High-throughput sequencing of small RNAs (sRNA-seq) is a popular method used to discover and annotate microRNAs (miRNAs), endogenous short interfering RNAs (siRNAs), and Piwi-associated RNAs ...(piRNAs). One of the key steps in sRNA-seq data analysis is alignment to a reference genome. sRNA-seq libraries often have a high proportion of reads that align to multiple genomic locations, which makes determining their true origins difficult. Commonly used sRNA-seq alignment methods result in either very low precision (choosing an alignment at random), or sensitivity (ignoring multi-mapping reads). Here, we describe and test an sRNA-seq alignment strategy that uses local genomic context to guide decisions on proper placements of multi-mapped sRNA-seq reads. Tests using simulated sRNA-seq data demonstrated that this local-weighting method outperforms other alignment strategies using three different plant genomes. Experimental analyses with real sRNA-seq data also indicate superior performance of local-weighting methods for both plant miRNAs and heterochromatic siRNAs. The local-weighting methods we have developed are implemented as part of the sRNA-seq analysis program ShortStack, which is freely available under a general public license. Improved genome alignments of sRNA-seq data should increase the quality of downstream analyses and genome annotation efforts.
The aim of this study was to investigate the repeatability of manual measurements of choroidal thickness in healthy subjects imaged on spectral domain optical coherence tomography (OCT) using the ...enhanced depth imaging (EDI) technique.
Fifty consecutive, healthy, young, adult volunteers with no known eye disease were enrolled prospectively. Two good-quality horizontal and vertical line scans through the fovea were obtained for each eye. Using the manual calipers provided by the software of the proprietary device, two experienced OCT readers measured the subfoveal choroidal thickness (SFCT) of the horizontal and vertical line scans for all eyes. The readers were masked to each other's readings. Intraobserver, interobserver, and intrasession coefficients of repeatability (CRs) were calculated.
Mean (standard deviation SD) age of the study subjects was 38 (5) years (range, 30-49 years). Mean (SD) subfoveal choroidal thickness was 332 (90) μm (right eyes) and 332 (91) μm (left eyes). Intraobserver CR was approximately 23 (95% confidence interval CI, 19-26) μm, whereas interobserver and intrasession CRs were greater at 32 (95% CI, 30-34) and 34 (95% CI, 32-36) μm, respectively. There was no significant difference in SFCT between all pairs of SFCT measurements except for the two intrasession vertical line scans.
A change of >32 μm was likely to exceed interobserver variability in SFCT. Future studies are required to estimate the repeatability of SFCT measurements in patients with chorioretinal pathology.
To report and analyze factors influencing topographical and interocular variations in choroidal thickness (CT) in a healthy adult population.
One hundred eyes of 50 healthy subjects underwent visual ...acuity and axial length measurements and optical coherence tomography (OCT) with enhanced depth imaging (EDI). CTs at the fovea and at 3 mm nasal, temporal, superior, and inferior to the fovea were measured manually. Topographic variation, relative interocular differences in CT and predictors of CT were analyzed. The relationships between interocular differences in CT and differences in age and interocular axial length were explored.
The mean (SD) foveal CT in the right and left eyes were 334 (95) and 333 (90) μm, respectively. For foveal CT, there was a high correlation between the two eyes (r = 0.90) with a relative interocular 95% limits of agreement of -80 to +83, and a median (range) absolute difference of 21 (0.4-135). There was no significant variation in the relative and absolute interocular differences in CT. Axial length was the main predictor of CT for nasal and foveal CT. Symmetry in CT in the horizontal and vertical meridians was seen in eyes with axial length shorter than 23.50 mm (P < 0.05).
There was no significant relative interocular difference in CT. Axial length contributes to some of the variances in CT but has a significant influence on the CT profile. Although relative interocular difference is not significant, absolute interocular differences in CT may reach 85 μm.
Purpose
The aim of this study is to image and describe the in vivo choroidal changes in various retinal dystrophies using the technique of enhanced depth imaging (EDI) optical coherence tomography ...(OCT) and to correlate these findings with the clinical appearance. Associations between choroidal change and genotype, visual acuity and results of retinal electrophysiology are also explored.
Design
Retrospective observational case series.
Methods
Twenty patients attending the medical retina clinics at Moorfields Eye Hospital underwent EDI OCT choroidal scans as part of the scanning protocol when they underwent OCT imaging with the Spectralis HRA and OCT. The choroidal images were obtained by moving the Spectralis camera close enough to obtain an inverted image of the retina. The scans were read by two experienced OCT readers assessing the choroidal thickness as well as the choroidal contour for focal areas of choroidal thinning corresponding to the areas of RPE/outer retinal atrophy. The spectrum of patients included those with Stargardt macular dystrophy, macular dystrophies secondary to known mutations such as
peripherin/RDS,
uncharacterised macular dystrophies, Best disease, bifocal chorioretinal atrophy, Bietti crystalline retinal dystrophy and choroideraemia.
Results
The choroidal appearance was symmetrical in all patients who had both eyes scanned. Ten patients showed no choroidal thinning, five had focal mild to moderate choroidal thinning, three had focal severe choroidal thinning, and two patients had diffuse severe choroidal thinning. There was no association between choroidal thinning and visual acuity Fisher’s exact test,
p
= 0.350 (right eye),
p
= 1.000 (left eye), or extent of retinal dysfunction on electrophysiology (Fisher’s exact test,
p
= 1.000).
Conclusion
Enhanced depth imaging using spectral domain OCT can be used to identify choroidal changes in inherited retinal disease. The pattern of choroidal change correlates well with the clinical appearance. It appears that the extent and pattern of choroidal thinning is dependent on the stage of the disease in some cases, and in others the causative gene defect.
To describe the features of an unusual syphilitic uveitis syndrome in a cluster of homosexual patients.
Retrospective case series.
Five consecutive patients diagnosed with syphilitic retinitis in our ...Melbourne uveitis clinic over a period of 8 months.
The case notes of patients diagnosed with syphilitic retinitis were reviewed and the clinical features are presented and discussed.
Description of retinal findings and documentation of any associated sequelae.
All patients were homosexual men. Two were human immunodeficiency virus positive. None of the patients had been previously diagnosed with syphilis, although 3 presented with systemic symptoms and signs of secondary syphilis. All patients had marked anterior uveitis and vitritis. All patients had acute retinal arteriolitis and inner retinitis, with distinctive, inner retinal and preretinal white dots. These retinal findings were remarkably similar in all patients, and resolved with little or no sequelae after standard systemic treatment for syphilis, combined with oral prednisolone.
Syphilitic retinitis may be an increasingly common clinical problem, reflecting the growing incidence of syphilis among homosexual men in Australia. Our patients showed stereotypical ocular and systemic features, which are useful in differentiating this condition clinically from other types of acute posterior uveitis, such as necrotizing viral retinitis.
Proprietary or commercial disclosure may be found after the references.
The extended clinical phenotype of dome-shaped macula Errera, Marie-Hélène; Michaelides, Michel; Keane, Pearse A. ...
Graefe's archive for clinical and experimental ophthalmology,
03/2014, Letnik:
252, Številka:
3
Journal Article
Recenzirano
Purpose
To describe the phenotype, associations, and complications of dome-shaped macula (DSM) through the combination of spectral-domain optical coherence tomography (OCT) imaging and B-scan ...ultrasonography, when available. This retroprospective cohort study aims to gain further pathophysiological understanding in eyes with DSM.
Methods
Fifty-eight eyes of 36 patients were identified as having OCT features of DSM. Retinal and choroidal thicknesses were determined from enhanced depth imaging (EDI)-OCT image sets, with scleral thickness subsequently calculated by subtraction from the B-scan ultrasound-derived measurements of posterior coat thickness.
Results
DSM was associated with myopia in 81 % of eyes. The underlying clinical diagnosis was variable: central serous chorioretinopathy (CSCR)-like entity, choroidal neovascularization, and inherited retinal disorders. The subfoveal choroidal thickness of the nine highly myopic eyes with a CSCR-like phenotype was thicker than the 25 eyes without CSCR (
p
= 0.169). The mean subfoveal scleral thickness of the highly myopic eyes was 585 ± 196 μm, which was significantly different from those with a refractive error less than 6 diopters (1133 ± 290 μm) (
P
< 0.0001).
Conclusions
This study highlights the novel observation of a thickened choroid when CSCR is present. In addition, we expand the associations of DSM to eyes with hypermetropia and acquired disease, and to those with inherited retinal dystrophies.
To assess the safety and efficacy of chronic electrical stimulation of the retina with a suprachoroidal visual prosthesis.
Seven normally-sighted feline subjects were implanted for 96-143 days with a ...suprachoroidal electrode array and six were chronically stimulated for 70-105 days at levels that activated the visual cortex. Charge balanced, biphasic, current pulses were delivered to platinum electrodes in a monopolar stimulation mode. Retinal integrity/function and the mechanical stability of the implant were assessed monthly using electroretinography (ERG), optical coherence tomography (OCT) and fundus photography. Electrode impedances were measured weekly and electrically-evoked visual cortex potentials (eEVCPs) were measured monthly to verify that chronic stimuli were suprathreshold. At the end of the chronic stimulation period, thresholds were confirmed with multi-unit recordings from the visual cortex. Randomized, blinded histological assessments were performed by two pathologists to compare the stimulated and non-stimulated retina and adjacent tissue.
All subjects tolerated the surgical and stimulation procedure with no evidence of discomfort or unexpected adverse outcomes. After an initial post-operative settling period, electrode arrays were mechanically stable. Mean electrode impedances were stable between 11-15 kΩ during the implantation period. Visually-evoked ERGs & OCT were normal, and mean eEVCP thresholds did not substantially differ over time. In 81 of 84 electrode-adjacent tissue samples examined, there were no discernible histopathological differences between stimulated and unstimulated tissue. In the remaining three tissue samples there were minor focal fibroblastic and acute inflammatory responses.
Chronic suprathreshold electrical stimulation of the retina using a suprachoroidal electrode array evoked a minimal tissue response and no adverse clinical or histological findings. Moreover, thresholds and electrode impedance remained stable for stimulation durations of up to 15 weeks. This study has demonstrated the safety and efficacy of suprachoroidal stimulation with charge balanced stimulus currents.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Purpose: Bevacizumab (Avastin) is a monoclonal antibody which targets all isoforms of vascular endothelial growth factor A. Its potent anti‐angiogenic effects have been shown to cause regression of ...neovascularization in proliferative diabetic retinopathy. The aim of this study is to investigate the role of Avastin as an adjunct to vitrectomy in the management of severe diabetic eye disease.
Methods: Sixteen patients (18 eyes) with severe proliferative diabetic retinopathy were recruited into the study. All eyes underwent a single intravitreal injection of bevacizumab 1.25 mg in 0.05 mL prior to vitrectomy surgery for the management of tractional retinal detachment or vitreous haemorrhage due to severe proliferative diabetic retinopathy.
Results: At 3 months, seven eyes had visual acuities which were better than baseline, four were unchanged and seven were worse. At 6 months, 14 eyes had visual acuities better than baseline, one was unchanged and three were worse. Seven of the 18 eyes (38.8%) had postoperative rebleeds, six of which required surgical washout.
Conclusion: Avastin improved the ease of the surgery in these complex eyes and the early results are encouraging. We have found it to be particularly useful in diabetic eyes with traction detachments of short duration in which there is still active neovascularization.
This review explores how optical coherence tomography has guided our assessment of vitreomacular disorders. Vitreomacular disorders (VMD), such as macular holes and epiretinal membranes are common ...and potentially sight threatening. The introduction and widespread use of optical coherence tomography (OCT) imaging technology has transformed our ability to visualise the vitreoretinal interface. This review discusses the pathogenesis and updated classification scheme for VMD in the OCT era. Imaging biomarkers and the treatment algorithm, including the role of novel therapeutics, for managing patients with VMD are presented.