cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6477287
title: PMD hypomethylation human (hg19) neural network scores

description: Global loss of DNA methylation in mammalian genomes occurs cumulatively as a mitotic process during aging and cancer, primarily in Partially Methylated Domains (PMDs). It has been shown that local sequence context (100bp) has a strong effect on the rate of demethylation of individual CpG dinucleotides within PMDs. Here, we train a deep learning model to characterize this sequence dependence further, finding that methylation loss can be predicted from a CpG’s 150bp sequence context alone with an AUC of 0.95. We use re-methylation rates of newly synthesized DNA to show that CpGs with fast-loss sequence context are inefficiently re-methylated. Interestingly, we find that the 10% of CpGs predicted to have the “slowest” rate of loss lose almost no DNA methylation in healthy cell types. These same slow-loss CpGs lose a significant amount of DNA methylation in cancer, suggesting that they could be responsible for deregulation of genes and transposable elements that are associated with DNA hypomethylation in cancer. This directory contains the Nov. 18, 2020 version of the human (hg19) CpG hypomethylation Neural network scores in a single tab-delimited (bedgraph) file:<br> <strong>multitissue-nn-scores.allCGs.0based.hg19.bedgraph.gz</strong><br> with the following columns:<br> 1: chromosome (hg19)<br> 2: start coord (hg19, 0-based)<br> 3: end coord (hg19, 0-based)<br> 4: multi-tissue NN score (0-1). Close to 0 is classified as slow-loss CpG, close to 1 is classified as fast loss CpG5: Num CpGs in 150 bp window (including central CpG, so minimum is 1). The full version of the NN scores with additional details are in the file <strong>zhou-bian.allCGs.1based.hg19.tsv.gz</strong> Each row is a CG which provides (1) chromosome, (2) the corresponding C coordinate on the forward (watson) strand of the reference genome in one-based coordinates, (3) Neural network score, (4) number of CpGs within the 150bp sequence centered on this CpG, including the center CpG, (5) CpG is within a CpG island (0, no; 1, yes), CpG is within ENCODE blacklist (0, no; 1, yes) Here the CpG islands are the union set of Irizarry (Irizarry et al. 2009, Nat Genet), Takai-Jones (Takai et al. 2002, PNAS), Gardner-Gardin CGIs (Gardner-Gardin et al. 1987, J Mol Biol.). The blacklist was downloaded from https://github.com/Boyle-Lab/Blacklist/tree/master/lists. Additional files are included here:<br> <strong>zhou_pmds.0based.hg19.bed.gz</strong>: Input PMD CpGs from the Zhou (multi-tissue) dataset<br> <strong>bian_pmds.crc01.0based.hg19.bed.gz</strong>: Input PMD CpGs from the Bian (intra-tumor) dataset<br> <strong>zhou_bian_train_test_data.tar.gz</strong>: All training and test CpGs, including labels and sequence windows.
DOI: 10.25573/data.19630062
title: Data: Attachment mechanism of epiphytic Anthurium obtusum

description: Datasets for anchorage strength analysis Peeling_Test.txt -&gt; Consolidated dataset for peeling test Shear_Test.txt -&gt; Consolidated dataset for shear test
DOI: 10.25573/data.19630062.v1
title: Data: Attachment mechanism of epiphytic Anthurium obtusum

description: Datasets for anchorage strength analysis Peeling_Test.txt -&gt; Consolidated dataset for peeling test Shear_Test.txt -&gt; Consolidated dataset for shear test
DOI: 10.6084/m9.figshare.5718379
title: A comparison of two conjunctival rotation autograft techniques in primary pterygium surgery

description: ABSTRACT Purpose: To compare the effects of 90° and 180° conjunctival rotational autograft (CRA) techniques used in primary pterygium surgery. Methods: Forty-five patients were included in this retrospective study. Visual acuity (VA), corneal topography, and auto-refractometer measurements, as well as detailed biomicroscopic examinations, were performed preoperatively and postoperatively. During surgery, the pterygium tissue was excised then rotated 90° in Group 1 and180° in Group 2, after which it was sutured to the bare sclera. Pterygium recurrence was defined as corneal invasion ≥1 mm. Results: Group 1 consisted of 21 patients with a mean age of 45.1 ± 11.8 years, while Group 2 comprised 24 patients with a mean age of 47.9 ± 13.8 years. The pterygia in Group 1 were graded as more advanced than those in Group 2. A similar number of recurrences were observed in Group 1 (14.3%) and in Group 2 (16.7%). There was no statistically significant difference in terms of the preoperative and postoperative VA and astigmatism values between the two groups. There was a statistically significant improvement in the postoperative VA and astigmatism values in Group 1 and in the postoperative astigmatism values in Group 2. Although postoperative redness was more common in Group 1, no statistically significant difference was found between the groups. Conclusion: BothCRA techniques can be successful in patients for whom it is desirable to avoid a conjunctival autograft and for patients without high cosmetic expectations.
DOI: 10.6084/m9.figshare.5718379.v1
title: A comparison of two conjunctival rotation autograft techniques in primary pterygium surgery

description: ABSTRACT Purpose: To compare the effects of 90° and 180° conjunctival rotational autograft (CRA) techniques used in primary pterygium surgery. Methods: Forty-five patients were included in this retrospective study. Visual acuity (VA), corneal topography, and auto-refractometer measurements, as well as detailed biomicroscopic examinations, were performed preoperatively and postoperatively. During surgery, the pterygium tissue was excised then rotated 90° in Group 1 and180° in Group 2, after which it was sutured to the bare sclera. Pterygium recurrence was defined as corneal invasion ≥1 mm. Results: Group 1 consisted of 21 patients with a mean age of 45.1 ± 11.8 years, while Group 2 comprised 24 patients with a mean age of 47.9 ± 13.8 years. The pterygia in Group 1 were graded as more advanced than those in Group 2. A similar number of recurrences were observed in Group 1 (14.3%) and in Group 2 (16.7%). There was no statistically significant difference in terms of the preoperative and postoperative VA and astigmatism values between the two groups. There was a statistically significant improvement in the postoperative VA and astigmatism values in Group 1 and in the postoperative astigmatism values in Group 2. Although postoperative redness was more common in Group 1, no statistically significant difference was found between the groups. Conclusion: BothCRA techniques can be successful in patients for whom it is desirable to avoid a conjunctival autograft and for patients without high cosmetic expectations.
DOI: 10.6084/m9.figshare.5718370
title: Repeatability and reproducibility of automatic segmentation of retinal layers in healthy subjects using Spectralis optical coherence tomography

description: ABSTRACT Purpose: To evaluate the repeatability and reproducibility of automatic segmentation in healthy subjects using a Spectralis optical coherence tomography (OCT) system. Methods: A total of 60 eyes from 60 patients were included in this prospective study. Spectral-domain optical coherence tomography images were generated using the Spectralis OCT system. An automated algorithm was used to segment the macular retina into nine layers and evaluate the thickness of each layer in the foveal, inner, and outer Early Treatment Diabetic Retinopathy Study (ETDRS) subfield rings. The eyes were imaged three times by an examiner to assess intraobserver repeatability and imaged once by a second examiner to assess interobserver reproducibility. The first scan was used for reference, whereas the second and third scans were collected using the device’s follow-up mode. Intraclass correlation coefficients (ICCs) of repeatability and reproducibility were analyzed. Results: The examiners achieved high repeatability and reproducibility for all parameters. Good agreement was found for all parameters in all ETDRS subdivisions with an ICC of &gt;0.96 for all measurements. Conclusion: It is possible to obtain cross-sections from the same location using the device’s follow-up mode, making it virtually impossible to distinguish between repeated measurements taken with the device by different examiners.
DOI: 10.6084/m9.figshare.5718370.v1
title: Repeatability and reproducibility of automatic segmentation of retinal layers in healthy subjects using Spectralis optical coherence tomography

description: ABSTRACT Purpose: To evaluate the repeatability and reproducibility of automatic segmentation in healthy subjects using a Spectralis optical coherence tomography (OCT) system. Methods: A total of 60 eyes from 60 patients were included in this prospective study. Spectral-domain optical coherence tomography images were generated using the Spectralis OCT system. An automated algorithm was used to segment the macular retina into nine layers and evaluate the thickness of each layer in the foveal, inner, and outer Early Treatment Diabetic Retinopathy Study (ETDRS) subfield rings. The eyes were imaged three times by an examiner to assess intraobserver repeatability and imaged once by a second examiner to assess interobserver reproducibility. The first scan was used for reference, whereas the second and third scans were collected using the device’s follow-up mode. Intraclass correlation coefficients (ICCs) of repeatability and reproducibility were analyzed. Results: The examiners achieved high repeatability and reproducibility for all parameters. Good agreement was found for all parameters in all ETDRS subdivisions with an ICC of &gt;0.96 for all measurements. Conclusion: It is possible to obtain cross-sections from the same location using the device’s follow-up mode, making it virtually impossible to distinguish between repeated measurements taken with the device by different examiners.
DOI: 10.6084/m9.figshare.5979946.v1
title: Recurrent idiopathic neuroretinitis as a spectrum of atypical optic neuritis: a case report and literature review

description: ABSTRACT Recurrent idiopathic neuroretinitis is an inflammatory optic neuropathy characterized by optic nerve edema and macular star, associated with painless and recurrent episodes of visual loss, poor visual prognosis, and visual field defects related to nerve fiber layer injury. The disorder is sometimes mistaken for atypical optic neuritis. However, early diagnosis is important for visual recovery. Long-term immunosuppression has been shown to reduce the rate of recurrence and protect against severe and irreversible vision loss.
DOI: 10.6084/m9.figshare.5979946
title: Recurrent idiopathic neuroretinitis as a spectrum of atypical optic neuritis: a case report and literature review

description: ABSTRACT Recurrent idiopathic neuroretinitis is an inflammatory optic neuropathy characterized by optic nerve edema and macular star, associated with painless and recurrent episodes of visual loss, poor visual prognosis, and visual field defects related to nerve fiber layer injury. The disorder is sometimes mistaken for atypical optic neuritis. However, early diagnosis is important for visual recovery. Long-term immunosuppression has been shown to reduce the rate of recurrence and protect against severe and irreversible vision loss.
DOI: 10.6084/m9.figshare.6388037
title: Undifferentiated pleomorphic sarcoma of the orbital region: a case report

description: ABSTRACT Undifferentiated pleomorphic sarcoma (UPS) is an extremely rare tumor that occurs in the head and neck region. Here, we report a unique case of a primary undifferentiated pleomorphic sarcoma in the orbital region. A 35-year-old woman presented with a progressive proptosis and periocular edema for 1 year. She had no previous history of surgery, skin malignancy, or radiation. Imaging tests showed an extraconal mass, not involving the muscles. The tumor was surgically removed and adjuvant radiotherapy was required after histological examination, which showed an undifferentiated pleomorphic sarcoma of the orbit. There was no recurrence after 1 year of follow-up. Though rare, undifferentiated pleomorphic sarcoma should be included in the differential diagnoses of orbital tumors.
DOI: 10.6084/m9.figshare.6388037.v1
title: Undifferentiated pleomorphic sarcoma of the orbital region: a case report

description: ABSTRACT Undifferentiated pleomorphic sarcoma (UPS) is an extremely rare tumor that occurs in the head and neck region. Here, we report a unique case of a primary undifferentiated pleomorphic sarcoma in the orbital region. A 35-year-old woman presented with a progressive proptosis and periocular edema for 1 year. She had no previous history of surgery, skin malignancy, or radiation. Imaging tests showed an extraconal mass, not involving the muscles. The tumor was surgically removed and adjuvant radiotherapy was required after histological examination, which showed an undifferentiated pleomorphic sarcoma of the orbit. There was no recurrence after 1 year of follow-up. Though rare, undifferentiated pleomorphic sarcoma should be included in the differential diagnoses of orbital tumors.
DOI: 10.6084/m9.figshare.19925520.v1
title: Cilioretinal artery branch avulsion secondary to surgical embolectomy: management and outcome. Case report

description: ABSTRACT We report the trans-operative approach and short-term outcome for a patient who suffered a traumatic avulsion of the cilioretinal artery branch during the surgical management of a cilioretinal arterial branch occlusion with intraocular embolectomy. The patient underwent a pars plana vitrectomy with in situ embolectomy. The blocked artery was incised using 25 Ga vertical scissors, and embolus manipulation was performed using microsurgical forceps. During embolus extraction, the occluded cilioretinal artery and its branch were inadvertently avulsed and torn with subsequent intense bleeding. Laser and endodiathermy were used for acute hemostasis. The maneuvers created an unintended retinochoroidal anastomosis. Visual-field improvement was noted three months after the surgery. In the event of a complicated surgical embolectomy with the avulsion of the artery, the formation of a retinochoroidal anastomosis and reperfusion of the occluded artery may occur along with the improvement of the visual field in some cases.
DOI: 10.6084/m9.figshare.19925520
title: Cilioretinal artery branch avulsion secondary to surgical embolectomy: management and outcome. Case report

description: ABSTRACT We report the trans-operative approach and short-term outcome for a patient who suffered a traumatic avulsion of the cilioretinal artery branch during the surgical management of a cilioretinal arterial branch occlusion with intraocular embolectomy. The patient underwent a pars plana vitrectomy with in situ embolectomy. The blocked artery was incised using 25 Ga vertical scissors, and embolus manipulation was performed using microsurgical forceps. During embolus extraction, the occluded cilioretinal artery and its branch were inadvertently avulsed and torn with subsequent intense bleeding. Laser and endodiathermy were used for acute hemostasis. The maneuvers created an unintended retinochoroidal anastomosis. Visual-field improvement was noted three months after the surgery. In the event of a complicated surgical embolectomy with the avulsion of the artery, the formation of a retinochoroidal anastomosis and reperfusion of the occluded artery may occur along with the improvement of the visual field in some cases.
DOI: 10.6084/m9.figshare.7075454
title: Oral omega 3 in different proportions of EPA, DHA, and antioxidants as adjuvant in treatment of keratoconjunctivitis sicca in dogs

description: ABSTRACT Purpose: To compare the efficacy of 0.03% topical tacrolimus in combination with oral omega (ω) 3 with different ratios of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and antioxidants as adjuvant in the treatment of keratoconjunctivitis sicca (KCS) in dogs. Methods: Forty-five dogs with KCS were evaluated monthly for 6 months. Evaluations included performance of the Schirmer tear, fluorescein, and lissamine green tests. Tear film break-up time (TBUT) was assessed. Conjunctival cytology was evaluated at the beginning, middle, and end of the study. Conjunctiva was biopsied at the beginning and end of the study. Dogs were randomly assigned to one of the three groups (n=15): Group T (topical tacrolimus 0.03%), Group TO (topical tacrolimus + ω-1.5 EPA: 1 DHA), or Group TOA (topical tacrolimus + ω-1 EPA:4.5 DHA + antioxidants). Results: There was a significant improvement in clinical signs in all groups. TBUT increased throughout treatment in all groups; this effect was most pronounced in Group TO. Cytological analysis performed at the end of the study period, showed decreased levels of lymphocytes, neutrophils, and metaplastic and squamous cells in Groups T, TO, and TOA. Histological analysis performed at the end of the study period showed decreased levels of lymphocytes and neutrophils and increased levels of goblet cells. These effects were most pronounced in Group TO. Conclusion: Oral treatment with ω-3 containing a higher proportion of EPA than DHA increased the effectiveness of topical tacrolimus 0.03% in the treatment of keratoconjunctivitis sicca in dogs.
DOI: 10.6084/m9.figshare.7075454.v1
title: Oral omega 3 in different proportions of EPA, DHA, and antioxidants as adjuvant in treatment of keratoconjunctivitis sicca in dogs

description: ABSTRACT Purpose: To compare the efficacy of 0.03% topical tacrolimus in combination with oral omega (ω) 3 with different ratios of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and antioxidants as adjuvant in the treatment of keratoconjunctivitis sicca (KCS) in dogs. Methods: Forty-five dogs with KCS were evaluated monthly for 6 months. Evaluations included performance of the Schirmer tear, fluorescein, and lissamine green tests. Tear film break-up time (TBUT) was assessed. Conjunctival cytology was evaluated at the beginning, middle, and end of the study. Conjunctiva was biopsied at the beginning and end of the study. Dogs were randomly assigned to one of the three groups (n=15): Group T (topical tacrolimus 0.03%), Group TO (topical tacrolimus + ω-1.5 EPA: 1 DHA), or Group TOA (topical tacrolimus + ω-1 EPA:4.5 DHA + antioxidants). Results: There was a significant improvement in clinical signs in all groups. TBUT increased throughout treatment in all groups; this effect was most pronounced in Group TO. Cytological analysis performed at the end of the study period, showed decreased levels of lymphocytes, neutrophils, and metaplastic and squamous cells in Groups T, TO, and TOA. Histological analysis performed at the end of the study period showed decreased levels of lymphocytes and neutrophils and increased levels of goblet cells. These effects were most pronounced in Group TO. Conclusion: Oral treatment with ω-3 containing a higher proportion of EPA than DHA increased the effectiveness of topical tacrolimus 0.03% in the treatment of keratoconjunctivitis sicca in dogs.
DOI: 10.6084/m9.figshare.7244522
title: Morphological and functional findings in Alström syndrome: a study of two families

description: ABSTRACT Alström syndrome is a rare disorder characterized by mutations to the ALMS1 gene and clinical findings of childhood obesity, diabetes mellitus, dilated cardiomyopathy, sensorineural hearing loss, and progressive cone-rod dystrophy, which may result in blindness. Ocular manifestations occur in the first decade of life with nystagmus, blepharospasm, and photophobia leading to progressive and severe reductions in visual acuity. This study describes the retinal structure and functional aspects of four patients (8 eyes) from two different families as determined by optical coherence tomography (OCT), fundus autofluorescence, and full-field electroretinography. There was a correlation between morphological and functional findings, evidenced by typical funduscopic changes of retinal dystrophy in spectral domain-OCT and electrophysiological analyses. Foveal characteristics include a single layer of undifferentiated photoreceptors with retinal disorganization mainly from external segments, in agreement with previous reports in the literature. Fundus autofluorescence showed areas of hyperautofluorescence interspersed by hypoautofluorescence dots suggesting, respectively, involvement and atrophy of retinal pigmented epithelial cells in the macular zone. Electroretinographic analyses showed early dysfunction of the cones followed by rapid rod deterioration.
DOI: 10.6084/m9.figshare.7244522.v1
title: Morphological and functional findings in Alström syndrome: a study of two families

description: ABSTRACT Alström syndrome is a rare disorder characterized by mutations to the ALMS1 gene and clinical findings of childhood obesity, diabetes mellitus, dilated cardiomyopathy, sensorineural hearing loss, and progressive cone-rod dystrophy, which may result in blindness. Ocular manifestations occur in the first decade of life with nystagmus, blepharospasm, and photophobia leading to progressive and severe reductions in visual acuity. This study describes the retinal structure and functional aspects of four patients (8 eyes) from two different families as determined by optical coherence tomography (OCT), fundus autofluorescence, and full-field electroretinography. There was a correlation between morphological and functional findings, evidenced by typical funduscopic changes of retinal dystrophy in spectral domain-OCT and electrophysiological analyses. Foveal characteristics include a single layer of undifferentiated photoreceptors with retinal disorganization mainly from external segments, in agreement with previous reports in the literature. Fundus autofluorescence showed areas of hyperautofluorescence interspersed by hypoautofluorescence dots suggesting, respectively, involvement and atrophy of retinal pigmented epithelial cells in the macular zone. Electroretinographic analyses showed early dysfunction of the cones followed by rapid rod deterioration.
DOI: 10.6084/m9.figshare.7075532
title: Nature as a source of drugs for ophthalmology

description: ABSTRACT Nature has always provided an unlimited source of biologically-active compounds. Since the beginning of mankind, humans have sought resources in fauna and flora to treat eye diseases. However, it was only after the Industrial Revolution that extracts of plants and substances of animal origin could be used safely, as has been determined by controlled interventional studies. Two major challenges faced by ocular pharmacology are the following: developing drugs that are able to reduce blindness due to glaucoma; and controlling the pain associated with eye surgery. The search for a drug that effectively lowers intraocular pressure and controls the progression of glaucoma has led to the development of various ocular hypotensive agents, such as physostigmine from the Physostigma venenosum plant. The anesthetic properties of cocaine, extracted from Erythroxylon coca, finally enabled surgical procedures in the eye. Several new natural compounds have been investigated in an attempt to identify substances with the potential to provide additional benefits to eye tissue and vision. Emerging evidence of anti-inflammatory, wound-healing, antimicrobial, antioxidant, antitumor, and antiangiogenic properties attributed to plant extracts and animal tissues has encouraged more investment in research in this area. Despite technological advances in synthesizing drugs, the pharmaceutical industry still seeks new active compounds from natural sources as well as from revisiting already-established naturally derived compounds. Although a large number of naturally-occurring compounds is known, this review article focuses on the bioactive substances with scientifically-proven benefits for ocular tissues.