the scleral wound in 33.3% rabbits of xenogenic HAM group (<i>p</i> &gt; .05), all the grafts were at the normal location and viable in autogenic PRF group. The inflammation and vascularization in autogenic PRF group was significantly lower than negative control and xenogenic HAM groups in HE (<i>p</i> p p p &gt; .05). For immunohistochemistry, the closest values to normal control group were detected in autogenic PRF group for all immunomarkers. <b>Conclusion</b>: Autogenic PRF showed superior features via its excellent anatomical and chemical composition for scleral regeneration when compared to single-layered xenogenic HAM and allogenic sclera grafts.
DOI: 10.6084/m9.figshare.12850052
title: <i>TBL1XR1</i> Mutations in Primary Marginal Zone Lymphomas of Ocular Adnexa are Associated with Unique Morphometric Phenotypes

description: Extranodal marginal zone B-cell lymphoma (EMZL) of mucosa-associated lymphoid tissue (MALT) that affects the ocular adnexa, also known as ocular adnexal MALT lymphomas (OAML), are low-grade lymphomas that mostly affect elderly individuals. This study was conducted to explore the genetic and microbial drivers of OMAL, and unique morphometric phenotypes associated with these mutations and infections. In this study, we performed targeted deep sequencing of 8 OAML cases to identify its potential genetic and microbial drivers. We additionally performed computational digital image analysis of cases to determine if morphologic features corresponded to genetic mutations and disease biology. We identified TBL1XR1 as recurrently mutated in OAML (4/8), and mutations in several other oncogenes, tumor suppressors, transcription regulators, and chromatin remodeling genes. Morphologically, OAML cases with mutations in TBL1XR1 showed lymphoma cells with significantly lower circularity and solidity by computational digital image analysis (<i>p</i>-value &lt;0.0001). Additionally, cases of OAML with mutations in TBL1XR1 showed equivalent or increased vascular density compared to cases without mutations in TBL1XR1. Finally, we did not find any infectious microbial organisms associated with OAML. Our study showed recurrent mutations in TBL1XR1 are associated with unique morphometric phenotypes in OMAL cases. Additionally, mutations in genes associated with the methylation status of histone 3, nuclear factor (NF)-κB pathway, and NOTCH pathway were enriched in OMAL cases. Our findings have biologic and clinical implications as mutations in TBL1XR1 and other genes have the potential to be used as markers for the diagnosis of OAML, and also demonstrate a specific biologic phenotypic manifestation of TBL1XR1 mutations.
DOI: 10.6084/m9.figshare.12850052.v1
title: <i>TBL1XR1</i> Mutations in Primary Marginal Zone Lymphomas of Ocular Adnexa are Associated with Unique Morphometric Phenotypes

description: Extranodal marginal zone B-cell lymphoma (EMZL) of mucosa-associated lymphoid tissue (MALT) that affects the ocular adnexa, also known as ocular adnexal MALT lymphomas (OAML), are low-grade lymphomas that mostly affect elderly individuals. This study was conducted to explore the genetic and microbial drivers of OMAL, and unique morphometric phenotypes associated with these mutations and infections. In this study, we performed targeted deep sequencing of 8 OAML cases to identify its potential genetic and microbial drivers. We additionally performed computational digital image analysis of cases to determine if morphologic features corresponded to genetic mutations and disease biology. We identified TBL1XR1 as recurrently mutated in OAML (4/8), and mutations in several other oncogenes, tumor suppressors, transcription regulators, and chromatin remodeling genes. Morphologically, OAML cases with mutations in TBL1XR1 showed lymphoma cells with significantly lower circularity and solidity by computational digital image analysis (<i>p</i>-value &lt;0.0001). Additionally, cases of OAML with mutations in TBL1XR1 showed equivalent or increased vascular density compared to cases without mutations in TBL1XR1. Finally, we did not find any infectious microbial organisms associated with OAML. Our study showed recurrent mutations in TBL1XR1 are associated with unique morphometric phenotypes in OMAL cases. Additionally, mutations in genes associated with the methylation status of histone 3, nuclear factor (NF)-κB pathway, and NOTCH pathway were enriched in OMAL cases. Our findings have biologic and clinical implications as mutations in TBL1XR1 and other genes have the potential to be used as markers for the diagnosis of OAML, and also demonstrate a specific biologic phenotypic manifestation of TBL1XR1 mutations.
DOI: 10.6084/m9.figshare.12248033.v1
title: Surgical and Immunohistochemical Outcomes of Scleral Reconstruction With Autogenic, Allogenic and Xenogenic Grafts: An Experimental Rabbit Model

description: <b>Purpose</b>: Choukroun’s platelet-rich fibrin (PRF), a second-generation platelet concentrate, has unique morphological and chemical features and may be considered as a scaffold for scleral reinforcement and regeneration. The purpose of this study was to compare the use of xenogenic human-derived amniotic membrane (HAM), allogenic sclera, and autogenic PRF in rabbit lamellar scleral defect model with respect to both anatomical and immunohistochemical improvement. <b>Methods</b>: A total of 45 adult New Zealand rabbits were randomized into 5 groups: normal control; without surgical procedure, negative control; scleral defect model (SDM), xenogenic HAM; SDM+HAM graft, allogenic sclera; SDM+allogenic sclera graft, autogenic PRF; SDM+autogenic PRF graft. Clinical findings, Hematoxylin&Eozin (HE), Masson Trichrome, Verhoeff Acid Fuchsin, Transforming Growth Factor β Receptor 1, Fibroblast Growth Factor, Bone Morphogenetic Protein 2, collagen type 1, aggrecan, and Matrix Metalloproteinase 2 were evaluated. <b>Results</b>: Ocular surface inflammation was significantly lower in normal control and autogenic PRF groups (p&lt;0.001). Graft was avascular and not integrated to scleral wound area in 25% rabbits of allogenic sclera group (<i>p</i>=0.02), was out of the scleral wound in 33.3% rabbits of xenogenic HAM group (<i>p</i>&gt;0.05), all the grafts were at the normal location and viable in autogenic PRF group. The inflammation and vascularization in autogenic PRF group was significantly lower than negative control and xenogenic HAM groups in HE (<i>p</i>&lt;0.001). The collagen score of negative control and xenogenic HAM groups were significantly lower than normal control (<i>p</i>&lt;0.001) and autogenic PRF (<i>p</i>&lt;0.001) groups. There were insignificant differences between allogenic sclera and autogenic PRF groups (p&gt;0.05). For immunohistochemistry, the closest values to normal control group were detected in autogenic PRF group for all immunomarkers. <b>Conclusion</b>: Autogenic PRF showed superior features via its excellent anatomical and chemical composition for scleral regeneration when compared to single-layered xenogenic HAM and allogenic sclera grafts.
DOI: 10.6084/m9.figshare.11551959
title: Infectious Keratitis Caused by Rare and Emerging Micro-Organisms

description: To provide a comprehensive review of rare and emerging micro-organisms causing infectious keratitis. A literature search was performed using PubMed Medline, Cochrane Library Database, EMBASE and Scopus (1960 onwards), using the terms: keratitis caused by rare pathogens; mycotic keratitis; fungal keratitis; bacterial keratitis; infectious keratitis; infective keratitis; atypical fungal keratitis; fungal keratitis caused by rare organisms; fungal keratitis caused by rare ocular pathogen; atypical bacterial keratitis; bacterial keratitis caused by rare organisms; bacterial keratitis caused by rare ocular pathogen. All relevant articles were included in this review. A total of 1232 articles matched our search strategy of which 124 articles were included in this mini-review. The rare and emerging bacteria causing keratitis include atypical mycobacteria, <i>Nocardia spp., Chrysebacterium spp., Delftia acidovorans, Kocuria spp., Enterococcus spp., Bartonella henslae, Achromobacter spp. and others</i>. The rare and emerging fungi causing keratitis include <i>Pythium spp., Alternaria spp., Acremonium spp., Cladosporium spp., Curvularia spp., Bipolaris spp., Microsporidia spp., Pseudallescheria spp., Colletotrichum spp</i>., and others. The clinical presentation of these cases is variable. While a few organisms produce characteristic clinical features, rest present similar to bacterial or fungal keratitis with variable response to routine treatment. A strong degree of suspicion is therefore essential for its diagnosis. Special investigations like polymerase chain reaction, gene sequencing, mass spectroscopy and enzyme-linked immunosorbent assay are required for accurate identification of these organisms. Culture-sensitivity is extremely useful as drug resistance to routinely used anti-microbial drugs is common. Prognosis is usually poor for keratitis with <i>Pythium spp., Pseudallescheria spp., Arthrographis spp., Purpureocillium spp., Kociria spp. and Achromobacter spp.</i> Keratitis caused by rare and emerging micro-organisms must be suspected in cases where the infection runs an unusual course or shows a poor response to standard anti-microbial drugs. Early diagnosis and timely treatment hold the key for a good outcome.
DOI: 10.6084/m9.figshare.12063147
title: Purinergic Signaling Involvement in Thymosin β4-mediated Corneal Epithelial Cell Migration

description: <b>Purpose</b>: This study aimed to determine the effect of thymosin beta 4 (Tβ4) on human corneal epithelial cell migration and the downstream signaling pathways. Tβ4 has a role in tissue development, cell migration, inflammation, and wound healing. A previous study showed that Tβ4 directly binds to F0-F1 ATP synthase. Other studies reported the role of extracellular ATP and purinergic receptors in cell migration with several cell types. Despite advancing to the clinical stage for treatment of eye disorders, the effect of Tβ4 on human corneal epithelial cell (HCEC) migration and proliferation and the precise downstream signaling pathway(s) have not been identified. <b>Methods</b>: Various concentrations of Tβ4 were tested in vitro on human corneal epithelial cell proliferation using the CCK-8 Kit and on cell migration using the gap closure migration assay. Additionally, ATP levels at various time points were determined using the ATP Lite One-Step Kit. The Fluo 8 NO Wash Calcium Assay Kit was used to measure the intracellular Ca<sup>2+</sup> concentration after treatment with various concentrations of Tβ4. P2X7 inhibitors were tested on ATP signaling and migration. Total- and phospho-ERK1/2 levels were determined in western blot. <b>Results</b>: Tβ4 enhanced HCEC proliferation and migration in a dose- and time-dependent manner. Moreover, these functions were related to increased extracellular ATP levels, intracellular Ca<sup>2+</sup> influx, and ERK1/2 phosphorylation. Tβ4-mediated HCEC migration was inhibited by specific P2X7 purinergic receptor antagonists suggesting the role of this receptor in Tβ4-mediated human corneal epithelial cell migration. <b>Conclusions</b>: These results suggest that Tβ4-mediated HCEC proliferation and migration are associated with increased ATP levels, P2X7 R-mediated Ca<sup>2+</sup> influx, and the ERK1/2 signaling pathway. This study begins to describe the mechanisms for Tβ4-mediated corneal healing and regeneration.
DOI: 10.6084/m9.figshare.12063147.v1
title: Purinergic Signaling Involvement in Thymosin β4-mediated Corneal Epithelial Cell Migration

description: <b>Purpose</b>: This study aimed to determine the effect of thymosin beta 4 (Tβ4) on human corneal epithelial cell migration and the downstream signaling pathways. Tβ4 has a role in tissue development, cell migration, inflammation, and wound healing. A previous study showed that Tβ4 directly binds to F0-F1 ATP synthase. Other studies reported the role of extracellular ATP and purinergic receptors in cell migration with several cell types. Despite advancing to the clinical stage for treatment of eye disorders, the effect of Tβ4 on human corneal epithelial cell (HCEC) migration and proliferation and the precise downstream signaling pathway(s) have not been identified. <b>Methods</b>: Various concentrations of Tβ4 were tested in vitro on human corneal epithelial cell proliferation using the CCK-8 Kit and on cell migration using the gap closure migration assay. Additionally, ATP levels at various time points were determined using the ATP Lite One-Step Kit. The Fluo 8 NO Wash Calcium Assay Kit was used to measure the intracellular Ca<sup>2+</sup> concentration after treatment with various concentrations of Tβ4. P2X7 inhibitors were tested on ATP signaling and migration. Total- and phospho-ERK1/2 levels were determined in western blot. <b>Results</b>: Tβ4 enhanced HCEC proliferation and migration in a dose- and time-dependent manner. Moreover, these functions were related to increased extracellular ATP levels, intracellular Ca<sup>2+</sup> influx, and ERK1/2 phosphorylation. Tβ4-mediated HCEC migration was inhibited by specific P2X7 purinergic receptor antagonists suggesting the role of this receptor in Tβ4-mediated human corneal epithelial cell migration. <b>Conclusions</b>: These results suggest that Tβ4-mediated HCEC proliferation and migration are associated with increased ATP levels, P2X7 R-mediated Ca<sup>2+</sup> influx, and the ERK1/2 signaling pathway. This study begins to describe the mechanisms for Tβ4-mediated corneal healing and regeneration.
DOI: 10.6084/m9.figshare.12143397
title: Electrolyte, Nitric Oxide and Oxidative Stress Levels of Aqueous Humor in Patients with Retinal Detachment and Silicone Oil Tamponade

description: <b>Purpose</b>: To enlighten the pathogenesis of silicone oil (SiO)-related complications via measuring aqueous humor levels of electrolytes, nitric oxide (NO), and oxidative stress in SiO, retinal detachment (RD), and control groups. <b>Materials and Methods</b>: In this prospective study, 56 patients were grouped as SiO (<i>n</i> = 29), RD (<i>n</i> = 12), and control (<i>n</i> = 15). The results of pre- and post-operative ophthalmological examinations, aqueous humor electrolyte and NO levels, total antioxidant and oxidant status (TAS, TOS) and oxidative stress index (OSI) were analyzed. <b>Results</b>: SiO group had a higher mean Na<sup>+</sup> level compared to controls (144.77 ± 11.48 vs 137.56 ± 6.57 mmol/kg, <i>p</i> = .02). Also, the mean Na<sup>+</sup> and Cl<sup>−</sup> levels of RD group were higher than controls (149.04 ± 12.05 vs. 137.56 ± 6.57 mmol/kg, <i>p</i> = .02, 115.2 ± 7.79 vs 106.23 ± 8.99 mmol/kg, <i>p</i> = .031 for Na<sup>+</sup> and Cl<sup>−</sup>, respectively). The mean NO level of RD group was higher than that of SiO group (51.07 ± 19.56 vs. 34.07 ± 13.84 μM, <i>p</i> = .009). The mean TAS and TOS were lower in SiO group compared to controls (1.92 ± 0.64 vs. 2.49 ± 0.56 μmolTroloxEqv./L, <i>p</i> = .021, 34.98 ± 26.55 vs. 61.46 ± 22.69 μmolH<sub>2</sub>O<sub>2</sub>Eqv./L, <i>p</i> = .004 for TAS and TOS, respectively). Intraocular retention time of SiO demonstrated positive correlation with post-operative visual acuity (logMAR) and negative correlation with TOS. <b>Conclusions</b>: Elevated aqueous humor Na<sup>+</sup> and Cl<sup>−</sup> in RD patients might reflect abolished function of ion channels on detached retina. Increased Na<sup>+</sup> and lack of NO response to elevated intraocular pressure in SiO-filled eyes might contribute to secondary cataract and glaucoma formation. SiO is associated with low levels of oxidative stress in aqueous humor; however, increased intraocular retention time of SiO is related to a poor visual outcome.
DOI: 10.6084/m9.figshare.12143397.v1
title: Electrolyte, Nitric Oxide and Oxidative Stress Levels of Aqueous Humor in Patients with Retinal Detachment and Silicone Oil Tamponade

description: <b>Purpose</b>: To enlighten the pathogenesis of silicone oil (SiO)-related complications via measuring aqueous humor levels of electrolytes, nitric oxide (NO), and oxidative stress in SiO, retinal detachment (RD), and control groups. <b>Materials and Methods</b>: In this prospective study, 56 patients were grouped as SiO (<i>n</i> = 29), RD (<i>n</i> = 12), and control (<i>n</i> = 15). The results of pre- and post-operative ophthalmological examinations, aqueous humor electrolyte and NO levels, total antioxidant and oxidant status (TAS, TOS) and oxidative stress index (OSI) were analyzed. <b>Results</b>: SiO group had a higher mean Na<sup>+</sup> level compared to controls (144.77 ± 11.48 vs 137.56 ± 6.57 mmol/kg, <i>p</i> = .02). Also, the mean Na<sup>+</sup> and Cl<sup>−</sup> levels of RD group were higher than controls (149.04 ± 12.05 vs. 137.56 ± 6.57 mmol/kg, <i>p</i> = .02, 115.2 ± 7.79 vs 106.23 ± 8.99 mmol/kg, <i>p</i> = .031 for Na<sup>+</sup> and Cl<sup>−</sup>, respectively). The mean NO level of RD group was higher than that of SiO group (51.07 ± 19.56 vs. 34.07 ± 13.84 μM, <i>p</i> = .009). The mean TAS and TOS were lower in SiO group compared to controls (1.92 ± 0.64 vs. 2.49 ± 0.56 μmolTroloxEqv./L, <i>p</i> = .021, 34.98 ± 26.55 vs. 61.46 ± 22.69 μmolH<sub>2</sub>O<sub>2</sub>Eqv./L, <i>p</i> = .004 for TAS and TOS, respectively). Intraocular retention time of SiO demonstrated positive correlation with post-operative visual acuity (logMAR) and negative correlation with TOS. <b>Conclusions</b>: Elevated aqueous humor Na<sup>+</sup> and Cl<sup>−</sup> in RD patients might reflect abolished function of ion channels on detached retina. Increased Na<sup>+</sup> and lack of NO response to elevated intraocular pressure in SiO-filled eyes might contribute to secondary cataract and glaucoma formation. SiO is associated with low levels of oxidative stress in aqueous humor; however, increased intraocular retention time of SiO is related to a poor visual outcome.
DOI: 10.5519/qd.nyxvosu6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (251 records)
DOI: 10.3886/e119191v2-85940
title: Weather & Summer Spatial Behavior of U.S. National Park Visitors (Flickr data 2006 - 2018)

description: This dataset corresponds to the following paper: Wilkins, E. J., Howe, P. D., & Smith, J. W. (2021). Social media data reveal ecoregional variation in how weather influences visitor behavior in U.S. National Park Service Units. Scientific Reports. https://doi.org/10.1038/s41598-021-82145-z<br><br>In this paper, we investigate how daily temperature and precipitation in the summer influence visitors' spatial behavior in 110 U.S. National Park Service Units. We use Flickr data from 2006 - 2018 to uncover visitors locations within parks, and connect each geotagged point to the weather at the date the photo was taken (using Daymet data), as well as nearby infrastructure and environmental features (using OpenStreetMap data). <br><br>While we cannot provide the raw Flickr data due to privacy concerns, we include the final database we used after all data collection, cleaning, and processing (all_ecoregions_Flickr.csv). All personally identifiable information is deleted from this database. This database was used to run the statistical tests presented in the paper, as well as generate the maps (R code included). <br><br>We also include maps of each of the 110 study sites that show the general summer spatial distributions of Flickr posts in each park, and well as how the spatial distributions differ by hot and cold summer days.
description: We collected all Flickr data within the study sites, and filtered the dataset to only include one post per user, per day, within a 10 meter radius.
description: Any visitor to 110 U.S. National Park Service Units who has uploaded a photo to Flickr. .
description: web scraping; All data was collected by writing Python and R scripts to interact with APIs.
DOI: 10.5281/zenodo.4705974
title: The Long Sinuous Rille System in Northern Oceanus Procellarum and its Relation to the Chang'e-5 Returned Samples

description: <strong>This dataset is for our work entitled "The Long Sinuous Rille System in Northern Oceanus Procellarum and its Relation to the Chang’e-5 Returned Samples"</strong> <strong>This dataset includes: 1) The geological boundaries for the Chang'e-5 landing region where we studied, 2) The geological features around the Chang'e-5 landing site, including sinuous rilles and wrinkle ridges, and 3) The CSFD ages for the Em4/P58 mare unit where Chang'e-5 landed.</strong>
description: {"references": ["Qian, Y., et al., 2018. Geology and Scientific Significance of the R\u00fcmker Region in Northern Oceanus Procellarum: China's Chang'E-5 Landing Region. J. Geophys. Res. Planets 123, 1407\u20131430. https://doi.org/10.1029/2018JE005595", "Qian, Y., et al., 2021. Young lunar mare basalts in the Chang'e-5 sample return region, northern Oceanus Procellarum. Earth Planet. Sci. Lett. 555, 116702. https://doi.org/10.1016/j.epsl.2020.116702", "Qian, Y., et al., 2021. The Long Sinuous Rille System in Northern Oceanus Procellarum and its Relation to the Chang'e-5 Returned Samples. Geophys. Res. Lett."]}
DOI: 10.5281/zenodo.4705973
title: The Long Sinuous Rille System in Northern Oceanus Procellarum and its Relation to the Chang'e-5 Returned Samples

description: <strong>This dataset is for our work entitled "The Long Sinuous Rille System in Northern Oceanus Procellarum and its Relation to the Chang’e-5 Returned Samples"</strong> <strong>This dataset includes: 1) The geological boundaries for the Chang'e-5 landing region where we studied, 2) The geological features around the Chang'e-5 landing site, including sinuous rilles and wrinkle ridges, and 3) The CSFD ages for the Em4/P58 mare unit where Chang'e-5 landed.</strong>
description: {"references": ["Qian, Y., et al., 2018. Geology and Scientific Significance of the R\u00fcmker Region in Northern Oceanus Procellarum: China's Chang'E-5 Landing Region. J. Geophys. Res. Planets 123, 1407\u20131430. https://doi.org/10.1029/2018JE005595", "Qian, Y., et al., 2021. Young lunar mare basalts in the Chang'e-5 sample return region, northern Oceanus Procellarum. Earth Planet. Sci. Lett. 555, 116702. https://doi.org/10.1016/j.epsl.2020.116702", "Qian, Y., et al., 2021. The Long Sinuous Rille System in Northern Oceanus Procellarum and its Relation to the Chang'e-5 Returned Samples. Geophys. Res. Lett."]}