Biomedical subjects

Bobby Paul

Publications and source records attributed to Bobby Paul.

3 recordsLinked to original sources

PubMed2026

SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.

Identification of unique and shared genomic regions between organisms has substantial translational potential for the development of marker-based diagnostic assays and sequence homology-driven taxonomic classification. An automated pipeline capable of performing genome comparisons at both the intra- and inter-species levels with minimal computational requirements can significantly advance genome-driven translational research. Species-specific genomic regions are particularly valuable for sequence-based species identification and for developing DNA amplification- or hybridization-based diagnostic assays. Here, we present SURE-Pipe, an automated and flexible pipeline for genome comparison and extraction of unique and shared genomic regions (https://github.com/BPaul-bioinfoLAB/SURE-Pipe). Benchmarking of this pipeline using simulated datasets demonstrated high accuracy for shared and unique region identification. Using the pairwise genome comparison module, six genome pairs from diverse microorganisms were analysed, and identified the unique and shared regions. In addition, the multigenome comparison module was applied to 96 genomes representing 24 Bacillus species and identified species-specific genomic regions. These regions were highly conserved among four strains of a species (>98% sequence identity) and exhibit little to no similarity with other species. Species-specific primers designed for all 24 Bacillus species showed no off-target amplification in in-silico polymerase chain reaction analysis, indicating their specificity. Overall, SURE-Pipe provides a robust and multipurpose framework for comparative genomics, and the outcomes can be used for species identification and the development of genome-based diagnostic approaches.

Genome, Bacterial↗

PubMed2006

Cataract surgery by appointment--a pilot study.

BACKGROUND: "Cataract Surgery by Appointment" is a new method of delivery of cataract surgery that reduces the time a patient spends in hospital by their direct arrival at the operating theatre, having self-prepared for surgery, thus avoiding admission to the ward or time spent in the Day Case Unit. The patient can stay as little as 20 minutes from their arrival to going home. We describe the process in detail, and seek to evaluate the visual outcome, safety and patient satisfaction of same. METHODS: Visual outcome and safety data were obtained from patients' medical records, prospectively. Patients were also surveyed by a questionnaire to determine their satisfaction with the service and viability as a prospect for providing a more efficient cataract surgery service. RESULTS: In 2002, fifty-one eyes of 39 consecutive patients underwent "Cataract Surgery by Appointment". There were 16 male and 23 female. The pre-operative best-corrected visual acuity was 6/9 or better in 17 (33%) eyes. The post-operative best-corrected visual acuity was 6/9 or better in 44 (86%) eyes. There were no per-operative complications. Post-operative complications occurred in 3 (6%) eyes. The average number of days from surgery to final discharge was 14.5 days. Twenty-eight (72%) completed questionnaires were returned. The results show that the majority of patients were satisfied with their overall experience of this mode of delivery for cataract surgery. CONCLUSION: "Cataract Surgery by Appointment" performed under local anaesthesia by a skilled ophthalmic surgeon appears to be safe and effective for highly selected cases. This method of delivery gave a high level of patient satisfaction, and is the ultimate form of day case cataract surgery. The method may gain widespread use should per-operative intracameral pupil dilatation prove to be effective and acceptable. Attention should be paid to risk-stratification, so complex cases are allocated more time on the operating list.

Appointments and Schedules↗

PubMedDate not supplied

The osteo-odonto-keratoprosthesis (OOKP).

The osteo-odonto-keratoprosthesis (OOKP), although described over 40 years ago, remains the keratoprosthesis of choice for end-stage corneal blindness not amenable to penetrating keratoplasty. It is particularly resilient to a hostile environment such as the dry keratinized eye resulting from severe Stevens-Johnson syndrome, ocular cicatricial pemphigoid, trachoma, and chemical injury. Its rigid optical cylinder gives excellent image resolution and quality. The desirable properties of the theoretical ideal keratoprosthesis is described. The indications, contraindications, and patient assessment (eye, tooth, buccal mucosa, psychology) for OOKP surgery are described. The surgical and anaesthetic techniques are described. Follow-up is life-long in order to detect and treat complications, which include oral, oculoplastic, glaucoma, vitreo-retinal complications and extrusion of the device. Resorption of the osteo-odonto-lamina is responsible for extrusion, and this is more pronounced in tooth allografts. Regular imaging with spiral-CT or electron beam tomography can help detect bone and dentine loss. The optical cylinder design is discussed. Preliminary work towards the development of a synthetic OOKP analogue is described. Finally, we describe how to set up an OOKP national referral center.

Alveolar Process↗