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4. Estimating RNA Secondary Structure by Maximizing Stacking Regions

Author

Sen, Piyali, Tula, Debapriya, Ray, Suvendra Kumar, Satapathy, Siddhartha Sankar, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Mandal, Jyotsna K., editor, Mukhopadhyay, Somnath, editor, and Roy, Alak, editor

Published
2021
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9. Detection of Diabetic Retinopathy from Ultra-Widefield Scanning Laser Ophthalmoscope Images: A Multicenter Deep Learning Analysis

Author

Tang, Fangyao, Luenam, Phoomraphee, Ran, An Ran, Quadeer, Ahmed Abdul, Raman, Rajiv, Sen, Piyali, Khan, Rehana, Giridhar, Anantharaman, Haridas, Swathy, Iglicki, Matias, Zur, Dinah, Loewenstein, Anat, Negri, Hermino P., Szeto, Simon, Lam, Bryce Ka Yau, Tham, Clement C., Sivaprasad, Sobha, Mckay, Matthew, and Cheung, Carol Y.

Published
2021
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10. A Web Portal to Calculate Codon Adaptation Index (CAI) with Organism Specific Reference Set of High Expression Genes for Diverse Bacteria Species

Author

Sen, Piyali, Waris, Abdul, Ray, Suvendra Kumar, Satapathy, Siddhartha Sankar, Bansal, Jagdish Chand, Series Editor, Deep, Kusum, Series Editor, Nagar, Atulya K., Series Editor, Singh Tomar, Geetam, editor, Chaudhari, Narendra S., editor, Barbosa, Jorge Luis V., editor, and Aghwariya, Mahesh Kumar, editor

Published
2020
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16. Difference in synonymous polymorphism related to codon degeneracy between co-transcribed genes in the genome of Escherichia coli.

Author

Beura, Pratyush Kumar, Sen, Piyali, Aziz, Ruksana, Chetia, Chayanika, Dash, Madhusmita, Satapathy, Siddhartha Shankar, and Ray, Suvendra Kumar

Subjects
*SCRAPIE, *ESCHERICHIA coli, *MOLECULAR evolution, *GENETIC code, *GENES, *GENETIC polymorphisms, *GENOMES
Abstract

In our study, we compared synonymous polymorphism in co-transcribed gene pairs within five well-known Escherichia coli operons (rpoB/C, lacZ/Y, kdpA/B, araB/A and bcsA/B). Interestingly, the transition to transversion ratio between gene pairs were different due to their compositional differences of two-fold and four-fold degenerate codons. The differences in polymorphism spectra were more pronounced in four-fold and six-fold codons compared to two-fold degenerate codons. Notably, rpoB and rpoC showed significant distinctions in UCC, GUA, CCG, GCU, GGC and CGC codons. Similar trends were observed in other gene pairs, particularly in higher degenerate codons. Notably, two-fold degenerate codons primarily exhibited synonymous polymorphisms through transitions, while higher degenerate codons encompassed both transition and transversion events. This underscores the intriguing role of degenerate codons in molecular evolution. [ABSTRACT FROM AUTHOR]

Published
2023
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21. RETINAL NONPERFUSION IN THE EARLY TREATMENT DIABETIC RETINOPATHY STUDY SEVEN FIELDS COMPARED WITH WIDEFIELD FLUORESCEIN ANGIOGRAPHY

Author

Martin-Gutierrez, Maria P., primary, Vermeirsch, Sandra, additional, Chandra, Shruti, additional, Agarwal, Aditi A. K., additional, Selvam, Senthil, additional, Thottarath, Sridevi, additional, Vazquez-Alfageme, Clara, additional, Sen, Piyali, additional, Sivaprasad, Sobha, additional, Hykin, Philip G., additional, and Nicholson, Luke, additional

Published
2022
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23. Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons

Author

Aziz, Ruksana, primary, Sen, Piyali, additional, Beura, Pratyush Kumar, additional, Das, Saurav, additional, Tula, Debapriya, additional, Dash, Madhusmita, additional, Namsa, Nima Dondu, additional, Deka, Ramesh Chandra, additional, Feil, Edward J, additional, Satapathy, Siddhartha Sankar, additional, and Ray, Suvendra Kumar, additional

Published
2022
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28. Detection of Diabetic Retinopathy from Ultrawide Field Scanning Laser Ophthalmoscope Images: A Multi-Center Deep Learning Analysis

Author

Tang, Fang Yao, Luenam, Phoomraphee, Ran, Ann Ran, Quadeer, Ahmed Abdul, Raman, Rajiv, Sen, Piyali, Khan, Rehana, Giridhar, Anantharaman, Haridas, Swathy, Iglicki, Matias, Zur, Dinah, Loewenstein, Anat, Negri, Hermino P., Szeto, Simon, Lam, Bryce Ka Yao, Tham, Clement C., Sivaprasad, Sobha, Mckay, Matthew Robert, Cheung, Carol. Y., Tang, Fang Yao, Luenam, Phoomraphee, Ran, Ann Ran, Quadeer, Ahmed Abdul, Raman, Rajiv, Sen, Piyali, Khan, Rehana, Giridhar, Anantharaman, Haridas, Swathy, Iglicki, Matias, Zur, Dinah, Loewenstein, Anat, Negri, Hermino P., Szeto, Simon, Lam, Bryce Ka Yao, Tham, Clement C., Sivaprasad, Sobha, Mckay, Matthew Robert, and Cheung, Carol. Y.

Abstract

Purpose: To develop a deep learning (DL) system that can detect referable diabetic retinopathy (RDR) and vision-threatening diabetic retinopathy (VTDR) from images obtained on ultra-widefield scanning laser ophthalmoscope (UWF-SLO). Design: Observational, cross-sectional study. Participants: A total of 9392 UWF-SLO images of 1903 eyes from 1022 subjects with diabetes from Hong Kong, the United Kingdom, India, and Argentina. Methods: All images were labeled according to the presence or absence of RDR and the presence or absence of VTDR. Labeling was performed by retina specialists from fundus examination, according to the International Clinical Diabetic Retinopathy Disease Severity Scale. Three convolutional neural networks (ResNet50) were trained with a transfer-learning procedure for assessing gradability and identifying VTDR and RDR. External validation was performed on 4 datasets spanning different geographical regions. Main Outcome Measures: Area under the receiver operating characteristic curve (AUROC); area under the precision-recall curve (AUPRC); sensitivity, specificity, and accuracy of the DL system in gradability assessment; and detection of RDR and VTDR. Results: For gradability assessment, the system achieved an AUROC of 0.923 (95% confidence interval [CI], 0.892–0.947), sensitivity of 86.5% (95% CI, 77.6–92.8), and specificity of 82.1% (95% CI, 77.3–86.2) for the primary validation dataset, and >0.82 AUROCs, >79.6% sensitivity, and >70.4% specificity for the geographical external validation datasets. For detecting RDR and VTDR, the AUROCs were 0.981 (95% CI, 0.977–0.984) and 0.966 (95% CI, 0.961–0.971), with sensitivities of 94.9% (95% CI, 92.3–97.9) and 87.2% (95% CI, 81.5–91.6), specificities of 95.1% (95% CI, 90.6–97.9) and 95.8% (95% CI, 93.3–97.6), and positive predictive values (PPVs) of 98.0% (95% CI, 96.1–99.0) and 91.1% (95% CI, 86.3–94.3) for the primary validation dataset, respectively. The AUROCs and accuracies for detecting both RDR and VT

Published
2021

39. Detection of Referable and Vision-Threatening Diabetic Retinopathy Using Deep Learning on Ultra-Wide Field Scanning Laser Ophthalmoscope Images

Author

Tang, Fangyao, Luenam, Phoomraphee, Quadeer, Ahmed Abdul, Ran, Anran, Sivaprasad, Sobha, Sen, Piyali, Raman, Rajiv, Anantharaman, Giridhar, Gopalakrishnan, Mahesh, Haridas, Swathy, Mckay, Matthew Robert, Cheung, Carol Yim-lui, Tang, Fangyao, Luenam, Phoomraphee, Quadeer, Ahmed Abdul, Ran, Anran, Sivaprasad, Sobha, Sen, Piyali, Raman, Rajiv, Anantharaman, Giridhar, Gopalakrishnan, Mahesh, Haridas, Swathy, Mckay, Matthew Robert, and Cheung, Carol Yim-lui

Published
2020

41. Outcomes of neovascular glaucoma in eyes presenting with moderate to good visual potential.

Author

Rani, Padmaja Kumari, Sen, Piyali, Sahoo, Niroj Kumar, Senthil, Sirisha, Chakurkar, Renuka, Anup, Manju, Behera, Umesh Chandra, Sivaprasad, Sobha, and Das, Taraprasad

Abstract

Purpose: To compare the disease characteristics and treatment outcomes of patients with neovascular glaucoma (NVG) presenting with visual acuity (VA) 6/60 or better in two different health systems. Methods: Retrospective chart review of consecutive patients with NVG who presented between January 2016 to January 2018 in 5 tertiary-centres in India and one eye-specialist centre in London (UK) was performed. The baseline characteristics, treatment provisions, and visual outcomes in the India and UK cohorts were compared. Results: At presentation, 18% (83 of 451) and 22% (59 of 270) of patients with NVG had VA 6/60 or better in India and the UK cohorts, respectively. The aetiologies of NVG were similar with proliferative diabetic retinopathy being the most common cause (60.9%, India; 64.4%, UK; p = 0.38). Previous panretinal photocoagulation was more prevalent in the UK cohort compared to the India cohort (94.9% versus 66.3%, respectively; p < 0.001). The mean number of intravitreal anti-VEGF injections per eye was higher in the Indian cohort (1.65 ± 0.97 versus 1.14 ± 1.02 injections; p < 0.001). The number of eyes with closed angles (36.9% India versus 30.5% UK; p = 0.45) and the number of eyes needing glaucoma interventions (52.1% India; 62.7% UK; p = 0.82) were similar in two cohorts. Among glaucoma surgeries, trabeculectomies were more commonly performed in the Indian cohort (23 vs 4; p < 0.001),while glaucoma drainage device surgeries were more prevalent in the UK cohort (18 vs 4 p < 0.001). After a median follow-up of 21 months (IQR 8.4–34.8 India; 24–36 months UK), favourable visual outcomes (vision stable or improved) were similar in both health systems (52.5% in the Indian cohort vs 43.4% in the UK cohort; p = 0.28). On multivariate regression analysis, the need for trans-scleral cyclophotocoagulation was associated with worse visual outcomes in both cohorts. Conclusions: The causes and clinical profile of neovascular glaucoma with presenting visual acuity 6/60 or better in India and the UK were similar. Only up to 50% of eyes achieved favourable visual outcomes with current management protocols in both health systems. [ABSTRACT FROM AUTHOR]

Published
2021
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