Automatic Protein Function Annotation through Candidate Ortholog Clusters from Incomplete Genomes

Annotation of protein function often arises in the context of partially complete genomes but is not adequately addressed. We present an annotation method by extracting ortholog clusters from incomplete genomes that are evolutionary closely related to the genome of interest. To construct clusters, our method focuses on sequence similarities across genomes rather than similarities between sequences within a genome. We use the quasi-concave set function optimization for extracting the ortholog clusters as extreme groups of sequences such that similarity of the least similar sequence in this group is maximum. A protein sequence is annotated with the ortholog cluster whose average similarity is highest. We have applied this method for annotating the Rice proteome based on clusters constructed on four partially complete cereal proteomes and the complete proteome from Arabidopsis. 1

Candidate Ortholog Clusters in Human, Mouse and Chicken genomes

Abstract- The recently completed chicken genome, and previously available human and mouse genomes provide us an opportunity to understand the evolutionary relationship between mammals and aves at the molecular level by finding groups of orthologs in these genomes. Using a recently developed tool for automatic large scale screening of candidate orthologs in a multi-genome data, we extracted candidate ortholog clusters in these complete genomes. We obtained 14,254 candidate ortholog clusters that cover 81 % of all genes in the three complete genomes. There are 9,733 candidate ortholog clusters that contain genes from all the three organisms. They cover about 70 % of all genes in these organisms. Based on the Pfam annotations of genes we found that 95 % of clusters are consistently annotated, since genes within each of these clusters are annotated by a single Pfam annotation. A comparison with manually curated 565 known ortholog triplets in these genomes shows that candidate ortholog clusters related to these ortholog triplets are the extensions of the ortholog triplets. Among the 565 known ortholog triplets, 549 were preserved in our results, demonstrating that our procedure was able to capture the essence of stringent criteria used by experts. Additionally, we were able to estimate the stability of the ortholog triplets and found that 562 of these are stable. I

Discriminative Patch Selection using Combinatorial and Statistical Models for Patch-Based Object Recognition

In an object recognition task where an image is represented as a constellation of image patches, often many patches correspond to the cluttered background. If such patches are used for object class recognition, they will adversely affect the recognition rate. In this paper, we present a two stage method for selecting image patches which characterize the target object class and are capable of discriminating between the positive images containing the target objects and the complementary negative images. The first stage selection is done using a novel combinatorial optimization formulation on a weighted multipartite graph representing similarities between images patches across different instances of the target object. The following stage is a statistical method for selecting those images patches from the positive images which, when used individually, have the power of discriminating between the positive and negative images in the evaluation data. The individual methods have a performance competitive with the state of the art methods on a popular benchmark data set and their sequential combination consistently outperforms the individual methods and most of the other known methods while approaching the best known results. 1

Generic and vision related quality of life associated with different types of cataract surgeries and different types of intraocular lens implantation.

ObjectivesTo assess the effects of different types of cataract surgeries and intraocular lenses on generic as well as vision related quality of life of cataract patients, using EQ-5D and IND-VFQ 33 instruments respectively.MethodsAn observational, longitudinal study of patients undergoing cataract surgery was carried out at three ophthalmology centres. Patients were prospectively admitted for surgery for age-related cataract. Generic quality of life was assessed by using Euroqol's EQ5D-5L questionnaire and vision related quality of life was assessed by the IND-VFQ-33 questionnaire. Data pertaining to vision function and quality of life were collected pre surgery and 4 weeks after the surgery.ResultsOut of total patients (n = 814) recruited for the study, 517 patients were interviewed for both pre-surgery and post-surgery for EQ5D and 519 patients were interviewed for both pre-surgery and post-surgery for IND VFQ 33 tool. The combined data from all three centres showed that Quality Adjusted Life Year (QALY) gains observed in patients undergoing phacoemulsification with foldable lens implantation (2.25 QALY) were significantly higher (0.57 QALY) as compared to Small Incision Cataract Surgery (SICS) with PMMA lens implantation (1.68 QALY). Highest improvement however, in all three subscales of IND-VFQ-33 tool were clearly observed for SICS with PMMA lens implantation.ConclusionsThe study has elicited the Health related and vision related Quality of Life scores for cataract surgeries and subsequent lens implantation. This study also offers Health State Utility Values along with visual outcomes for different surgical procedures, lenses and for the combination of surgery with lens implantation for cataract procedures providing a useful resource for future economic evaluation studies