An Image Processing Approach Toward a Visual Intra-Cortical Stimulator

Abstract Visual impairment may be caused by various factors varying from trauma, birth-defects, and diseases. Until today there are no viable medical treatments for this condition; hence bio-medical approaches are being employed to overcome that. The Cortivision team has been working on an intra-cortical implant that can bypass the retina and optic nerve and directly stimulate the visual cortex. In this work we aimed to implement a modular, reusable, and parameterizable object recognition system that tends to ``simplify'' video data prior to stimulation; hence opening new horizons for partial vision restoration, navigational and even recognition abilities. We identified the Scale Invariant Feature Transform (SIFT) algorithm as being a robust candidate for our application's needs. A multithreaded software prototype of the SIFT and Lucas-Kanade tracker was implemented to ensure proper overall operation. The feature extractor, difference of Gaussians (DoG) part of the SIFT, being the most computationally expensive, was migrated to an FPGA implementation due to the real-time restrictions that is not achievable on a host machine. The VHDL implementation is highly parameterizable for different application needs and tradeoffs. We introduced a novel architecture employing the sub-kernel trick to reduce resource usage compared to preexisting architectures while still being comparably accurate to a software floating point implementation. In order to alleviate transmission bottlenecks, the system also includes a new parallel Huffman encoder design that is capable of performing lossless compression of both images and scale space image pyramids taking into account spatial and scale data correlations during the predictor phase. The encoder was able to achieve compression ratios of 27.3% on the Caltech-256 data-set. Furthermore, a new camera and fiducial markers setup based on image processing was proposed in order to target the phosphene map estimation problem which affects the quality of the final stimulation that is perceived by the patient.----------RÉSUMÉ Introduction et objectifs La déficience visuelle, qui est définie par la perte totale ou partielle de la vision, n'est actuellement pas médicalement traitable. Des approches biomédicales modernes sont utilisées pour stimuler électriquement la vision; ces approches peuvent être divisées en trois groupes principaux: le premier ciblant les implants rétiniens Humayun et al. (2003), Kim et al. (2004), Chow et al. (2004); Palanker et al. (2005), Toledo et al. (2005); Yanai et al. (2007), Winter et al. (2007); Zrenner et al. (2011), le deuxième ciblant les implants du nerf optique Veraart et al. (2003), Sakaguchi et al. (2009), et le troisième ciblant les implants intra-corticaux Doljanu et Sawan (2007); Coulombe et al. (2007); Srivastava et al. (2007). L’inconvénient principal des deux premiers groupes, c'est qu'ils ne sont pas suffisamment génériques pour surmonter la majorité des maladies de déficience visuelle, car ils dépendent du fait que le patient doit avoir un nerf optique intact et/ou une rétine partiellement opérationnelle ; ce qui n'est pas le cas pour le troisième groupe. L'équipe du Laboratoire Polystim Neurotechnologies travaille actuellement sur un implant intra-cortical qui stimule directement le cortex visuel primaire (région V1) ; le nom du projet global est Cortivision. Le système utilise une caméra, un module de traitement d'image, un transmetteur RF (radiofréquence) et un stimulateur implantable. Cette méthode est robuste et générique car elle contourne l'oeil et le nerf optique. Un des défis majeurs est le traitement d'image nécessaire pour «simplifier» les données antérieures à la stimulation, l'extraction de l’information utile en écartant les données superflues. Les pixels qui sont capturés par la caméra n'ont pas de correspondance un-à-un sur le cortex visuel comme dans une image rectangulaire, ils sont plutôt mis en correspondance avec une carte complexe de «phosphènes» Coulombe et al. (2007); Srivastava et al. (2007). Les phosphènes sont des points lumineux qui apparaissent dans le champ de vision du patient quand le cerveau est stimulé électriquement. Ces points changent en terme de taille, de luminosité et d’emplacement en fonction de la façon dont la stimulation électrique est effectuée (c'est à dire un changement dans la fréquence, la tension, la durée, etc. ...) et même par le placement physique des électrodes dans le cortex visuel. Les approches actuelles visent à stimuler des images de phosphènes monochromes à basse résolution. Sachant cela, nous nous attendons plutôt à une vision de faible qualité qui rend des activités comme naviguer, interpréter des objets, ou encore lire, difficile pour le patient. Ceci est principalement dû à la complexité de l’étalonnage de la carte phosphène et sa correspondance, et aussi à la non-trivialité de savoir comment simplifier les données à partir des images qui viennent de la camera de façon qu’on conserve seulement les données pertinentes. La Figure 1.1 est un exemple qui démontre la non-trivialité de transformer une image grise en stimulation phosphène

High Accuracy of Common HIV-Related Oral Disease Diagnoses by Non-Oral Health Specialists in the AIDS Clinical Trial Group

Objective: Many studies include oral HIV-related endpoints that may be diagnosed by non-oral-health specialists (non-OHS) like nurses or physicians. Our objective was to assess the accuracy of clinical diagnoses of HIV-related oral lesions made by non-OHS compared to diagnoses made by OHS. Methods: A5254, a cross-sectional study conducted by the Oral HIV/AIDS Research Alliance within the AIDS Clinical Trial Group, enrolled HIV-1-infected adults participants from six clinical trial units (CTU) in the US (San Francisco, New York, Chapel Hill, Cleveland, Atlanta) and Haiti. CTU examiners (non-OHS) received standardized training on how to perform an oral examination and make clinical diagnoses of specific oral disease endpoints. Diagnoses by calibrated non-OHS were compared to those made by calibrated OHS, and sensitivity and specificity computed. Results: Among 324 participants, the majority were black (73%), men (66%), and the median CD4+ cell count 138 cells/mm3. The overall frequency of oral mucosal disease diagnosed by OHS was 43% in US sites, and 90% in Haiti. Oral candidiasis (OC) was detected in 153 (47%) by OHS, with erythematous candidiasis (EC) the most common type (39%) followed by pseudomembranous candidiasis (PC; 26%). The highest prevalence of OC (79%) was among participants in Haiti, and among those with CD4+ cell count ≤ 200 cells/mm3 and HIV-1 RNA > 1000 copies/mL (71%). The sensitivity and specificity of OC diagnoses by non-OHS were 90% and 92% (for EC: 81% and 94%; PC: 82% and 95%). Sensitivity and specificity were also high for KS (87% and 94%, respectively), but sensitivity was < 60% for HL and oral warts in all sites combined. The Candida culture confirmation of OC clinical diagnoses (as defined by ≥ 1 colony forming unit per mL of oral/throat rinse) was ≥ 93% for both PC and EC. Conclusion: Trained non-OHS showed high accuracy of clinical diagnoses of OC in comparison with OHS, suggesting their usefulness in studies in resource-poor settings, but detection of less common lesions may require OHS

Characterization of the Fungal Microbiota (Mycobiome) in Healthy and Dandruff-Afflicted Human Scalps

The human scalp harbors a vast community of microbial mutualists, the composition of which is difficult to elucidate as many of the microorganisms are not culturable using current culture techniques. Dandruff, a common scalp disorder, is known as a causative factor of a mild seborrheic dermatitis as well as pityriasis versicolor, seborrheic dermatitis, and atopic dermatitis. Lipophilic yeast Malassezia is widely accepted to play a role in dandruff, but relatively few comprehensive studies have been reported. In order to investigate fungal biota and genetic resources of dandruff, we amplified the 26S rRNA gene from samples of healthy scalps and dandruff-afflicted scalps. The sequences were analyzed by a high throughput method using a GS-FLX 454 pyrosequencer. Of the 74,811 total sequence reads, Basidiomycota (Filobasidium spp.) was the most common phylum associated with dandruff. In contrast, Ascomycota (Acremonium spp.) was common in the healthy scalps. Our results elucidate the distribution of fungal communities associated with dandruff and provide new avenues for the potential prevention and treatment of dandruff

In vitro activity of CAY-1, a saponin from Capsicum frutescens, against Microsporum and Trichophyton species.

Dermatomycoses are among the world's most common diseases and their incidence has increased over recent years, particularly in immunosuppressed patients. In previous studies, the saponin CAY-1 from cayenne pepper (Capsicum frutescens), has shown antifungal activities against Candida albicans and Aspergillus spp. We therefore studied the in vitro antifungal activity of CAY-1 against non-germinating conidia and hyphae of clinical isolates of the dermatophytes Trichophyton mentagrophytes, T. rubrum, T. tonsurans and Microsporum canis. We used a microdilution method to assess the growth inhibitory activities of CAY-1 against conidia (CLSI document M38-A) and a colorimetric procedure (XTT method) to investigate the metabolic inhibitory activity of CAY-1 against hyphae. The minimal inhibitory concentrations (complete visual growth inhibition) of CAY-1 against non-germinating conidia ranged from 10-20 microg/ml for all dermatophyte isolates included in this investigation. In addition, we found >90% inhibition of hyphal metabolic activity of these same isolates with 10-20 microg/ml of CAY-1. Results indicate that CAY-1 merits further investigation as a potential agent for the treatment of dermatomycoses

In vitro activity of CAY-1, a saponin from Capsicum frutescens, against Microsporum and Trichophyton species

Dermatomycoses are among the world’s most common diseases and their incidence has increased over recent years, particularly in immunosuppressed patients. In previous studies, the saponin CAY-1 from cayenne pepper (Capsicum frutescens), has shown antifungal activities against Candida albicans and Aspergillus spp. We therefore studied the in vitro antifungal activity of CAY-1 against non-germinating conidia and hyphae of clinical isolates of the dermatophytes Trichophyton mentagrophytes, T. rubrum, T. tonsurans and Microsporum canis. We used a microdilution method to assess the growth inhibitory activities of CAY-1 against conidia (CLSI document M38-A) and a colorimetric procedure (XTT method) to investigate the metabolic inhibitory activity of CAY-1 against hyphae. The minimal inhibitory concentrations (complete visual growth inhibition) of CAY-1 against non-germinating conidia ranged from 10-20 g/ml for all dermatophyte isolates included in this investigation. In addition, we found 90% inhibition of hyphal metabolic activity of these same isolates with 10-20 g/ml of CAY-1. Results indicate that CAY-1 merits further investigation as a potential agent for the treatment of dermatomycoses

Oral shedding of herpesviruses in HIV-infected patients with varying degrees of immune status

ObjectiveHerpesvirus shedding in the oral cavity was analyzed to determine if presence in the oral compartment correlates with systemic changes in HIV-associated immune deficiency as measured by CD4 cell counts, plasma HIV viral load and presence of AIDS-defining events.DesignA5254 is a multicenter, cross-sectional, single-visit study to evaluate oral complications of HIV/AIDS and determine the association between clinical appearance, herpesvirus shedding, and immune status as ascertained by CD4 cell count and HIV viral load. In total, 307 HIV-infected individuals were evaluated and throat wash collected.MethodsFisher's exact test and Kruskal-Wallis test were used to assess the association between presence of herpesviruses and the state of immunodeficiency as stratified by a combination of CD4 cell count and HIV viral load. Relationship between pathogens and HIV viral load in plasma was modeled by logistic regression.ResultsThe presence of cytomegalovirus (CMV) and herpes simplex virus-1 in throat wash was associated with decreased CD4 cell counts. By contrast, Kaposi sarcoma-associated herpesvirus and Epstein-Barr virus were similarly detectable across all levels of CD4 cell counts. One unit increase in log10 (HIV viral load) was associated with 1.31 times higher odds of detecting CMV in throat wash when controlling for oral candidiasis, CD4 cell count, and sites (95% confidence interval 1.04-1.65, P = 0.02).ConclusionOral CMV shedding was significantly higher in highly immunocompromised HIV participants. Our finding supports the recommendations to start antiretroviral therapy independent of CD4 cell count as this may have the added benefit to lower the risk of herpesvirus transmission among persons infected with HIV and their partners

High Accuracy of Common HIV-Related Oral Disease Diagnoses by Non-Oral Health Specialists in the AIDS Clinical Trial Group

AbstractObjectiveMany studies include oral HIV-related endpoints that may be diagnosed by non-oral-healthspecialists (non-OHS) like nurses or physicians. Our objective was to assess the accuracyof clinical diagnoses of HIV-related oral lesions made by non-OHS compared to diagnosesmade by OHS.MethodsA5254, a cross-sectional study conducted by the Oral HIV/AIDS Research Alliance withinthe AIDS Clinical Trial Group, enrolled HIV-1-infected adults participants from six clinicaltrial units (CTU) in the US (San Francisco, New York, Chapel Hill, Cleveland, Atlanta) andHaiti. CTU examiners (non-OHS) received standardized training on how to perform an oralexamination and make clinical diagnoses of specific oral disease endpoints. Diagnoses bycalibrated non-OHS were compared to those made by calibrated OHS, and sensitivity andspecificity computed.ResultsAmong 324 participants, the majority were black (73%), men (66%), and the median CD4+cell count 138 cells/mm3. The overall frequency of oral mucosal disease diagnosed by OHSwas 43% in US sites, and 90% in Haiti. Oral candidiasis (OC) was detected in 153 (47%) byOHS, with erythematous candidiasis (EC) the most common type (39%) followed by pseudomembranouscandidiasis (PC; 26%). The highest prevalence of OC (79%) was amongparticipants in Haiti, and among those with CD4+ cell count 200 cells/mm3 and HIV-1RNA > 1000 copies/mL (71%). The sensitivity and specificity of OC diagnoses by non-OHSwere 90% and 92% (for EC: 81% and 94%; PC: 82% and 95%). Sensitivity and specificitywere also high for KS (87% and 94%, respectively), but sensitivity was < 60% for HL andoral warts in all sites combined. The Candida culture confirmation of OC clinical diagnoses(as defined by 1 colony forming unit per mL of oral/throat rinse) was 93% for both PCand EC.ConclusionTrained non-OHS showed high accuracy of clinical diagnoses of OC in comparison withOHS, suggesting their usefulness in studies in resource-poor settings, but detection of lesscommon lesions may require OHS

Saccharomyces cerevisiae, candida albicans and adherent-invasive escherichia coli (AIEC) intestinal colonization is not associated with asca detection in Crohn's disease

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