Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential

In this article, we focus on the analysis of competitive gene set methods for detecting the statistical significance of pathways from gene expression data. Our main result is to demonstrate that some of the most frequently used gene set methods, GSEA, GSEArot and GAGE, are severely influenced by the filtering of the data in a way that such an analysis is no longer reconcilable with the principles of statistical inference, rendering the obtained results in the worst case inexpressive. A possible consequence of this is that these methods can increase their power by the addition of unrelated data and noise. Our results are obtained within a bootstrapping framework that allows a rigorous assessment of the robustness of results and enables power estimates. Our results indicate that when using competitive gene set methods, it is imperative to apply a stringent gene filtering criterion. However, even when genes are filtered appropriately, for gene expression data from chips that do not provide a genome-scale coverage of the expression values of all mRNAs, this is not enough for GSEA, GSEArot and GAGE to ensure the statistical soundness of the applied procedure. For this reason, for biomedical and clinical studies, we strongly advice not to use GSEA, GSEArot and GAGE for such data sets.

Use of contact lenses in patients with filtering blebs

Purpose: The purpose of this study was to describe the outcome of patients with filtering blebs who were fit with contact lenses. Methods: We retrospectively studied patients with filtering blebs secondary to glaucoma or cataract surgery who were fit with contact lenses. Eight eyes from seven patients were identified. Results: Five patients (six eyes) were fit with gas permeable contact lenses and two patients (two eyes) were fit with soft contact lenses. Successful fits were achieved in all patients. No complications were observed after a mean follow-up of 64.6±28.5 months. Conclusions: No significant complications were recorded in our series of patients with filtering blebs who were fit with contact lenses. We think that when indications for fitting contact lenses are justified, patients with filtering blebs are acceptable candidates for contact lens use. However, adequate selection of cases, careful contact lens fitting, patient education, and close follow-up are necessary.

Dysfunctional filtering blebs

Guarded filtration surgery is commonly used to control the intraocular pressure (IOP) in glaucomatous patients. Filtration surgery lowers the IOP by creating a fistula between the inner compartments of the eye and the subconjunctival space (i.e., filtering bleb). There are several options to improve the function of filtering blebs and to prevent their failure. However, improvement of IOP control after guarded filtration procedures is associated with a higher frequency of bleb-related complications. Early (e.g., bleb leak, excessive filtration, flat anterior chamber, filtration failure) and late (e.g., bleb leak, excessive filtration and hypotony, symptomatic blebs, bleb encapsulation, filtration failure, bleb infection) complications associated with filtering procedures should be managed adequately to prevent further problems. Techniques to improve the function of filtering blebs and to treat postoperative complications have progressed over the past decade.

Encapsulated filtering blebs after trabeculectomy with mitomycin-C

BACKGROUND AND OBJECTIVE: To determine the frequency of encapsulated blebs after guarded filtration procedures with mitomycin-C. PATIENTS AND METHODS: The authors reviewed the charts of all patients who had undergone a guarded filtration procedure with mitomycin-C. There were 235 patients (283 cases) who had more than 1 month of follow-up. RESULTS: An encapsulated bleb developed in 7 eyes (2.47%) of 6 patients. Identification of bleb encapsulation occurred at a mean follow-up time of 29.7 ± 14.6 days after surgery. The mean intraocular pressure at that point was 24.2 ± 13.5 mm Hg in the affected eyes. Three eyes were treated medically, and needling was performed in 4 eyes. CONCLUSION: There is a low frequency of encapsulated bleb formation after guarded filtration procedures with adjunctive mitomycin- C.

Mean shift based gradient vector flow for image segmentation

In recent years, gradient vector flow (GVF) based algorithms have been successfully used to segment a variety of 2-D and 3-D imagery. However, due to the compromise of internal and external energy forces within the resulting partial differential equations, these methods may lead to biased segmentation results. In this paper, we propose MSGVF, a mean shift based GVF segmentation algorithm that can successfully locate the correct borders. MSGVF is developed so that when the contour reaches equilibrium, the various forces resulting from the different energy terms are balanced. In addition, the smoothness constraint of image pixels is kept so that over- or under-segmentation can be reduced. Experimental results on publicly accessible datasets of dermoscopic and optic disc images demonstrate that the proposed method effectively detects the borders of the objects of interest.

Documents and Dependencies: an Exploration of Vector Space Models for Semantic Composition

In most previous research on distributional semantics, Vector Space Models (VSMs) of words are built either from topical information (e.g., documents in which a word is present), or from syntactic/semantic types of words (e.g., dependency parse links of a word in sentences), but not both. In this paper, we explore the utility of combining these two representations to build VSM for the task of semantic composition of adjective-noun phrases. Through extensive experiments on benchmark datasets, we find that even though a type-based VSM is effective for semantic composition, it is often outperformed by a VSM built using a combination of topic- and type-based statistics. We also introduce a new evaluation task wherein we predict the composed vector representation of a phrase from the brain activity of a human subject reading that phrase. We exploit a large syntactically parsed corpus of 16 billion tokens to build our VSMs, with vectors for both phrases and words, and make them publicly available.

A Vector Approach for the Analysis and Synthesis of Directional Modulation Transmitters

In order to formalize and extend on previous ad-hoc analysis and synthesis methods a theoretical treatment using vector representations of directional modulation (DM) systems is introduced and used to achieve DM transmitter characteristics. An orthogonal vector approach is proposed which allows the artificial orthogonal noise concept derived from information theory to be brought to bear on DM analysis and synthesis. The orthogonal vector method is validated and discussed via bit error rate (BER) simulations.

Vector representation of directional modulation transmitters

Directional Modulation (DM) is a recently proposed technique for securing wireless communication. In this paper we point out that modulation-directionality is a consequence of varying the beamforming network, either in baseband or in the RF stage, at the information rate In order to formalize and extend on previous analysis and synthesis methods a new theoretical treatment using vector representations of directional modulation (DM) systems is introduced and used to obtain the necessary and sufficient con

Adaptive Fusion Of Particle Filtering And Spatio-Temporal Motion Energy For Human Tracking

Object tracking is an active research area nowadays due to its importance in human computer interface, teleconferencing and video surveillance. However, reliable tracking of objects in the presence of occlusions, pose and illumination changes is still a challenging topic. In this paper, we introduce a novel tracking approach that fuses two cues namely colour and spatio-temporal motion energy within a particle filter based framework. We conduct a measure of coherent motion over two image frames, which reveals the spatio-temporal dynamics of the target. At the same time, the importance of both colour and motion energy cues is determined in the stage of reliability evaluation. This determination helps maintain the performance of the tracking system against abrupt appearance changes. Experimental results demonstrate that the proposed method outperforms the other state of the art techniques in the used test datasets.