Micropulse trans-scleral diode laser cyclophotocoagulation in refractory glaucoma: an initial experience in Indian eyes.

PURPOSE: To evaluate the efficacy and safety of micro-pulse trans-scleral diode laser cyclophotocoagulation (MP-TSCPC) in Indian eyes with refractory glaucoma. METHODS: A prospective interventional short-term study was carried out with relatively small sample size of 55 eyes with refractory glaucoma. All eyes had visual acuity (VA) and intraocular pressure (IOP) measurements at baseline, 1 week (1w), 1 month (1 m) and 3 months (3 m). A single surgeon treated all eyes with recommended MP-TSCPC treatment settings. Surgical success was defined as achieving an IOP between 8-21 mmHg or achieving > 20% IOP reduction. RESULTS: The age of participants was 56.98 ± 15.74 years. Our study had more number of males. VA (in logMAR) at baseline was 1.38 ± 0.99. VA was 1.43 ± 0.93 at 1w, 1.47 ± 0.94 at 1 m and 1.47 ± 0.96 at 3 m (p > 0.05 for all). IOP (in mmHg) at baseline was 30.38 ± 10.70. IOP was 15.72 ± 6.85 at 1w, 16.98 ± 8.72 at 1 m and 17.60 ± 8.40 at 3 m (p < 0.001 for all). At 3 m, 49 (89.1%) eyes had surgical success. Surgical success was lesser in primary open angle glaucoma (p = 0.03). IOP at baseline showed significant correlation with percentage reduction in IOP at each review (p < 0.05). Use of glaucoma medication reduced from 2.94 ± 0.98 to 2.01 ± 1.16 at 3 m (p < 0.001). At 3 m, hypotony was noted in 4 (7.3%) eyes and reduction in visual acuity was seen in 15 (27.3%) eyes. CONCLUSION: Initial experience in Indian eyes has shown that MP-TSCPC is safe and effective for refractory glaucoma. Patients can expect significant IOP lowering along with reduction in number of topical medications required for control of IOP.

Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients.

BACKGROUND: Rheumatoid arthritis and osteoarthritis are two common musculoskeletal disorders that affect the joints. Despite high prevalence rates, etiological factors involved in these disorders remain largely unknown. Dissecting the molecular aspects of these disorders will significantly contribute to improving their diagnosis and clinical management. In order to identify proteins that are differentially expressed between these two conditions, a quantitative proteomic profiling of synovial fluid obtained from rheumatoid arthritis and osteoarthritis patients was carried out by using iTRAQ labeling followed by high resolution mass spectrometry analysis. RESULTS: We have identified 575 proteins out of which 135 proteins were found to be differentially expressed by ≥3-fold in the synovial fluid of rheumatoid arthritis and osteoarthritis patients. Proteins not previously reported to be associated with rheumatoid arthritis including, coronin-1A (CORO1A), fibrinogen like-2 (FGL2), and macrophage capping protein (CAPG) were found to be upregulated in rheumatoid arthritis. Proteins such as CD5 molecule-like protein (CD5L), soluble scavenger receptor cysteine-rich domain-containing protein (SSC5D), and TTK protein kinase (TTK) were found to be upregulated in the synovial fluid of osteoarthritis patients. We confirmed the upregulation of CAPG in rheumatoid arthritis synovial fluid by multiple reaction monitoring assay as well as by Western blot. Pathway analysis of differentially expressed proteins revealed a significant enrichment of genes involved in glycolytic pathway in rheumatoid arthritis. CONCLUSIONS: We report here the largest identification of proteins from the synovial fluid of rheumatoid arthritis and osteoarthritis patients using a quantitative proteomics approach. The novel proteins identified from our study needs to be explored further for their role in the disease pathogenesis of rheumatoid arthritis and osteoarthritis.Sartaj Ahmad and Raja Sekhar Nirujogi contributed equally to this article.

Proteomic analysis of human osteoarthritis synovial fluid.

BACKGROUND: Osteoarthritis is a chronic musculoskeletal disorder characterized mainly by progressive degradation of the hyaline cartilage. Patients with osteoarthritis often postpone seeking medical help, which results in the diagnosis being made at an advanced stage of cartilage destruction. Sustained efforts are needed to identify specific markers that might help in early diagnosis, monitoring disease progression and in improving therapeutic outcomes. We employed a multipronged proteomic approach, which included multiple fractionation strategies followed by high resolution mass spectrometry analysis to explore the proteome of synovial fluid obtained from osteoarthritis patients. In addition to the total proteome, we also enriched glycoproteins from synovial fluid using lectin affinity chromatography. RESULTS: We identified 677 proteins from synovial fluid of patients with osteoarthritis of which 545 proteins have not been previously reported. These novel proteins included ADAM-like decysin 1 (ADAMDEC1), alanyl (membrane) aminopeptidase (ANPEP), CD84, fibulin 1 (FBLN1), matrix remodelling associated 5 (MXRA5), secreted phosphoprotein 2 (SPP2) and spondin 2 (SPON2). We identified 300 proteins using lectin affinity chromatography, including the glycoproteins afamin (AFM), attractin (ATRN), fibrillin 1 (FBN1), transferrin (TF), tissue inhibitor of metalloproteinase 1 (TIMP1) and vasorin (VSN). Gene ontology analysis confirmed that a majority of the identified proteins were extracellular and are mostly involved in cell communication and signaling. We also confirmed the expression of ANPEP, dickkopf WNT signaling pathway inhibitor 3 (DKK3) and osteoglycin (OGN) by multiple reaction monitoring (MRM) analysis of osteoarthritis synovial fluid samples. CONCLUSIONS: We present an in-depth analysis of the synovial fluid proteome from patients with osteoarthritis. We believe that the catalog of proteins generated in this study will further enhance our knowledge regarding the pathophysiology of osteoarthritis and should assist in identifying better biomarkers for early diagnosis.

Characterizing the normal proteome of human ciliary body.

BACKGROUND: The ciliary body is the circumferential muscular tissue located just behind the iris in the anterior chamber of the eye. It plays a pivotal role in the production of aqueous humor, maintenance of the lens zonules and accommodation by changing the shape of the crystalline lens. The ciliary body is the major target of drugs against glaucoma as its inhibition leads to a drop in intraocular pressure. A molecular study of the ciliary body could provide a better understanding about the pathophysiological processes that occur in glaucoma. Thus far, no large-scale proteomic investigation has been reported for the human ciliary body. RESULTS: In this study, we have carried out an in-depth LC-MS/MS-based proteomic analysis of normal human ciliary body and have identified 2,815 proteins. We identified a number of proteins that were previously not described in the ciliary body including importin 5 (IPO5), atlastin-2 (ATL2), B-cell receptor associated protein 29 (BCAP29), basigin (BSG), calpain-1 (CAPN1), copine 6 (CPNE6), fibulin 1 (FBLN1) and galectin 1 (LGALS1). We compared the plasma proteome with the ciliary body proteome and found that the large majority of proteins in the ciliary body were also detectable in the plasma while 896 proteins were unique to the ciliary body. We also classified proteins using pathway enrichment analysis and found most of proteins associated with ubiquitin pathway, EIF2 signaling, glycolysis and gluconeogenesis. CONCLUSIONS: More than 95% of the identified proteins have not been previously described in the ciliary body proteome. This is the largest catalogue of proteins reported thus far in the ciliary body that should provide new insights into our understanding of the factors involved in maintaining the secretion of aqueous humor. The identification of these proteins will aid in understanding various eye diseases of the anterior segment such as glaucoma and presbyopia.

The RIKEN integrated database of mammals.

The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.

Taming the polar bear: Ten tips to manage posterior polar cataract.

Background: Posterior polar cataracts are challenging even for skilled cataract surgeons due to the high risk of posterior capsule rupture and vitreous loss during cataract surgery; hence, it is important to know how to manage such cases. Purpose: In this video, we describe the necessary precautions and steps to be taken to prevent and manage complications in phacoemulsification cataract surgery for posterior polar cataracts. Synopsis: The video contains ten tips to follow to avoid complications while performing phacoemulsification cataract surgery in patients with posterior polar cataracts and includes preoperative identification on slit-lamp examination, size of capsulorhexis, avoidance of hydrodissection, technique of nucleus management, viscoelastic injection to keep the anterior chamber formed, epinucleus and cortical matter removal, posterior capsular rupture management, anterior vitrectomy, and intraocular lens (IOL) implantation in eyes with posterior capsular rupture. Highlights: The video highlights ten different steps to be followed in the surgical management of patients with posterior polar cataract which, if followed meticulously, can give excellent outcomes in these patients. Conclusion: Posterior polar cataracts can be managed with phacoemulsification, with good visual outcomes if these precautions are followed. Video link: https://youtu.be/TeoLckE83xM. Additional information: Won Best Educational Video in a contest by phacotraining.org.

A Rare Complication Causing Another Rare Complication: Corneal Dellen with Infiltration Secondary to Subconjunctival Silicon Oil.

The usage of silicon oil (SO) in vitreoretinal surgery is associated with potential complications. One such complication is the extravasation of SO into the subconjunctival space through open sclerotomies. Subconjunctival SO (SCSO) can cause irregularities in the ocular surface which predisposes to complications like corneal dellen. This corneal dellen can get infected in rare situations. SCSO needs to be removed to stabilize the ocular surface. We present a case of corneal dellen with infiltration which developed as a consequence of SCSO and its management.

Management of acute hydrops with pre-Descemet's deep anterior lamellar keratoplasty.

This case report describes a 23-year-old female patient who had bilateral keratoconus and a history of right eye penetrating keratoplasty who presented with acute hydrops in the left eye which did not respond to conservative management. Pre-Descemet's deep anterior lamellar keratoplasty was performed in the acute stage for management of the impending perforation with good visual outcomes.

RAPID: Resource of Asian Primary Immunodeficiency Diseases.

Availability of a freely accessible, dynamic and integrated database for primary immunodeficiency diseases (PID) is important both for researchers as well as clinicians. To build a PID informational platform and also as a part of action to initiate a network of PID research in Asia, we have constructed a web-based compendium of molecular alterations in PID, named Resource of Asian Primary Immunodeficiency Diseases (RAPID), which is available as a worldwide web resource at http://rapid.rcai.riken.jp/. It hosts information on sequence variations and expression at the mRNA and protein levels of all genes reported to be involved in PID patients. The main objective of this database is to provide detailed information pertaining to genes and proteins involved in primary immunodeficiency diseases along with other relevant information about protein-protein interactions, mouse studies and microarray gene-expression profiles in various organs and cells of the immune system. RAPID also hosts a tool, mutation viewer, to predict deleterious and novel mutations and also to obtain mutation-based 3D structures for PID genes. Thus, information contained in this database should help physicians and other biomedical investigators to further investigate the role of these molecules in PID.

Human Protein Reference Database--2009 update.

Human Protein Reference Database (HPRD--http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system--Human Proteinpedia (http://www.humanproteinpedia.org/)--through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15,000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome.

PathBuilder--open source software for annotating and developing pathway resources.

SUMMARY: We have developed PathBuilder, an open-source web application to annotate biological information pertaining to signaling pathways and to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events either manually or through automated importing of data from other databases. Salient features of PathBuilder include automatic validation of data formats, built-in modules for visualization of pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving existing pathway datasets. AVAILABILITY: PathBuilder is freely available for download at http://pathbuilder.sourceforge.net/ under the terms of GNU lesser general public license (LGPL: http://www.gnu.org/copyleft/lesser.html). The software is platform independent and has been tested on Windows and Linux platforms. CONTACT: pandey@jhmi.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Towards label-free 3D segmentation of optical coherence tomography images of the optic nerve head using deep learning.

Recently proposed deep learning (DL) algorithms for the segmentation of optical coherence tomography (OCT) images to quantify the morphological changes to the optic nerve head (ONH) tissues during glaucoma have limited clinical adoption due to their device specific nature and the difficulty in preparing manual segmentations (training data). We propose a DL-based 3D segmentation framework that is easily translatable across OCT devices in a label-free manner (i.e. without the need to manually re-segment data for each device). Specifically, we developed 2 sets of DL networks: the 'enhancer' (enhance OCT image quality and harmonize image characteristics from 3 devices) and the 'ONH-Net' (3D segmentation of 6 ONH tissues). We found that only when the 'enhancer' was used to preprocess the OCT images, the 'ONH-Net' trained on any of the 3 devices successfully segmented ONH tissues from the other two unseen devices with high performance (Dice coefficients > 0.92). We demonstrate that is possible to automatically segment OCT images from new devices without ever needing manual segmentation data from them.

Glued intraocular lens implantation for eyes with inadequate capsular support: Analysis of the postoperative visual outcome.

AIM: The aim of this study is to analyze the postoperative visual outcomes of fibrin glue-assisted, suture-less posterior chamber (PC) intraocular lens (IOL) implantation technique in eyes with inadequate capsule support at a tertiary eye care hospital in South India. SETTING AND DESIGN: This is a retrospective, nonrandomized case series. PATIENTS AND METHODS: This study analyzes 94 eyes which underwent PC-IOL implantation by fibrin glue-assisted, suture-less technique. All patients who had IOL implants by the fibrin glue-assisted PC-IOL technique from August 2009 to January 2014 were included in the study. Intra- and post-operative complications were analyzed. The postoperative best spectacle-corrected visual acuity (BSCVA) was evaluated and recorded at the end of 6 months. STATISTICAL ANALYSIS: The data were analyzed using SPSS version 16.1 (SPSS Inc., Chicago, Illinois, USA) using two sample paired t-test and independent t-test. RESULTS: A total of 94 eyes of 92 patients that underwent glued IOL implantation over a period of 5 years were analyzed. Out of 94 eyes, 77 eyes (84.6%) maintained or improved on their preoperative BSCVA (P = 0.012). CONCLUSION: We conclude that glued IOL implantation is a feasible option in rehabilitating patients with aphakia without adequate capsular support.

Human protein reference database as a discovery resource for proteomics.

The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein-protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.