Differentially used codons among essential genes in bacteria identified by machine learning-based analysis.

Codon usage bias (CUB), the uneven usage of synonymous codons encoding the same amino acid, differs among genes within and across bacteria genomes. CUB is known to be influenced by gene expression and accordingly, CUB differs between the high-expression and low-expression genes in several bacteria. In this article, we have extended codon usage study considering gene essentiality as a feature.

Transcribed intergenic regions exhibit a lower frequency of nucleotide polymorphism than the untranscribed intergenic regions in the genomes of and .

The temporary exposure of single-stranded regions in the genome during the process of replication and transcription makes the region vulnerable to cytosine deamination resulting in a higher rate of C→T transition. Intraoperon intergenic regions undergo transcription along with adjacent co-transcribed genes in an operon, whereas interoperon intergenic regions are usually devoid of transcription. Hence these two types of intergenic regions (IGRs) can be compared to find out the contribution of replication-associated mutations (RAM) and transcription-associated mutations (TrAM) towards bringing variation in genomes.

Machine learning approach identifies prominent codons from different degenerate groups influencing gene expression in bacteria.

Unequal usage of synonymous codons is known as codon usage bias (CUB), which is generally different between the high-expression genes (HEG) and low-expression genes (LEG) in organisms is not yet adequately reported across different bacteria. In this study, a machine learning-based approach was implemented initially to find out codons that are significantly different between the HEG and LEG in Escherichia coli. It identified Cys codons such as UGU and UGC, Lys codons such as AAA and AAG that were least influenced by gene expression.

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

A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons.

Correlation of Optical Coherence Tomography Angiography Characteristics with Visual Function to Define Vision-Threatening Diabetic Macular Ischemia.

The thresholds of macular microvasculature parameters associated with mild visual impairment in diabetic macular ischemia (DMI) patients are unclear. Therefore, this prospective observational study is aimed at demonstrating the optical coherence tomography angiography parameters that best correlate with mild visual impairment (<70 Early Treatment Diabetic Retinopathy Study (ETDRS) letters, Snellen equivalent 20/40) in DMI. The study was completed at the Moorfields Eye Hospital from December 2019 to August 2021.

RETINAL NONPERFUSION IN THE EARLY TREATMENT DIABETIC RETINOPATHY STUDY SEVEN FIELDS COMPARED WITH WIDEFIELD FLUORESCEIN ANGIOGRAPHY: Correlation and Use of Extrapolation Factor.

Background: In previous landmark studies on central retinal vein occlusion, retinal nonperfusion assessments were obtained using 7-field (7F) angiography. The widespread current use of widefield imaging allows better visualization of the peripheral retina and more comprehensive estimation of the total area of nonperfusion. The relationship between nonperfusion measurement of 7F and widefield angiography (WFA) in central retinal vein occlusion has not been studied.

Stem Region of tRNA Genes Favors Transition Substitution Towards Keto Bases in Bacteria.

Transversion and transition mutations have variable effects on the stability of RNA secondary structure considering that the former destabilizes the double helix geometry to a greater extent by introducing purine:purine (R:R) or pyrimidine:pyrimidine (Y:Y) base pairs. Therefore, transversion frequency is likely to be lower than that of transition in the secondary structure regions of RNA genes. Here, we performed an analysis of transition and transversion frequencies in tRNA genes defined well with secondary structure and compared with the intergenic regions in five bacterial species namely Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae using a large genome sequence data set.

Visual Outcomes Associated With Patterns of Macular Edema Resolution in Central Retinal Vein Occlusion Treated With Anti-Vascular Endothelial Growth Factor Therapy: A Post Hoc Analysis of the Lucentis, Eylea, Avastin in Vein Occlusion (LEAVO) Trial.

Importance: It is unclear how visual outcomes vary between patterns of macular edema (ME) resolution in eyes with central retinal vein occlusion (CRVO).

Objective: To assess best-corrected visual acuity (BCVA) outcomes at 100 weeks based on macular fluid resolution patterns by 52 and 100 weeks among patients receiving anti-vascular endothelial growth factor therapy for CRVO-related ME.

Design, Setting, And Participants: Post hoc analysis of the prospective, 3-arm, double-masked, randomized noninferiority trial Lucentis, Eylea, Avastin in Vein Occlusion (LEAVO), which evaluated intravitreal aflibercept (2.

The clinical relevance of ultra-widefield angiography findings in patients with central retinal vein occlusion and macular oedema receiving anti-VEGF therapy.

Aims: To report, using ultra-widefield angiography (UWFA) the area, distribution, and change in retinal capillary nonperfusion (RCNP) at baseline and 100 weeks in eyes with central retinal vein occlusion (CRVO) receiving anti-VEGF for macula oedema.

Methods: Prospective longitudinal multi-centre cohort study. Adults with CRVO treated with anti-VEGF therapy for macular oedema underwent UWFA at baseline and week-100.

Functional clinical endpoints and their correlations in eyes with AMD with and without subretinal drusenoid deposits-a pilot study.

Purpose: To evaluate functional clinical endpoints and their structural correlations in AMD, with a focus on subretinal drusenoid deposits (SDD).

Methods: This prospective study enroled 50 participants (11 controls, 17 intermediate AMD (iAMD) with no SDD, 11 iAMD with SDD and 11 non-foveal atrophic AMD). Participants underwent best-corrected visual acuity (BCVA), low luminance visual acuity (LLVA), low luminance questionnaire (LLQ), scotopic thresholds, rod-intercept time (RIT), photopic flicker electroretinograms and multimodal imaging.

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

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.

Inter-rater reliability for diagnosis of geographic atrophy using spectral domain OCT in age-related macular degeneration.

Purpose: To evaluate the inter-rater reliability for identification of complete retinal pigment epithelium and outer retinal atrophy (cRORA) on SD-OCT images as defined by the Classification of Atrophy Meetings (CAM) group.

Methods: Fifty images of anonymized SD-OCT line scans of eyes with cRORA due to AMD were selected. Each .

Looking Ahead: Visual and Anatomical Endpoints in Future Trials of Diabetic Macular Ischemia.

Diabetic macular ischemia (DMI) is a common complication of diabetic retinopathy that can lead to progressive and irreversible visual loss. Despite substantial clinical burden, there are no treatments for DMI, no validated clinical trial endpoints, and few clinical trials focusing on DMI. Therefore, generating consensus on validated endpoints that can be used in DMI for the development of effective interventions is vital.

Predictors of Visual Acuity Outcomes after Anti-Vascular Endothelial Growth Factor Treatment for Macular Edema Secondary to Central Retinal Vein Occlusion.

Purpose: To evaluate whether baseline demographic, clinical, and OCT characteristics predict visual acuity (VA) outcomes in patients receiving anti-vascular endothelial growth factor (VEGF) therapy for macular edema (ME) due to central retinal vein occlusion (CRVO).

Design: Post hoc analysis of the randomized noninferiority trial (Lucentis, Eylea, Avastin in CRVO) LEAVO Study from December 12, 2014, to December 16, 2016, carried out across 44 UK National Health Service ophthalmology departments.

Participants: Data on 267 participants with a baseline best-corrected mean visual acuity (BCVA) range of 19 to 78 Early Treatment Diabetic Retinopathy Study letter score (approximate Snellen equivalent, 20/32 to 20/320) who had central subfield thickness (CST) ≥ 320 μm on Spectralis OCT (Heidelberg Engineering) were analyzed.

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

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.

Low Luminance Visual Acuity and Low Luminance Deficit in Proliferative Diabetic Retinopathy.

This study aimed to determine the relation of best corrected visual acuity (BCVA) and low luminance visual acuity (LLVA) in proliferative diabetic retinopathy (PDR) following treatment with either aflibercept or pan-retinal photocoagulation (PRP). The study was conducted as a post-hoc analysis of the CLARITY trial in which naïve and PRP treated PDR patients were randomised to receive either aflibercept or PRP. BCVA and LLVA were assessed at baseline and at week 52.

Long-term follow-up of a case of posterior microphthalmos (PRSS56) with hyperautofluorescent retinal pigment epithelial deposits.

Purpose: To report a case of posterior microphthalomos (PM) related to PRSS56 gene mutation with long term follow up with multimodal imaging findings.

Methods: Single retrospective case report.

Results: A 43-year old male patient presented in 2009 with bilateral reduced vision.

Deep Learning-Based Segmentation and Quantification of Retinal Capillary Non-Perfusion on Ultra-Wide-Field Retinal Fluorescein Angiography.

Reliable outcome measures are required for clinical trials investigating novel agents for preventing progression of capillary non-perfusion (CNP) in retinal vascular diseases. Currently, accurate quantification of topographical distribution of CNP on ultrawide field fluorescein angiography (UWF-FA) by retinal experts is subjective and lack standardisation. A U-net style network was trained to extract a dense segmentation of CNP from a newly created dataset of 75 UWF-FA images.

Profitability, energetics and GHGs emission estimation from rice-based cropping systems in the coastal saline zone of West Bengal, India.

This study compares thirteen rice-based cropping systems in the coastal part of West Bengal, India in terms of productivity, profitability, energetics, and emissions. Information on the crop management practices of these systems was collected on 60 farms through a questionnaire survey. Rice-bitter gourd system was observed to have the highest system yield (49.