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Sample records for coherence domain molecular

  1. Dental optical coherence domain reflectometry explorer

    Energy Technology Data Exchange (ETDEWEB)

    Everett, Matthew J. (Livermore, CA); Colston, Jr., Billy W. (Livermore, CA); Sathyam, Ujwal S. (Livermore, CA); Da Silva, Luiz B. (Pleasanton, CA)

    2001-01-01

    A hand-held, fiber optic based dental device with optical coherence domain reflectometry (OCDR) sensing capabilities provides a profile of optical scattering as a function of depth in the tissue at the point where the tip of the dental explorer touches the tissue. This system provides information on the internal structure of the dental tissue, which is then used to detect caries and periodontal disease. A series of profiles of optical scattering or tissue microstructure are generated by moving the explorer across the tooth or other tissue. The profiles are combined to form a cross-sectional, or optical coherence tomography (OCT), image.

  2. Coherent combining pulse bursts in time domain

    Science.gov (United States)

    Galvanauskas, Almantas

    2018-01-09

    A beam combining and pulse stacking technique is provided that enhances laser pulse energy by coherent stacking pulse bursts (i.e. non-periodic pulsed signals) in time domain. This energy enhancement is achieved by using various configurations of Fabry-Perot, Gires-Tournois and other types of resonant cavities, so that a multiple-pulse burst incident at either a single input or multiple inputs of the system produces an output with a solitary pulse, which contains the summed energy of the incident multiple pulses from all beams. This disclosure provides a substantial improvement over conventional coherent-combining methods in that it achieves very high pulse energies using a relatively small number of combined laser systems, thus providing with orders of magnitude reduction in system size, complexity, and cost compared to current combining approaches.

  3. Submicron Resolution Spectral-Domain Optical Coherence Tomography

    KAUST Repository

    Alarousu, Erkki; Jabbour, Ghassan

    2013-01-01

    Apparatuses and systems for submicron resolution spectral-domain optical coherence tomography (OCT) are disclosed. The system may use white light sources having wavelengths within 400-1000 nanometers, and achieve resolution below 1 .mu

  4. Fourier phase in Fourier-domain optical coherence tomography

    Science.gov (United States)

    Uttam, Shikhar; Liu, Yang

    2015-01-01

    Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulations are presented to explain and support the theoretical results. These results are further used to show how Fourier phase allows the estimation of an axial mean spatial frequency profile of the sample, along with depth-resolved characterization of localized optical density change and sample heterogeneity. Finally, a Fourier phase-based explanation of Doppler optical coherence tomography is also provided. PMID:26831383

  5. Fourier phase in Fourier-domain optical coherence tomography.

    Science.gov (United States)

    Uttam, Shikhar; Liu, Yang

    2015-12-01

    Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulations are presented to explain and support the theoretical results. These results are further used to show how Fourier phase allows the estimation of an axial mean spatial frequency profile of the sample, along with depth-resolved characterization of localized optical density change and sample heterogeneity. Finally, a Fourier phase-based explanation of Doppler optical coherence tomography is also provided.

  6. Spectral-domain optical coherence tomography of roth spots.

    Science.gov (United States)

    Giovinazzo, Jerome; Mrejen, Sarah; Freund, K Bailey

    2013-01-01

    To describe the retinal findings of subacute bacterial endocarditis, their evolution after treatment, and analysis with spectral-domain optical coherence tomography. Retrospective chart review. A 21-year-old man presented with the sudden onset of a central scotoma in his left eye because of a sub-internal limiting membrane hemorrhage overlying the left fovea. When examined 2 weeks later, Roth spots were noted in his right eye. The patient was immediately referred to his internist and diagnosed with subacute bacterial endocarditis with cultures positive for Streptococcus viridans. He subsequently underwent aortic valve replacement surgery after 4 weeks of intravenous antibiotic therapy. When examined 4 weeks after valve replacement surgery, there was regression of the Roth spots. The present case demonstrates the importance of a funduscopic examination in the early diagnosis and management of subacute bacterial endocarditis. The analysis of Roth spots with spectral-domain optical coherence tomography suggested that they were septic emboli.

  7. Submicron Resolution Spectral-Domain Optical Coherence Tomography

    KAUST Repository

    Alarousu, Erkki

    2013-11-14

    Apparatuses and systems for submicron resolution spectral-domain optical coherence tomography (OCT) are disclosed. The system may use white light sources having wavelengths within 400-1000 nanometers, and achieve resolution below 1 .mu.m. The apparatus is aggregated into a unitary piece, and a user can connect the apparatus to a user provided controller and/or light source. The light source may be a supercontinuum source.

  8. Posterior lattice degeneration characterized by spectral domain optical coherence tomography.

    Science.gov (United States)

    Manjunath, Varsha; Taha, Mohammed; Fujimoto, James G; Duker, Jay S

    2011-03-01

    The purpose of this study was to use high-resolution spectral domain optical coherence tomography in the characterization of retinal and vitreal morphological changes overlying posterior lattice degeneration. A cross-sectional retrospective analysis was performed on 13 eyes of 13 nonconsecutive subjects with posterior lattice degeneration seen at the New England Eye Center, Tufts Medical Center between October 2009 and January 2010. Spectral domain optical coherence tomography images taken through the region of lattice degeneration were qualitatively analyzed. Four characteristic changes of the retina and vitreous were seen in the 13 eyes with lattice degeneration: 1) anterior/posterior U-shaped vitreous traction; 2) retinal breaks; 3) focal retinal thinning; and 4) vitreous membrane formation. The morphologic appearance of vitreous traction and retinal breaks were found to be consistent with previous histologic reports. It is possible to image posterior lattice degeneration in many eyes using spectral domain optical coherence tomography and to visualize the spectrum of retinal and vitreous changes throughout the area of lattice degeneration.

  9. Spectral domain optical coherence tomography characteristics in diabetic retinopathy

    Directory of Open Access Journals (Sweden)

    Laxmi Gella

    2014-01-01

    Full Text Available Purpose: To report the appearance of diabetic retinopathy lesions using spectral domain optical coherence tomography (SD-OCT. Materials and Methods: A total of 287 eyes of 199 subjects were included. All the subjects underwent complete ophthalmic examination including SD-OCT. Results: The appearance of various lesions of diabetic retinopathy and the retinal layers involved were reported. In subjects with macular edema the prevalence of incomplete PVD was 55.6%. Conclusion: SD-OCT brings new insights into the morphological changes of the retina in diabetic retinopathy.

  10. High resolution coherence domain depth-resolved nailfold capillaroscopy based on correlation mapping optical coherence tomography

    Science.gov (United States)

    Subhash, Hrebesh M.; O'Gorman, Sean; Neuhaus, Kai; Leahy, Martin

    2014-03-01

    In this paper we demonstrate a novel application of correlation mapping optical coherence tomography (cm-OCT) for volumetric nailfold capillaroscopy (NFC). NFC is a widely used non-invasive diagnostic method to analyze capillary morphology and microvascular abnormalities of nailfold area for a range of disease conditions. However, the conventional NFC is incapable of providing volumetric imaging, when volumetric quantitative microangiopathic parameters such as plexus morphology, capillary density, and morphologic anomalies of the end row loops most critical. cm-OCT is a recently developed well established coherence domain magnitude based angiographic modality, which takes advantage of the time-varying speckle effect, which is normally dominant in the vicinity of vascular regions compared to static tissue region. It utilizes the correlation coefficient as a direct measurement of decorrelation between two adjacent B-frames to enhance the visibility of depth-resolved microcirculation.

  11. Extending the Effective Ranging Depth of Spectral Domain Optical Coherence Tomography by Spatial Frequency Domain Multiplexing

    Directory of Open Access Journals (Sweden)

    Tong Wu

    2016-11-01

    Full Text Available We present a spatial frequency domain multiplexing method for extending the imaging depth range of a spectral domain optical coherence tomography (SDOCT system without any expensive device. This method uses two galvo scanners with different pivot-offset distances in two independent reference arms for spatial frequency modulation and multiplexing. The spatial frequency contents corresponding to different depth regions of the sample can be shifted to different frequency bands. The spatial frequency domain multiplexing SDOCT system provides an approximately 1.9-fold increase in the effective ranging depth compared with that of a conventional full-range SDOCT system. The reconstructed images of phantom and biological tissue demonstrate the expected increase in ranging depth. The parameters choice criterion for this method is discussed.

  12. Integral ceramic superstructure evaluation using time domain optical coherence tomography

    Science.gov (United States)

    Sinescu, Cosmin; Bradu, Adrian; Topala, Florin I.; Negrutiu, Meda Lavinia; Duma, Virgil-Florin; Podoleanu, Adrian G.

    2014-02-01

    Optical Coherence Tomography (OCT) is a non-invasive low coherence interferometry technique that includes several technologies (and the corresponding devices and components), such as illumination and detection, interferometry, scanning, adaptive optics, microscopy and endoscopy. From its large area of applications, we consider in this paper a critical aspect in dentistry - to be investigated with a Time Domain (TD) OCT system. The clinical situation of an edentulous mandible is considered; it can be solved by inserting 2 to 6 implants. On these implants a mesostructure will be manufactured and on it a superstructure is needed. This superstructure can be integral ceramic; in this case materials defects could be trapped inside the ceramic layers and those defects could lead to fractures of the entire superstructure. In this paper we demonstrate that a TD-OCT imaging system has the potential to properly evaluate the presence of the defects inside the ceramic layers and those defects can be fixed before inserting the prosthesis inside the oral cavity. Three integral ceramic superstructures were developed by using a CAD/CAM technology. After the milling, the ceramic layers were applied on the core. All the three samples were evaluated by a TD-OCT system working at 1300 nm. For two of the superstructures evaluated, no defects were found in the most stressed areas. The third superstructure presented four ceramic defects in the mentioned areas. Because of those defects the superstructure may fracture. The integral ceramic prosthesis was send back to the dental laboratory to fix the problems related to the material defects found. Thus, TD-OCT proved to be a valuable method for diagnosing the ceramic defects inside the integral ceramic superstructures in order to prevent fractures at this level.

  13. Optical coherence tomography and optical coherence domain reflectometry for deep brain stimulation probe guidance

    Science.gov (United States)

    Jeon, Sung W.; Shure, Mark A.; Baker, Kenneth B.; Chahlavi, Ali; Hatoum, Nagi; Turbay, Massud; Rollins, Andrew M.; Rezai, Ali R.; Huang, David

    2005-04-01

    Deep Brain Stimulation (DBS) is FDA-approved for the treatment of Parkinson's disease and essential tremor. Currently, placement of DBS leads is guided through a combination of anatomical targeting and intraoperative microelectrode recordings. The physiological mapping process requires several hours, and each pass of the microelectrode into the brain increases the risk of hemorrhage. Optical Coherence Domain Reflectometry (OCDR) in combination with current methodologies could reduce surgical time and increase accuracy and safety by providing data on structures some distance ahead of the probe. For this preliminary study, we scanned a rat brain in vitro using polarization-insensitive Optical Coherence Tomography (OCT). For accurate measurement of intensity and attenuation, polarization effects arising from tissue birefringence are removed by polarization diversity detection. A fresh rat brain was sectioned along the coronal plane and immersed in a 5 mm cuvette with saline solution. OCT images from a 1294 nm light source showed depth profiles up to 2 mm. Light intensity and attenuation rate distinguished various tissue structures such as hippocampus, cortex, external capsule, internal capsule, and optic tract. Attenuation coefficient is determined by linear fitting of the single scattering regime in averaged A-scans where Beer"s law is applicable. Histology showed very good correlation with OCT images. From the preliminary study using OCT, we conclude that OCDR is a promising approach for guiding DBS probe placement.

  14. Photoreceptor layer map using spectral-domain optical coherence tomography.

    Science.gov (United States)

    Lee, Ji Eun; Lim, Dae Won; Bae, Han Yong; Park, Hyun Jin

    2009-12-01

    To develop a novel method for analysis of the photoreceptor layer map (PLM) generated using spectral-domain optical coherence tomography (OCT). OCT scans were obtained from 20 eyes, 10 with macular holes (MH) and 10 with central serous chorioretinopathy (CSC) using the Macular Cube (512 x 128) protocol of the Cirrus HD-OCT (Carl Zeiss). The scanned data were processed using embedded tools of the advanced visualization. A partial thickness OCT fundus image of the photoreceptor layer was generated by setting the region of interest to a 50-microm thick layer that was parallel and adjacent to the retinal pigment epithelium. The resulting image depicted the photoreceptor layer as a map of the reflectivity in OCT. The PLM was compared with fundus photography, auto-fluorescence, tomography, and retinal thickness map. The signal from the photoreceptor layer of every OCT scan in each case was demonstrated as a single image of PLM in a fundus photograph fashion. In PLM images, detachment of the sensory retina is depicted as a hypo-reflective area, which represents the base of MH and serous detachment in CSC. Relative hypo-reflectivity, which was also noted at closed MH and at recently reattached retina in CSC, was associated with reduced signal from the junction between the inner and outer segments of photoreceptors in OCT images. Using PLM, changes in the area of detachment and reflectivity of the photoreceptor layer could be efficiently monitored. The photoreceptor layer can be analyzed as a map using spectral-domain OCT. In the treatment of both MH and CSC, PLM may provide new pathological information about the photoreceptor layer to expand our understanding of these diseases.

  15. Spectral Domain Optical Coherence Tomography Findings in Posterior Microphthalmia

    Directory of Open Access Journals (Sweden)

    Emine Tınkır Kayıtmazbatır

    2014-05-01

    Full Text Available The retinal spectral domain optical coherence tomography (SD-OCT findings of two posterior microphthalmia cases are presented in this case report. For this purpose, the findings of two siblings aged five and seven years who presented to our clinic with the complain of far-sightedness and high hypermetropia were evaluated. Both cases diagnosed to have posterior microphthalmia demonstrated normal biomicroscopic anterior segment examination and gonioscopy findings and the axial lengths were measured to be shorter than 17mm. The SD-OCT analysis of papillomacular folds detected in fundus examination revealed contribution of only neurosensorial retina. Beneath the retinal fold, we observed bilateral cysts in the intraretinal area in one of the cases and a triangle-shaped hyporeflective space with an apex corresponding to that of the retinal fold in the subretinal area in both cases. SD-OCT is an adjunctive imaging tool for diagnosis and follow-up of degenerative changes in posterior microphthalmia. These changes may be also important for visual prognosis. (Turk J Ophthalmol 2014; 44: 240-2

  16. Retinal Imaging of Infants on Spectral Domain Optical Coherence Tomography

    Directory of Open Access Journals (Sweden)

    Anand Vinekar

    2015-01-01

    Full Text Available Spectral domain coherence tomography (SD OCT has become an important tool in the management of pediatric retinal diseases. It is a noncontact imaging device that provides detailed assessment of the microanatomy and pathology of the infant retina with a short acquisition time allowing office examination without the requirement of anesthesia. Our understanding of the development and maturation of the infant fovea has been enhanced by SD OCT allowing an in vivo assessment that correlates with histopathology. This has helped us understand the critical correlation of foveal development with visual potential in the first year of life and beyond. In this review, we summarize the recent literature on the clinical applications of SD OCT in studying the pathoanatomy of the infant macula, its ability to detect subclinical features, and its correlation with disease and vision. Retinopathy of prematurity and macular edema have been discussed in detail. The review also summarizes the current status of SD OCT in other infant retinal conditions, imaging the optic nerve, the choroid, and the retinal nerve fibre in infants and children, and suggests future areas of research.

  17. Differences between time domain and Fourier domain optical coherence tomography in imaging tissues.

    Science.gov (United States)

    Gao, W; Wu, X

    2017-11-01

    It has been numerously demonstrated that both time domain and Fourier domain optical coherence tomography (OCT) can generate high-resolution depth-resolved images of living tissues and cells. In this work, we compare the common points and differences between two methods when the continuous and random properties of live tissue are taken into account. It is found that when relationships that exist between the scattered light and tissue structures are taken into account, spectral interference measurements in Fourier domain OCT (FDOCT) is more advantageous than interference fringe envelope measurements in time domain OCT (TDOCT) in the cases where continuous property of tissue is taken into account. It is also demonstrated that when random property of tissue is taken into account FDOCT measures the Fourier transform of the spatial correlation function of the refractive index and speckle phenomena will limit the effective limiting imaging resolution in both TDOCT and FDOCT. Finally, the effective limiting resolution of both TDOCT and FDOCT are given which can be used to estimate the effective limiting resolution in various practical applications. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

  18. Spectral-domain optical coherence tomography of macula in myopia.

    Science.gov (United States)

    Choovuthayakorn, Janejit; Laowong, Taksaorn; Watanachai, Nawat; Patikulsila, Direk; Chaikitmongkol, Voraporn

    2016-06-01

    The aim of this study is to determine the associations between regional macular thickness and gender, age, axial length, and degree of myopia in young and middle-aged healthy myopic eyes. One hundred and seventy-one subjects with -0.5 diopters of myopia or worse underwent prospective macular thickness measurement by Spectralis spectral-domain optical coherence tomography. Subjects' mean age was 32.40 ± 8.25 years (range 18 to 49 years), with 45 % being male. The mean degree of myopia was -4.57 ± 3.52 diopters, with a mean axial length of 25.09 ± 1.67 mm. Multivariate regression analysis demonstrated significantly thicker central (mean 9.13 µm thicker) and inner subfields (mean 8.55 µm thicker) in males (P values were <0.001 and 0.002, respectively). In addition, in both genders, for each millimeter of increased axial length, the central subfield thickness increased by 2.11 µm, the inner subfield decreased by 2.25 µm, and the outer subfield decreased by 3.62 µm (P values were 0.010, <0.001, and <0.001, respectively). Factors including gender and axial length affect baseline regional macular thickness in young and middle-age myopic subjects. The central subfield and inner subfield were affected by both gender and axial length, while the outer subfield was affected only by axial length. The macular thickness of myopic subjects with macular disease should be interpreted in light of these factors.

  19. Handbook of Coherent-Domain Optical Methods Biomedical Diagnostics, Environmental Monitoring, and Materials Science

    CERN Document Server

    2013-01-01

    This Handbook provides comprehensive coverage of laser and coherent-domain methods as applied to biomedicine, environmental monitoring, and materials science. Worldwide leaders in these fields describe the fundamentals of light interaction with random media and present an overview of basic research. The latest results on coherent and polarization properties of light scattered by random media, including tissues and blood, speckles formation in multiple scattering media, and other non-destructive interactions of coherent light with rough surfaces and tissues, allow the reader to understand the principles and applications of coherent diagnostic techniques. The expanded second edition has been thoroughly updated with particular emphasis on novel coherent-domain techniques and their applications in medicine and environmental science. Volume 1 describes state-of-the-art methods of coherent and polarization optical imaging, tomography and spectroscopy; diffusion wave spectroscopy; elastic, quasi-elastic and inelasti...

  20. Spectral domain optical coherence tomography findings in tamoxifen retinopathy--a case report.

    Science.gov (United States)

    Nair, Sandhya Narayanan; Anantharaman, Giridhar; Gopalakrishnan, Mahesh; Vyas, Jyothiprakash

    2013-01-01

    To report spectral domain optical coherence tomography findings in a case of typical tamoxifen retinopathy. In this observational case report, a patient with tamoxifen retinopathy was imaged with spectral domain optical coherence tomography and fundus auto fluorescence. Spectral domain optical coherence tomography showed numerous hyperreflective spots within the retina, mainly in the inner retinal layers in both the eyes. The external limiting membrane, the Inner Segment-Outer Segment junction, and the photoreceptors were not discernable at the fovea in the right eye. In the left eye, there was foveal atrophy with total loss of photoreceptors. The autofluorescent images showed macular hypofluorescence with foveal hyperfluorescence. Spectral domain optical coherence tomography demonstrated abnormalities in the outer retinal layers in tamoxifen retinopathy. There were also characteristic alterations in the autofluorescence pattern at the macula in tamoxifen retinopathy.

  1. Keratometric index obtained by Fourier-domain optical coherence tomography.

    Directory of Open Access Journals (Sweden)

    Yanjun Hua

    Full Text Available To determine the keratometric indices calculated based on parameters obtained by Fourier-domain optical coherence tomography (FD-OCT.The ratio of anterior corneal curvature to posterior corneal curvature (Ratio and keratometric index (N were calculated within central 3 mm zone with the RTVue FD-OCT (RTVue, Optovue, Inc. in 186 untreated eyes, 60 post-LASIK/PRK eyes, and 39 keratoconus eyes. The total corneal powers were calculated using different keratometric indices: Kcal based on the mean calculated keratometric index, K1.3315 calculated by the keratometric index of 1.3315, and K1.3375 calculated by the keratometric index of 1.3375. In addition, the total corneal powers based on Gaussian optics formula (Kactual were calculated.The means for Ratio in untreated controls, post-LASIK/PRK group and keratoconus group were 1.176 ± 0.022 (95% confidence interval (CI, 1.172-1.179, 1.314 ± 0.042 (95%CI, 1.303-1.325 and 1.229 ± 0.118 (95%CI, 1.191-1.267, respectively. And the mean calculated keratometric index in untreated controls, post-LASIK/PRK group and keratoconus group were 1.3299 ± 0.00085 (95%CI, 1.3272-1.3308, 1.3242 ± 0.00171 (95%CI, 1.3238-1.3246 and 1.3277 ± 0.0046 (95%CI, 1.3263-1.3292, respectively. All the parameters were normally distributed. The differences between Kcal and Kactual, K1.3315 and Kactual, and K1.3375 and Kactual were 0.00 ± 0.11 D, 0.21 ± 0.11 D and 0.99 ± 0.12 D, respectively, in untreated controls; -0.01 ± 0.20 D, 0.85 ± 0.18 D and 1.56 ± 0.16 D, respectively, in post-LASIK/PRK group; and 0.03 ± 0.67 D, 0.56 ± 0.70 D and 1.40 ± 0.76 D, respectively, in keratoconus group.The calculated keratometric index is negatively related to the ratio of anterior corneal curvature to posterior corneal curvature in untreated, post-LASIK/PRK, and keratoconus eyes, respectively. Using the calculated keratometric index may improve the prediction accuracies of total corneal powers in untreated controls, but not in post

  2. Full-range k-domain linearization in spectral-domain optical coherence tomography.

    Science.gov (United States)

    Jeon, Mansik; Kim, Jeehyun; Jung, Unsang; Lee, Changho; Jung, Woonggyu; Boppart, Stephen A

    2011-03-10

    A full-bandwidth k-domain linearization method for spectral-domain optical coherence tomography (SD-OCT) is demonstrated. The method uses information of the wavenumber-pixel-position provided by a translating-slit-based wavelength filter. For calibration purposes, the filter is placed either after a broadband source or at the end of the sample path, and the filtered spectrum with a narrowed line width (∼0.5 nm) is incident on a line-scan camera in the detection path. The wavelength-swept spectra are co-registered with the pixel positions according to their central wavelengths, which can be automatically measured with an optical spectrum analyzer. For imaging, the method does not require a filter or a software recalibration algorithm; it simply resamples the OCT signal from the detector array without employing rescaling or interpolation methods. The accuracy of k-linearization is maximized by increasing the k-linearization order, which is known to be a crucial parameter for maintaining a narrow point-spread function (PSF) width at increasing depths. The broadening effect is studied by changing the k-linearization order by undersampling to search for the optimal value. The system provides more position information, surpassing the optimum without compromising the imaging speed. The proposed full-range k-domain linearization method can be applied to SD-OCT systems to simplify their hardware/software, increase their speed, and improve the axial image resolution. The experimentally measured width of PSF in air has an FWHM of 8 μm at the edge of the axial measurement range. At an imaging depth of 2.5 mm, the sensitivity of the full-range calibration case drops less than 10 dB compared with the uncompensated case.

  3. Handbook of coherent domain optical methods biomedical diagnostics, environmental and material science

    CERN Document Server

    2004-01-01

    For the first time in one set of books, coherent-domain optical methods are discussed in the framework of various applications, which are characterized by a strong light scattering. A few chapters describe basic research containing the updated results on coherent and polarized light non-destructive interactions with a scattering medium, in particular, diffraction, interference, and speckle formation at multiple scattering. These chapters allow for understanding coherent-domain diagnostic techniques presented in later chapters. A large portion of Volume I is dedicated to analysis of various aspects of optical coherence tomography (OCT) - a very new and growing field of coherent optics. Two chapters on laser scanning confocal microscopy give insight to recent extraordinary results on in vivo imaging and compare the possibilities and achievements of confocol, excitation multiphoton, and OCT microscopy. This two volume reference contains descriptions of holography, interferometry and optical heterodyning techniqu...

  4. Spectral-domain optical coherence tomography on a silicon chip

    NARCIS (Netherlands)

    Akça, B.I.

    2012-01-01

    Optical coherence tomography (OCT) is a non-invasive optical technique for high-resolution cross-sectional imaging of specimens, with many applications in clinical medicine and industry (e.g. materials testing, quality assurance, and process control). Current state-of-the-art OCT systems operate in

  5. Agreement of angle closure assessments between gonioscopy, anterior segment optical coherence tomography and spectral domain optical coherence tomography

    OpenAIRE

    Tay, Elton Lik Tong; Yong, Vernon Khet Yau; Lim, Boon Ang; Sia, Stelson; Wong, Elizabeth Poh Ying; Yip, Leonard Wei Leon

    2015-01-01

    AIM: To determine angle closure agreements between gonioscopy and anterior segment optical coherence tomography (AS-OCT), as well as gonioscopy and spectral domain OCT (SD-OCT). A secondary objective was to quantify inter-observer agreements of AS-OCT and SD-OCT assessments. METHODS: Seventeen consecutive subjects (33 eyes) were recruited from the study hospital’s Glaucoma clinic. Gonioscopy was performed by a glaucomatologist masked to OCT results. OCT images were read independently by 2 ...

  6. INTRASURGICAL MICROSCOPE-INTEGRATED SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY-ASSISTED MEMBRANE PEELING.

    Science.gov (United States)

    Falkner-Radler, Christiane I; Glittenberg, Carl; Gabriel, Max; Binder, Susanne

    2015-10-01

    To evaluate microscope-integrated intrasurgical spectral domain optical coherence tomography during macular surgery in a prospective monocenter study. Before pars plana vitrectomy and before, during, and after membrane peeling, 512 × 128 macular cube scans were performed using a Carl Zeiss Meditec Cirrus high-definition OCT system adapted to the optical pathway of a Zeiss OPMI VISU 200 surgical microscope and compared with retinal staining. The study included 51 patients with epiretinal membranes, with 8 of those having additional lamellar macular holes, 11 patients with vitreomacular traction, and 8 patients with full-thickness macular holes. Intraoperative spectral domain optical coherence tomography allowed performing membrane peeling without using retinal dyes in 40% of cases (28 of 70 patients). No residual membranes were found in 94.3% of patients (66 of 70 patients) in intrasurgical spectral domain optical coherence tomography and subsequent (re)staining. In patients with vitreomacular traction, intrasurgical spectral domain optical coherence tomography scans facilitated decisions on the need for an intraocular tamponade after membrane peeling. Intraoperative spectral domain optical coherence tomography was comparable with retinal dyes in confirming success after membrane peeling. However, the visualization of flat membranes was better after staining.

  7. Dynamic coherence in excitonic molecular complexes under various excitation conditions

    Energy Technology Data Exchange (ETDEWEB)

    Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz

    2014-08-17

    Highlights: • Dynamic coherence does not improve energy transfer efficiency in natural conditions. • Photo-induced quantum jumps are discussed in classical context. • Natural time scale of a light excitation event is identified. • Coherence in FMO complex averages out under excitation by neighboring antenna. • This result is valid even in absence of dissipation. - Abstract: We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity – an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna–Matthews–Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.

  8. In vivo sweat film layer thickness measured with Fourier-domain optical coherence tomography

    CSIR Research Space (South Africa)

    Jonathan, E

    2008-01-01

    Full Text Available s Centre form the f th s pr t fi d id Keywords: Fourier-domain optical coherence tomography; Human sweat secretion; Sweat gland; Sweat duct; Hyperhidrosis growing list of triggers include cancer, glucose control disorder, mental stress, social..., that is, the gland, duct and pore(s). However, due to a slow imaging time, COCT is largely restricted to morphometry of human tissue and thickness measurement of biologic and biologic samples [12,13]. ARTICLE IN PRESS Fourier-domain optical coherence...

  9. Flow patterns on spectral-domain optical coherence tomography reveal flow directions at retinal vessel bifurcations

    DEFF Research Database (Denmark)

    Willerslev, Anne; Li, Xiao Q; Munch, Inger C

    2014-01-01

    PURPOSE: To study intravascular characteristics of flowing blood in retinal vessels using spectral-domain optical coherence tomography (SD-OCT). METHODS: Examination of selected arterial bifurcations and venous sites of confluence in 25 healthy 11-year-old children recruited as an ad hoc subsample...

  10. Broadband Fourier domain mode-locked laser for optical coherence tomography at 1060 nm

    DEFF Research Database (Denmark)

    Marschall, Sebastian; Klein, Thomas; Wieser, Wolfgang

    2012-01-01

    Optical coherence tomography (OCT) in the 1060nm range is interesting for in vivo imaging of the human posterior eye segment (retina, choroid, sclera) due to low absorption in water and deep penetration into the tissue. Rapidly tunable light sources, such as Fourier domain mode-locked (FDML) lasers...

  11. Linearity of Air-Biased Coherent Detection for Terahertz Time-Domain Spectroscopy

    DEFF Research Database (Denmark)

    Wang, Tianwu; Iwaszczuk, Krzysztof; Wrisberg, Emil Astrup

    2016-01-01

    The performance of air-biased coherent detection (ABCD) in a broadband two-color laser-induced air plasma system for terahertz time-domain spectroscopy (THz-TDS) has been investigated. Fundamental parameters of the ABCD detection, including signal-to-noise ratio (SNR), dynamic range (DR), and lin...

  12. Extracting structural features of rat sciatic nerve using polarization-sensitive spectral domain optical coherence tomography

    NARCIS (Netherlands)

    Islam, M.S.; Oliveira, M.C.; Wang, Y.; Henry, F.P.; Randolph, M.A.; Park, B. H.; de Boer, J.F.

    2012-01-01

    We present spectral domain polarization-sensitive optical coherence tomography (SD PS-OCT) imaging of peripheral nerves. Structural and polarization-sensitive OCT imaging of uninjured rat sciatic nerves was evaluated both qualitatively and quantitatively. OCT and its functional extension, PS-OCT,

  13. Online monitoring of printed electronics by Spectral-Domain Optical Coherence Tomography

    KAUST Repository

    Alarousu, Erkki; Alsaggaf, Ahmed; Jabbour, Ghassan E.

    2013-01-01

    Spectral-Domain Optical Coherence Tomography (SD-OCT) is an optical method capable of 3D imaging of object's internal structure with micron-scale resolution. Modern SD-OCT tools offer the speed capable of online monitoring of printed devices

  14. Digital coherent detection research on Brillouin optical time domain reflectometry with simplex pulse codes

    International Nuclear Information System (INIS)

    Hao Yun-Qi; Ye Qing; Pan Zheng-Qing; Cai Hai-Wen; Qu Rong-Hui

    2014-01-01

    The digital coherent detection technique has been investigated without any frequency-scanning device in the Brillouin optical time domain reflectometry (BOTDR), where the simplex pulse codes are applied in the sensing system. The time domain signal of every code sequence is collected by the data acquisition card (DAQ). A shift-averaging technique is applied in the frequency domain for the reason that the local oscillator (LO) in the coherent detection is fix-frequency deviated from the primary source. With the 31-bit simplex code, the signal-to-noise ratio (SNR) has 3.5-dB enhancement with the same single pulse traces, accordant with the theoretical analysis. The frequency fluctuation for simplex codes is 14.01 MHz less than that for a single pulse as to 4-m spatial resolution. The results are believed to be beneficial for the BOTDR performance improvement. (general)

  15. Improved Plane-Wave Ultrasound Beamforming by Incorporating Angular Weighting and Coherent Compounding in Fourier Domain.

    Science.gov (United States)

    Chen, Chuan; Hendriks, Gijs A G M; van Sloun, Ruud J G; Hansen, Hendrik H G; de Korte, Chris L

    2018-05-01

    In this paper, a novel processing framework is introduced for Fourier-domain beamforming of plane-wave ultrasound data, which incorporates coherent compounding and angular weighting in the Fourier domain. Angular weighting implies spectral weighting by a 2-D steering-angle-dependent filtering template. The design of this filter is also optimized as part of this paper. Two widely used Fourier-domain plane-wave ultrasound beamforming methods, i.e., Lu's f-k and Stolt's f-k methods, were integrated in the framework. To enable coherent compounding in Fourier domain for the Stolt's f-k method, the original Stolt's f-k method was modified to achieve alignment of the spectra for different steering angles in k-space. The performance of the framework was compared for both methods with and without angular weighting using experimentally obtained data sets (phantom and in vivo), and data sets (phantom) provided by the IEEE IUS 2016 plane-wave beamforming challenge. The addition of angular weighting enhanced the image contrast while preserving image resolution. This resulted in images of equal quality as those obtained by conventionally used delay-and-sum (DAS) beamforming with apodization and coherent compounding. Given the lower computational load of the proposed framework compared to DAS, to our knowledge it can, therefore, be concluded that it outperforms commonly used beamforming methods such as Stolt's f-k, Lu's f-k, and DAS.

  16. Autofluorescence and spectral-domain optical coherence tomography of optic disk melanocytoma.

    Science.gov (United States)

    Guerra, Ricardo Luz Leitão; Marback, Eduardo Ferrari; Silva, Igor Sandes Pessoa da; Maia Junior, Otacílio de Oliveira; Marback, Roberto Lorens

    2014-01-01

    The authors report fundus autofluorescence (FAF) and spectral-domain optical coherence tomography (OCT) findings of two consecutive patients who presented with optic disk melanocytoma (ODM). A retrospective study was performed by reviewing medical records and ophthalmic imaging examinations. Optical coherence tomography findings were sloped and brightly reflective anterior tumor surface, adjacent retinal desorganization and abrupt posterior optical shadowing. Vitreous seeds were found in one patient. Fundus autofluorescence revealed outstanding hypoautofluorescence at the tumor area and isoautofluorescence at the remaining retina. Optical coherence tomography findings of the reported cases are consistent with those reported in the reviewed literature. Fundus autofluorescence has been used in the assessment of choroidal melanocytic tumors, but not yet in melanocytomas. We assume that this is the first report of these findings and believe that when its pattern has become clearly defined, fundus autofluorescence will be a useful tool to avoid misdiagnosis in suspicious cases and for follow-up.

  17. Autofluorescence and spectral-domain optical coherence tomography of optic disk melanocytoma

    Directory of Open Access Journals (Sweden)

    Ricardo Luz Leitão Guerra

    2014-12-01

    Full Text Available The authors report fundus autofluorescence (FAF and spectral-domain optical coherence tomography (OCT findings of two consecutive patients who presented with optic disk melanocytoma (ODM. A retrospective study was performed by reviewing medical records and ophthalmic imaging examinations. Optical coherence tomography findings were sloped and brightly reflective anterior tumor surface, adjacent retinal desorganization and abrupt posterior optical shadowing. Vitreous seeds were found in one patient. Fundus autofluorescence revealed outstanding hypoautofluorescence at the tumor area and isoautofluorescence at the remaining retina. Optical coherence tomography findings of the reported cases are consistent with those reported in the reviewed literature. Fundus autofluorescence has been used in the assessment of choroidal melanocytic tumors, but not yet in melanocytomas. We assume that this is the first report of these findings and believe that when its pattern has become clearly defined, fundus autofluorescence will be a useful tool to avoid misdiagnosis in suspicious cases and for follow-up.

  18. Probing molecular chirality by coherent optical absorption spectra

    Energy Technology Data Exchange (ETDEWEB)

    Jia, W. Z. [Quantum Optoelectronics Laboratory, School of Physics and Technology, Southwest Jiaotong University, Chengdu 610031 (China); Wei, L. F. [Quantum Optoelectronics Laboratory, School of Physics and Technology, Southwest Jiaotong University, Chengdu 610031 (China); State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-Sen University, Guangzhou 510275 (China)

    2011-11-15

    We propose an approach to sensitively probe the chirality of molecules by measuring their coherent optical-absorption spectra. It is shown that quantum dynamics of the cyclic three-level chiral molecules driven by appropriately designed external fields is total-phase dependent. This will result in chirality-dependent absorption spectra for the probe field. As a consequence, the charality-dependent information in the spectra (such as the locations and relative heights of the characteristic absorption peaks) can be utilized to identify molecular chirality and determinate enantiomer excess (i.e., the percentages of different enantiomers). The feasibility of the proposal with chiral molecules confined in hollow-core photonic crystal fiber is also discussed.

  19. Transient spectral domain optical coherence tomography findings in classic MEWDS: a case report.

    Science.gov (United States)

    Lavigne, Luciana Castro; Isaac, David Leonardo Cruvinel; Duarte Júnior, José Osório; Avila, Marcos Pereira de

    2014-01-01

    The purpose of this study was to describe a patient with multiple evanescent white dot syndrome (MEWDS) who presented with classic retinal findings and transient changes in outer retinal anatomy. A 20-year-old man presented with mild blurred vision in the left eye, reporting flu-like symptoms 1 week before the visual symptoms started. Fundus examination of the left eye revealed foveal granularity and multiple scattered spots deep to the retina in the posterior pole. Fluorescein angiography and indocyanine green angiography showed typical MEWDS findings. Spectral Domain Optical Coherence Tomography has shown transient changes in outer retinal anatomy with disappearance of inner segment-outer segment junction and mild attenuation of external limiting membrane. Six months later, Spectral Domain Optical Coherence Tomography has shown complete resolution with recovery of normal outer retinal aspect.

  20. Spectral domain optical coherence tomography imaging of subretinal bands associated with chronic retinal detachments

    OpenAIRE

    Kothari, Nikisha; Kuriyan, Ajay E; Flynn, Harry W

    2016-01-01

    Nikisha Kothari, Ajay E Kuriyan, Harry W Flynn JrDepartment of Ophthalmology, Bascom Palmer Eye Institute, Miller School of Medicine, University of Miami, Miami, FL, USAAbstract: We report three patients with subretinal bands associated with retinal detachment in chronic retinal detachments who underwent successful retinal reattachment. Subretinal bands before and after surgery can be identified on clinical examination and spectral domain optical coherence tomography. Removal of subr...

  1. Fundus auto fluorescence and spectral domain ocular coherence tomography in the early detection of chloroquine retinopathy

    OpenAIRE

    Megan B. Goodman; Ari Ziskind

    2015-01-01

    Purpose: To determine the sensitivity of spectral domain ocular coherence tomography (SD-OCT) and fundus auto fluorescence (FAF) images as a screening test to detect early changes in the retina prior to the onset of chloroquine retinopathy. Method: The study was conducted using patients taking chloroquine (CQ), referred by the Rheumatology Department to the Ophthalmology Department at Tygerberg Academic Hospital. Group A consisted of 59 patients on CQ for less than 5 years, and Group B co...

  2. Study on the coherence degree of magnetization reversal in Permalloy single-domain nano-ellipses

    Energy Technology Data Exchange (ETDEWEB)

    Júnior, D.S. Vieira [Departamento Acadêmico de Matemática, Física, e Estatística, Instituto Federal de Educação, Ciência e Tecnologia do Sudeste de Minas Gerais – Campus Rio Pomba, Rio Pomba, Minas Gerais 36180-000 (Brazil); Leonel, S.A. [Departamento de Física, Laboratório de Simulação Computacional, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36036-330 (Brazil); Toscano, D., E-mail: danilotoscano@fisica.ufjf.br [Departamento de Física, Laboratório de Simulação Computacional, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36036-330 (Brazil); Sato, F.; Coura, P.Z.; Dias, R.A. [Departamento de Física, Laboratório de Simulação Computacional, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36036-330 (Brazil)

    2017-03-15

    Numerical simulations have been performed to study the magnetization reversal in Permalloy nano-ellipses, under combined in-plane magnetic fields along the longitudinal and the transverse directions. We have considered nano-ellipses with two different aspect ratios and five thicknesses: 220×80×t nm{sup 3} and 70×50×t nm{sup 3}, where t ranging from 5 to 25 nm in steps of 5 nm. We found that the mechanism of magnetization reversal is not only dependent on the parameters of the magnetic field pulse but also related to the ellipse dimensions. It is known that the reversal time is related to the mechanism behind the magnetization reversal. In particular, ultrafast magnetization reversals occur by coherent rotation, when applying a field oriented mainly perpendicular to the initial magnetization. In order to evaluate the degree of coherence of the magnetization reversal we have introduced a quantity called “coherence index”. Besides complementing the previous studies by including the effect of the thickness on the magnetization reversal, our results indicate that it is possible to obtain magnetization reversals with high degree of coherence in small nano-ellipses by adjusting the geometric factors of the ellipse and the parameters of the magnetic field pulse simultaneously. - Highlights: • Magnetization reversals in single-domain nano-ellipses were investigated. • A parameter to evaluate the degree of coherence of the magnetization reversal was proposed. • A higher coherence index indicates a complete, coherent, rotation of the magnetization.

  3. Three-dimensional, time-resolved profiling of ferroelectric domain wall dynamics by spectral-domain optical coherence tomography

    International Nuclear Information System (INIS)

    Haussmann, Alexander; Schmidt, Sebastian; Wehmeier, Lukas; Eng, Lukas M.; Kirsten, Lars; Cimalla, Peter; Koch, Edmund

    2017-01-01

    We apply here spectral-domain optical coherence tomography (SD-OCT) for the precise detection and temporal tracking of ferroelectric domain walls (DWs) in magnesium-doped periodically poled lithium niobate (Mg:PPLN). We reproducibly map static DWs at an axial (depth) resolution down to ∝ 0.6 μm, being located up to 0.5 mm well inside the single crystalline Mg:PPLN sample. We show that a full 3-dimensional (3D) reconstruction of the DW geometry is possible from the collected data, when applying a special algorithm that accounts for the nonlinear optical dispersion of the material. Our OCT investigation provides valuable reference information on the DWs' polarization charge distribution, which is known to be the key to the electrical conductivity of ferroelectric DWs in such systems. Hence, we carefully analyze the SD-OCT signal dependence both when varying the direction of incident polarization, and when applying electrical fields along the polar axis. Surprisingly, the large backreflection intensities recorded under extraordinary polarization are not affected by any electrical field, at least for field strengths below the switching threshold, while no significant signals above noise floor are detected under ordinary polarization. Finally, we employed the high-speed SD-OCT setup for the real-time DW tracking upon ferroelectric domain switching under high external fields. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  4. Three-dimensional, time-resolved profiling of ferroelectric domain wall dynamics by spectral-domain optical coherence tomography

    Energy Technology Data Exchange (ETDEWEB)

    Haussmann, Alexander; Schmidt, Sebastian; Wehmeier, Lukas; Eng, Lukas M. [Technische Universitaet Dresden, Institute of Applied Physics and Center for Advancing Electronics Dresden (cfaed), Dresden (Germany); Kirsten, Lars; Cimalla, Peter; Koch, Edmund [Technische Universitaet Dresden, Faculty of Medicine Carl Gustav Carus, Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, Dresden (Germany)

    2017-08-15

    We apply here spectral-domain optical coherence tomography (SD-OCT) for the precise detection and temporal tracking of ferroelectric domain walls (DWs) in magnesium-doped periodically poled lithium niobate (Mg:PPLN). We reproducibly map static DWs at an axial (depth) resolution down to ∝ 0.6 μm, being located up to 0.5 mm well inside the single crystalline Mg:PPLN sample. We show that a full 3-dimensional (3D) reconstruction of the DW geometry is possible from the collected data, when applying a special algorithm that accounts for the nonlinear optical dispersion of the material. Our OCT investigation provides valuable reference information on the DWs' polarization charge distribution, which is known to be the key to the electrical conductivity of ferroelectric DWs in such systems. Hence, we carefully analyze the SD-OCT signal dependence both when varying the direction of incident polarization, and when applying electrical fields along the polar axis. Surprisingly, the large backreflection intensities recorded under extraordinary polarization are not affected by any electrical field, at least for field strengths below the switching threshold, while no significant signals above noise floor are detected under ordinary polarization. Finally, we employed the high-speed SD-OCT setup for the real-time DW tracking upon ferroelectric domain switching under high external fields. (copyright 2017 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  5. Generation and relaxation of high rank coherences in AX3 systems in a selectively methionine labelled SH2 domain

    International Nuclear Information System (INIS)

    Kloiber, Karin; Fischer, Michael; Ledolter, Karin; Nagl, Michael; Schmid, Walther; Konrat, Robert

    2007-01-01

    The usefulness of selective isotope labelling patterns is demonstrated using the C-terminal SH2 domain of PLC-γ1 selectively 13 C labelled at methionine methyl groups. We demonstrate the generation and relaxation of coherences that are second rank in protons and first rank in carbons that derive from quadrupolar order in protons. The decay rates of second rank double quantum proton coherences are measured. These terms exhibit fewer channels for cross-correlated relaxation compared to single quantum coherences. Our results indicate the potential application of the measurement of high order proton coherences to the analysis of dynamics in methyl-bearing side chains

  6. Spectral domain optical coherence tomography imaging of spectacular ecdysis in the royal python (Python regius).

    Science.gov (United States)

    Tusler, Charlotte A; Maggs, David J; Kass, Philip H; Paul-Murphy, Joanne R; Schwab, Ivan R; Murphy, Christopher J

    2015-01-01

    To describe using spectral domain optical coherence tomography (SD-OCT), digital slit-lamp biomicroscopy, and external photography, changes in the ophidian cuticle, spectacle, and cornea during ecdysis. Four normal royal pythons (Python regius). Snakes were assessed once daily throughout a complete shed cycle using nasal, axial, and temporal SD-OCT images, digital slit-lamp biomicroscopy, and external photography. Spectral domain optical coherence tomography (SD-OCT) images reliably showed the spectacular cuticle and stroma, subcuticular space (SCS), cornea, anterior chamber, iris, and Schlemm's canal. When visible, the subspectacular space (SSS) was more distended peripherally than axially. Ocular surface changes throughout ecdysis were relatively conserved among snakes at all three regions imaged. From baseline (7 days following completion of a full cycle), the spectacle gradually thickened before separating into superficial cuticular and deep, hyper-reflective stromal components, thereby creating the SCS. During spectacular separation, the stroma regained original reflectivity, and multiple hyper-reflective foci (likely fragments from the cuticular-stromal interface) were noted within the SCS. The cornea was relatively unchanged in character or thickness throughout all stages of ecdysis. Slit-lamp images did not permit observation of these changes. Spectral domain optical coherence tomography (SD-OCT) provided excellent high-resolution images of the snake anterior segment, and especially the cuticle, spectacle, and cornea of manually restrained normal snakes at all stages of ecdysis and warrants investigation in snakes with anterior segment disease. The peripheral spectacle may be the preferred entry point for diagnostic or therapeutic injections into the SSS and for initiating spectacular surgery. © 2014 American College of Veterinary Ophthalmologists.

  7. Molecular Frame Reconstruction Using Time-Domain Photoionization Interferometry.

    Science.gov (United States)

    Marceau, Claude; Makhija, Varun; Platzer, Dominique; Naumov, A Yu; Corkum, P B; Stolow, Albert; Villeneuve, D M; Hockett, Paul

    2017-08-25

    Photoionization of molecular species is, essentially, a multipath interferometer with both experimentally controllable and intrinsic molecular characteristics. In this work, XUV photoionization of impulsively aligned molecular targets (N_{2}) is used to provide a time-domain route to "complete" photoionization experiments, in which the rotational wave packet controls the geometric part of the photoionization interferometer. The data obtained is sufficient to determine the magnitudes and phases of the ionization matrix elements for all observed channels, and to reconstruct molecular frame interferograms from lab frame measurements. In principle, this methodology provides a time-domain route to complete photoionization experiments and the molecular frame, which is generally applicable to any molecule (no prerequisites), for all energies and ionization channels.

  8. High-resolution retinal imaging using adaptive optics and Fourier-domain optical coherence tomography

    Science.gov (United States)

    Olivier, Scot S.; Werner, John S.; Zawadzki, Robert J.; Laut, Sophie P.; Jones, Steven M.

    2010-09-07

    This invention permits retinal images to be acquired at high speed and with unprecedented resolution in three dimensions (4.times.4.times.6 .mu.m). The instrument achieves high lateral resolution by using adaptive optics to correct optical aberrations of the human eye in real time. High axial resolution and high speed are made possible by the use of Fourier-domain optical coherence tomography. Using this system, we have demonstrated the ability to image microscopic blood vessels and the cone photoreceptor mosaic.

  9. Extended depth of focus adaptive optics spectral domain optical coherence tomography

    Science.gov (United States)

    Sasaki, Kazuhiro; Kurokawa, Kazuhiro; Makita, Shuichi; Yasuno, Yoshiaki

    2012-01-01

    We present an adaptive optics spectral domain optical coherence tomography (AO-SDOCT) with a long focal range by active phase modulation of the pupil. A long focal range is achieved by introducing AO-controlled third-order spherical aberration (SA). The property of SA and its effects on focal range are investigated in detail using the Huygens-Fresnel principle, beam profile measurement and OCT imaging of a phantom. The results indicate that the focal range is extended by applying SA, and the direction of extension can be controlled by the sign of applied SA. Finally, we demonstrated in vivo human retinal imaging by altering the applied SA. PMID:23082278

  10. Nanoscale nuclear architecture for cancer diagnosis by spatial-domain low-coherence quantitative phase microscopy

    Science.gov (United States)

    Wang, Pin; Bista, Rajan K.; Khalbuss, Walid E.; Qiu, Wei; Staton, Kevin D.; Zhang, Lin; Brentnall, Teresa A.; Brand, Randall E.; Liu, Yang

    2011-03-01

    Alterations in nuclear architecture are the hallmark diagnostic characteristic of cancer cells. In this work, we show that the nuclear architectural characteristics quantified by spatial-domain low-coherence quantitative phase microscopy (SL-QPM), is more sensitive for the identification of cancer cells than conventional cytopathology. We demonstrated the importance of nuclear architectural characteristics in both an animal model of intestinal carcinogenesis - APC/Min mouse model and human cytology specimens with colorectal cancer by identifying cancer from cytologically noncancerous appearing cells. The determination of nanoscale nuclear architecture using this simple and practical optical instrument is a significant advance towards cancer diagnosis.

  11. Novel developments in Fourier domain optical coherence tomography and nonlinear tomographic interferometry

    OpenAIRE

    Mallat, Kamel

    2014-01-01

    In this thesis we present novel methods to improve the limitations in Optical Coherence Tomography (OCT). They are divided into two parts. The first part deals with the axial resolution limitation in OCT systems. We give a description of the Fourier Domain OCT (FDOCT), and then we show theoretically how to enhance the axial resolution in a particular case of a two-layer sample where one of the two layers is moving continuously, while these two layers are separated by a distance lower than the...

  12. Time domain optical coherence tomography investigation of bone matrix interface in rat femurs

    Science.gov (United States)

    Rusu, Laura-Cristina; Negruá¹±iu, Meda-Lavinia; Sinescu, Cosmin; Hoinoiu, Bogdan; Topala, Florin-Ionel; Duma, Virgil-Florin; Rominu, Mihai; Podoleanu, Adrian G.

    2013-08-01

    The materials used to fabricate scaffolds for tissue engineering are derived from synthetic polymers, mainly from the polyester family, or from natural materials (e.g., collagen and chitosan). The mechanical properties and the structural properties of these materials can be tailored by adjusting the molecular weight, the crystalline state, and the ratio of monomers in the copolymers. Quality control and adjustment of the scaffold manufacturing process are essential to achieve high standard scaffolds. Most scaffolds are made from highly crystalline polymers, which inevitably result in their opaque appearance. Their 3-D opaque structure prevents the observation of internal uneven surface structures of the scaffolds under normal optical instruments, such as the traditional light microscope. The inability to easily monitor the inner structure of scaffolds as well as the interface with the old bone poses a major challenge for tissue engineering: it impedes the precise control and adjustment of the parameters that affect the cell growth in response to various mimicked culture conditions. The aim of this paper is to investigate the interface between the femur rat bone and the new bone that is obtained using a method of tissue engineering that is based on different artificial matrixes inserted in previously artificially induced defects. For this study, 15 rats were used in conformity with ethical procedures. In all the femurs a round defect was induced by drilling with a 1 mm spherical Co-Cr surgical drill. The matrixes used were Bioss and 4bone. These materials were inserted into the induced defects. The femurs were investigated at 1 week, 1 month, 2 month and three month after the surgical procedures. The interfaces were examined using Time Domain (TD) Optical Coherence Tomography (OCT) combined with Confocal Microscopy (CM). The optical configuration uses two single mode directional couplers with a superluminiscent diode as the source centered at 1300 nm. The scanning

  13. Limitations in imaging common conjunctival and corneal pathologies with fourier-domain optical coherence tomography.

    Science.gov (United States)

    Demirci, Hakan; Steen, Daniel W

    2014-01-01

    To describe the limitations of Fourier-domain optical coherence tomography (OCT) in imaging common conjunctival and corneal pathology. Retrospective, single-center case series of 40 patients with conjunctival and cornea pathology. Fourier-domain OCT imaged laser in situ keratomileusis (LASIK) flaps in detail, including its relation to other corneal structures and abnormalities. Similarly, in infectious or degenerative corneal disorders, Fourier-domain OCT successfully showed the extent of infiltration or material deposition, which appeared as hyper-reflective areas. In cases with pterygium, the underlying cornea could not be imaged. All cases of common conjunctival pathologies, such as nevus or pinguecula, were successfully imaged in detail. Nevi, scleritis, pterygium, pinguecula, and subconjunctival hemorrhage were hyper-reflective lesions, while cysts and lymphangiectasia were hyporeflective. The details of the underlying sclera were not uniformly imaged in conjunctival pathologies. Fourier-domain OCT imaged the trabeculectomy bleb in detail, whereas the details of structures of the anterior chamber angle were not routinely visualized in all cases. Light scatter through vascularized, densely inflamed, or thick lesions limits the imaging capabilities of Fourier-domain anterior segment OCT.

  14. Indistinguishability and interference in the coherent control of atomic and molecular processes

    International Nuclear Information System (INIS)

    Gong Jiangbin; Brumer, Paul

    2010-01-01

    The subtle and fundamental issue of indistinguishability and interference between independent pathways to the same target state is examined in the context of coherent control of atomic and molecular processes, with emphasis placed on possible 'which-way' information due to quantum entanglement established in the quantum dynamics. Because quantum interference between independent pathways to the same target state occurs only when the independent pathways are indistinguishable, it is first shown that creating useful coherence between nondegenerate states of a molecule for subsequent quantum interference manipulation cannot be achieved by collisions between atoms or molecules that are prepared in momentum and energy eigenstates. Coherence can, however, be transferred from light fields to atoms or molecules. Using a particular coherent control scenario, it is shown that this coherence transfer and the subsequent coherent phase control can be readily realized by the most classical states of light, i.e., coherent states of light. It is further demonstrated that quantum states of light may suppress the extent of phase-sensitive coherent control by leaking out some which-way information while 'incoherent interference control' scenarios proposed in the literature have automatically ensured the indistinguishability of multiple excitation pathways. The possibility of quantum coherence in photodissociation product states is also understood in terms of the disentanglement between photodissociation fragments. Results offer deeper insights into quantum coherence generation in atomic and molecular processes.

  15. Directly assessing interpersonal RSA influences in the frequency domain: An illustration with generalized partial directed coherence.

    Science.gov (United States)

    Liu, Siwei; Gates, Kathleen M; Blandon, Alysia Y

    2018-06-01

    Despite recent research indicating that interpersonal linkage in physiology is a common phenomenon during social interactions, and the well-established role of respiratory sinus arrhythmia (RSA) in socially facilitative physiological regulation, little research has directly examined interpersonal influences in RSA, perhaps due to methodological challenges in analyzing multivariate RSA data. In this article, we aim to bridge this methodological gap by introducing a new method for quantifying interpersonal RSA influences. Specifically, we show that a frequency-domain statistic, generalized partial directed coherence (gPDC), can be used to capture lagged relations in RSA between social partners without first estimating RSA for each person. We illustrate its utility by examining the relation between gPDC and marital conflict in a sample of married couples. Finally, we discuss how gPDC complements existing methods in the time domain and provide guidelines for choosing among these different statistical techniques. © 2018 Society for Psychophysiological Research.

  16. Glaucoma diagnosis by mapping macula with Fourier domain optical coherence tomography

    Science.gov (United States)

    Tan, Ou; Lu, Ake; Chopra, Vik; Varma, Rohit; Hiroshi, Ishikawa; Schuman, Joel; Huang, David

    2008-03-01

    A new image segmentation method was developed to detect macular retinal sub-layers boundary on newly-developed Fourier-Domain Optical Coherence Tomography (FD-OCT) with macular grid scan pattern. The segmentation results were used to create thickness map of macular ganglion cell complex (GCC), which contains the ganglion cell dendrites, cell bodies and axons. Overall average and several pattern analysis parameters were defined on the GCC thickness map and compared for the diagnosis of glaucoma. Intraclass correlation (ICC) is used to compare the reproducibility of the parameters. Area under receiving operative characteristic curve (AROC) was calculated to compare the diagnostic power. The result is also compared to the output of clinical time-domain OCT (TD-OCT). We found that GCC based parameters had good repeatability and comparable diagnostic power with circumpapillary nerve fiber layer (cpNFL) thickness. Parameters based on pattern analysis can increase the diagnostic power of GCC macular mapping.

  17. Spectral-domain optical coherence tomography staging and autofluorescence imaging in achromatopsia.

    Science.gov (United States)

    Greenberg, Jonathan P; Sherman, Jerome; Zweifel, Sandrine A; Chen, Royce W S; Duncker, Tobias; Kohl, Susanne; Baumann, Britta; Wissinger, Bernd; Yannuzzi, Lawrence A; Tsang, Stephen H

    2014-04-01

    IMPORTANCE Evidence is mounting that achromatopsia is a progressive retinal degeneration, and treatments for this condition are on the horizon. OBJECTIVES To categorize achromatopsia into clinically identifiable stages using spectral-domain optical coherence tomography and to describe fundus autofluorescence imaging in this condition. DESIGN, SETTING, AND PARTICIPANTS A prospective observational study was performed between 2010 and 2012 at the Edward S. Harkness Eye Institute, New York-Presbyterian Hospital. Participants included 17 patients (aged 10-62 years) with full-field electroretinography-confirmed achromatopsia. MAIN OUTCOMES AND MEASURES Spectral-domain optical coherence tomography features and staging system, fundus autofluorescence and near-infrared reflectance features and their correlation to optical coherence tomography, and genetic mutations served as the outcomes and measures. RESULTS Achromatopsia was categorized into 5 stages on spectral-domain optical coherence tomography: stage 1 (2 patients [12%]), intact outer retina; stage 2 (2 patients [12%]), inner segment ellipsoid line disruption; stage 3 (5 patients [29%]), presence of an optically empty space; stage 4 (5 patients [29%]), optically empty space with partial retinal pigment epithelium disruption; and stage 5 (3 patients [18%]), complete retinal pigment epithelium disruption and/or loss of the outer nuclear layer. Stage 1 patients showed isolated hyperreflectivity of the external limiting membrane in the fovea, and the external limiting membrane was hyperreflective above each optically empty space. On near infrared reflectance imaging, the fovea was normal, hyporeflective, or showed both hyporeflective and hyperreflective features. All patients demonstrated autofluorescence abnormalities in the fovea and/or parafovea: 9 participants (53%) had reduced or absent autofluorescence surrounded by increased autofluorescence, 4 individuals (24%) showed only reduced or absent autofluorescence, 3

  18. Photoreceptor inner segment ellipsoid band integrity on spectral domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Saxena S

    2014-12-01

    Full Text Available Sandeep Saxena,1 Khushboo Srivastav,1 Chui M Cheung,2 Joanne YW Ng,3 Timothy YY Lai3 1Retina Service, Department of Ophthalmology, King George’s Medical University Lucknow, India; 2Singapore National Eye Centre, Singapore; 3Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Kowloon, Hong Kong Abstract: Spectral domain optical coherence tomography cross-sectional imaging of the macula has conventionally been resolved into four bands. However, some doubts were raised regarding authentication of the existence of these bands. Recently, a number of studies have suggested that the second band appeared to originate from the inner segment ellipsoids of the foveal cone photoreceptors, and therefore the previously called inner segment-outer segment junction is now referred to as inner segment ellipsoidband. Photoreceptor dysfunction may be a significant predictor of visual acuity in a spectrum of surgical and medical retinal diseases. This review aims to provide an overview and summarizes the role of the photoreceptor inner segment ellipsoid band in the management and prognostication of various vitreoretinal diseases. Keywords: spectral domain optical coherence tomography, inner segment-outer segment junction, external limiting membrane, macular hole, diabetic macular edema, age relate macular degeneration

  19. Repeatability of pachymetric mapping using fourier domain optical coherence tomography in corneas with opacities.

    Science.gov (United States)

    Samy El Gendy, Nehal M; Li, Yan; Zhang, Xinbo; Huang, David

    2012-04-01

    To evaluate the repeatability of Fourier domain optical coherence tomography (OCT) pachymetric mapping in patients with corneal opacities and to assess the reliability of Fourier domain OCT with 830 nm wavelength as a pachymetric measurement tool in opaque corneas. A Fourier domain OCT system was used to map the corneal thickness of patients with corneal scars or dystrophy. A retrospective study of a consecutive series was conducted. The repeatability was measured using pooled standard deviation of repeated measurements. A slit-scanning tomography device provided pachymetric mapping for comparison. Seventeen eyes of 12 patients with corneal scars (7 trauma and 3 post infection) or dystrophy (2 Reis-Bucklers and 5 granular dystrophy) were included. The posterior corneal boundary was detectable in all cases. The average corneal thickness measured by OCT was 536 ± 89 μm in central 2 mm area, 553 ± 76 μm in pericentral 2- to 5-mm area, and 508 ± 93 μm for the minimum corneal thickness. The slit-scanning tomography central corneal thickness, 433 ± 111 μm, was significantly lower than OCT readings (mean difference -91.1 ± 33.3 μm, P = 0.002). Repeatability of the OCT measurements was 2.1 μm centrally and 1.2 μm pericentrally. Pachymetric mapping with Fourier domain OCT was highly repeatable. Fourier domain OCT is a reliable pachymetric tool in opaque corneas. In comparison, corneal thickness measured by the slit-scanning tomography is significantly thinner than those measured by the Fourier domain OCT in the presence of corneal opacities.

  20. Agreement of angle closure assessments between gonioscopy, anterior segment optical coherence tomography and spectral domain optical coherence tomography.

    Science.gov (United States)

    Tay, Elton Lik Tong; Yong, Vernon Khet Yau; Lim, Boon Ang; Sia, Stelson; Wong, Elizabeth Poh Ying; Yip, Leonard Wei Leon

    2015-01-01

    To determine angle closure agreements between gonioscopy and anterior segment optical coherence tomography (AS-OCT), as well as gonioscopy and spectral domain OCT (SD-OCT). A secondary objective was to quantify inter-observer agreements of AS-OCT and SD-OCT assessments. Seventeen consecutive subjects (33 eyes) were recruited from the study hospital's Glaucoma clinic. Gonioscopy was performed by a glaucomatologist masked to OCT results. OCT images were read independently by 2 other glaucomatologists masked to gonioscopy findings as well as each other's analyses of OCT images. Totally 84.8% and 45.5% of scleral spurs were visualized in AS-OCT and SD-OCT images respectively (Pgonioscopy was fair at k=0.31 (95% confidence interval, CI: 0.03-0.59) and k=0.35 (95% CI: 0.07-0.63) for reader 1 and 2 respectively. The agreement for angle closure between SD-OCT and gonioscopy was fair at k=0.21 (95% CI: 0.07-0.49) and slight at k=0.17 (95% CI: 0.08-0.42) for reader 1 and 2 respectively. The inter-reader agreement for angle closure in AS-OCT images was moderate at 0.51 (95% CI: 0.13-0.88). The inter-reader agreement for angle closure in SD-OCT images was slight at 0.18 (95% CI: 0.08-0.45). Significant proportion of scleral spurs were not visualised with SD-OCT imaging resulting in weaker inter-reader agreements. Identifying other angle landmarks in SD-OCT images will allow more consistent angle closure assessments. Gonioscopy and OCT imaging do not always agree in angle closure assessments but have their own advantages, and should be used together and not exclusively.

  1. Agreement of angle closure assessments between gonioscopy, anterior segment optical coherence tomography and spectral domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Elton Lik Tong Tay

    2015-04-01

    Full Text Available AIM: To determine angle closure agreements between gonioscopy and anterior segment optical coherence tomography (AS-OCT, as well as gonioscopy and spectral domain OCT (SD-OCT. A secondary objective was to quantify inter-observer agreements of AS-OCT and SD-OCT assessments. METHODS: Seventeen consecutive subjects (33 eyes were recruited from the study hospital’s Glaucoma clinic. Gonioscopy was performed by a glaucomatologist masked to OCT results. OCT images were read independently by 2 other glaucomatologists masked to gonioscopy findings as well as each other’s analyses of OCT images. RESULTS: Totally 84.8% and 45.5% of scleral spurs were visualized in AS-OCT and SD-OCT images respectively (P<0.01. The agreement for angle closure between AS-OCT and gonioscopy was fair at k=0.31 (95% confidence interval, CI: 0.03-0.59 and k=0.35 (95% CI: 0.07-0.63 for reader 1 and 2 respectively. The agreement for angle closure between SD-OCT and gonioscopy was fair at k=0.21 (95% CI: 0.07-0.49 and slight at k=0.17 (95% CI: 0.08-0.42 for reader 1 and 2 respectively. The inter-reader agreement for angle closure in AS-OCT images was moderate at 0.51 (95% CI: 0.13-0.88. The inter-reader agreement for angle closure in SD-OCT images was slight at 0.18 (95% CI: 0.08-0.45. CONCLUSION: Significant proportion of scleral spurs were not visualised with SD-OCT imaging resulting in weaker inter-reader agreements. Identifying other angle landmarks in SD-OCT images will allow more consistent angle closure assessments. Gonioscopy and OCT imaging do not always agree in angle closure assessments but have their own advantages, and should be used together and not exclusively.

  2. Evaluation of time domain and spectral domain optical coherence tomography in the measurement of diabetic macular edema.

    Science.gov (United States)

    Forooghian, Farzin; Cukras, Catherine; Meyerle, Catherine B; Chew, Emily Y; Wong, Wai T

    2008-10-01

    To evaluate macular thickness and volume measurements and their intrasession repeatability in two optical coherence tomography (OCT) systems: the Stratus OCT, a time domain system, and the Cirrus HD-OCT, a spectral domain system (both by Carl Zeiss Meditec, Inc., Dublin, CA), in the context of diabetic macular edema (DME). Thirty-three eyes of 33 diabetic patients with clinically significant macular edema (CSME) were scanned in a single session by a single operator on both OCT systems. Macular thickness measurements of nine standard macular subfields and total macular volume were obtained and analyzed. Bland-Altman plots were constructed to assess agreement in macular measurements. Intraclass correlation coefficients (ICCs), coefficients of repeatability (CR(W)), and coefficients of variation (CV(W)) were used to assess intrasession repeatability. Macular thickness in nine retinal subfields and macular volume were significantly higher in the Cirrus HD-OCT system compared with the Stratus OCT system. Subfield thickness and total volume measurements, respectively, were 30 to 55 microm and 3.2 mm(3) greater for the Cirrus HD-OCT system compared with the Stratus OCT system. Both Stratus OCT and Cirrus HD-OCT systems demonstrated high intrasession repeatability, with overlapping ranges for CR(W), CV(W), and ICC. Repeatability measures (CR(W) and CV(W)) differed significantly between systems in only one of nine subfields (outer temporal subfield). Absolute measures of macular thickness and volume in patients with DME differed significantly in magnitude between the Stratus OCT and Cirrus HD-OCT systems. However, both OCT systems demonstrated high intrasessional repeatability. Although the two systems may not be used interchangeably, they appear equally reliable in generating macular measurements for clinical practice and research.

  3. Management of Patients with Graves’ Disease and Orbital Involvement: Role of Spectral Domain Optical Coherence Tomography

    Directory of Open Access Journals (Sweden)

    Alice Bruscolini

    2018-01-01

    Full Text Available Purpose. To investigate the role of choroidal thickness evaluation with spectral domain optical coherence tomography (SDOCT and enhanced depth imaging (EDI technique in the management of patients with Graves’ disease and orbitopathy (GO. Methods. Thirty-six eyes of 18 patients with GO and 36 eyes of 18 age-matched control subjects were included in this retrospective observational study. All the subjects underwent a complete ophthalmological evaluation, including clinical activity score (CAS and exophthalmometry. The SDOCT images of the choroid were obtained by EDI modality. Results. Choroidal thickness was significantly increased in GO than in control eyes (p<0.01. A significant correlation was found between choroidal thickness and CAS, proptosis, and the duration of disease (p<0.05. Conclusion. This study shows that choroidal thickness, evaluated with EDI-OCT, is significantly increased in patients with GO and correlates with the activity of the disease, proptosis, and duration of the disease. The choroidal thickening may reflect the ocular hemodynamic changes, and enhanced depth imaging optical coherence tomography may be a useful tool for the evaluation of orbital congestion and management of patients with Graves’ disease and orbital involvement.

  4. Single-shot parallel full range complex Fourier-domain optical coherence tomography

    International Nuclear Information System (INIS)

    Huang Bingjie; Bu Peng; Nan Nan; Wang Xiangzhao

    2011-01-01

    We present a method of parallel full range complex Fourier-domain optical coherence tomography (FDOCT) that is capable of acquiring an artifacts-free two-dimensional (2-D) cross-sectional image, i.e. a full range B-scan tomogram, by a single shot of 2-D CCD camera. This method is based on a spatial carrier technique, in which the spatial carrier-frequency is instantaneously introduced into the 2-D spectral interferogram registered in parallel FDOCT by using a grating-generated reference beam. The spatial-carrier-contained 2-D spectral interferogram is processed through Fourier transformation to obtain a complex 2-D spectral interferogram. From the 2-D complex spectral interferomgram, a full range B-scan tomogram is reconstructed. The principle of our method is confirmed by imaging an onion sample.

  5. Two-harmonic complex spectral-domain optical coherence tomography using achromatic sinusoidal phase modulation

    Science.gov (United States)

    Lu, Sheng-Hua; Huang, Siang-Ru; Chou, Che-Chung

    2018-03-01

    We resolve the complex conjugate ambiguity in spectral-domain optical coherence tomography (SD-OCT) by using achromatic two-harmonic method. Unlike previous researches, the optical phase of the fiber interferometer is modulated by an achromatic phase shifter based on an optical delay line. The achromatic phase modulation leads to a wavelength-independent scaling coefficient for the two harmonics. Dividing the mean absolute value of the first harmonic by that of the second harmonic in a B-scan interferogram directly gives the scaling coefficient. It greatly simplifies the determination of the magnitude ratio between the two harmonics without the need of third harmonic and cumbersome iterative calculations. The inverse fast Fourier transform of the complex-valued interferogram constructed with the scaling coefficient, first and second harmonics yields a full-range OCT image. Experimental results confirm the effectiveness of the proposed achromatic two-harmonic technique for suppressing the mirror artifacts in SD-OCT images.

  6. High-speed spectral domain optical coherence tomography using non-uniform fast Fourier transform

    Science.gov (United States)

    Chan, Kenny K. H.; Tang, Shuo

    2010-01-01

    The useful imaging range in spectral domain optical coherence tomography (SD-OCT) is often limited by the depth dependent sensitivity fall-off. Processing SD-OCT data with the non-uniform fast Fourier transform (NFFT) can improve the sensitivity fall-off at maximum depth by greater than 5dB concurrently with a 30 fold decrease in processing time compared to the fast Fourier transform with cubic spline interpolation method. NFFT can also improve local signal to noise ratio (SNR) and reduce image artifacts introduced in post-processing. Combined with parallel processing, NFFT is shown to have the ability to process up to 90k A-lines per second. High-speed SD-OCT imaging is demonstrated at camera-limited 100 frames per second on an ex-vivo squid eye. PMID:21258551

  7. Quantifying Optical Microangiography Images Obtained from a Spectral Domain Optical Coherence Tomography System

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    Roberto Reif

    2012-01-01

    Full Text Available The blood vessel morphology is known to correlate with several diseases, such as cancer, and is important for describing several tissue physiological processes, like angiogenesis. Therefore, a quantitative method for characterizing the angiography obtained from medical images would have several clinical applications. Optical microangiography (OMAG is a method for obtaining three-dimensional images of blood vessels within a volume of tissue. In this study we propose to quantify OMAG images obtained with a spectral domain optical coherence tomography system. A technique for determining three measureable parameters (the fractal dimension, the vessel length fraction, and the vessel area density is proposed and validated. Finally, the repeatability for acquiring OMAG images is determined, and a new method for analyzing small areas from these images is proposed.

  8. Spectral-domain optical coherence tomography findings of the macula in 500 consecutive patients with uveitis.

    Science.gov (United States)

    Grajewski, R S; Boelke, A C; Adler, W; Meyer, S; Caramoy, A; Kirchhof, B; Cursiefen, C; Heindl, L M

    2016-11-01

    PurposeTo analyze the macular structure in a large series of consecutive patients with different types of uveitis using spectral-domain optical coherence tomography (SD-OCT).Patients and methodsFive hundred eyes of 500 consecutive patients with anterior, intermediate, posterior, and panuveitis underwent standardized macular examination using SD-OCT. Central retinal thickness (CRT), macular volume (MV), and presence of cystoid macular edema (CME), diffuse macular edema (DME), serous retinal detachment (SRD), epiretinal membrane with (ERM+) and without (ERM-) retinal surface wrinkling were determined.ResultsThe anatomic location of inflammation affected significantly CRT and MV (Pmacula is recommended for all uveitis patients. CRT, MV, and the incidence of CME were highest in intermediate and panuveitis.

  9. Online monitoring of printed electronics by Spectral-Domain Optical Coherence Tomography

    KAUST Repository

    Alarousu, Erkki

    2013-03-28

    Spectral-Domain Optical Coherence Tomography (SD-OCT) is an optical method capable of 3D imaging of object\\'s internal structure with micron-scale resolution. Modern SD-OCT tools offer the speed capable of online monitoring of printed devices. This paper demonstrates the use of SD-OCT in a simulated roll-to-roll (R2R) process through monitoring some structural properties of moving screen printed interdigitated electrodes. It is shown that structural properties can be resolved for speeds up to ca. 1m/min, which is the first step towards application of this method in real manufacturing processes, including roll-to-roll (R2R) printing.

  10. Sizes of X-ray radiation coherent domains in thin SmS films and their visualization

    Science.gov (United States)

    Sharenkova, N. V.; Kaminskii, V. V.; Petrov, S. N.

    2011-09-01

    The size of X-ray radiation coherent domains (250 ± 20 Å) is determined in a thin polycrystalline SmS film using X-ray diffraction patterns (θ-2θ scanning, DRON-2 diffractometer, Cu K α radiation) and the Selyakov-Scherrer formula with allowance for the effect of microstrains. An image of this film is taken with a transmission electron microscope, and regions with a characteristic size of 240 Å are clearly visible in it. It is concluded that X-ray radiation coherent domains are visualized.

  11. Clinical manifestations of optic pit maculopathy as demonstrated by spectral domain optical coherence tomography

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    Tzu JH

    2013-01-01

    Full Text Available Jonathan H Tzu, Harry W Flynn Jr, Audina M Berrocal, William E Smiddy, Timothy G Murray, Yale L FisherDepartment of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USAPurpose: The purpose of this retrospective study was to evaluate the characteristic features, including spectral-domain optical coherence tomography (SD-OCT, clinical course, and outcome of treatment if given for patients with optic disc pit maculopathy.Methods: We investigated a consecutive series of patients with a diagnosis of optic pit maculopathy treated between 2001 and 2012 at the Bascom Palmer Eye Institute. Patients were divided into two main groups, ie, patients who were observed without surgery and patients who received surgical intervention. The main outcome measures were presenting and final visual acuity, and changes in SD-OCT imaging were recorded. Other data including age, gender, eye, age of onset, length of follow-up, location of optic pit, and location of fluid by OCT were also recorded.Results: On OCT, 67% (12/18 of the eyes showed schisis-like cavities, 22% (4/18 had only subretinal fluid, and 17% (3/18 had only a schisis-like cavity without subretinal fluid. In the patients managed by observation, visual acuity was ≥20/200 in 6/8 eyes initially and 6/8 eyes at last follow-up. Ten of 18 patients received either focal laser, surgery or both. Six of 10 eyes undergoing surgery had initial visual acuity ≥ 20/200, and 8 of 10 eyes undergoing surgery had a visual acuity of ≥20/200 at last follow-up.Conclusion: In this study, many eyes were observed and remained stable during follow-up. In eyes with reduced vision, surgical intervention produced variable outcomes, and persistent intraretinal/subretinal fluid was a common occurrence.Keywords: optic pit maculopathy, spectral-domain optical coherence tomography

  12. Study of Anterior Chamber Aqueous Tube Shunt by Fourier-Domain Optical Coherence Tomography

    Directory of Open Access Journals (Sweden)

    Chunhui Jiang

    2012-01-01

    Full Text Available Purpose. This cross-sectional, observational study used Fourier-domain optical coherence tomography (OCT to examine the position, patency, and the interior entrance site of anterior chamber (AC aqueous tube shunts. Methods. The OCT, slitlamp biomicroscopy, and gonioscopy findings of 23 eyes of 18 patients with AC shunts were collected and compared. Results. OCT images demonstrated the shunt position and patency in all 23 eyes, and the details of the AC entrance in 16 eyes. The position of the tube varied, with the majority (14/23 on the surface of the iris. The exact position of the AC entrance relative to Schwalbe’s line (SL could be determined in 9 eyes (posterior to SL in 7 eyes, anterior in 2 eyes. At the AC entrance, growth of fibrous scar tissue was present between the tube and the corneal endothelium in all 16 eyes in which the entrance could be clearly visualized. It’s a new finding that could not be visualized by slitlamp examination or lower resolution OCT. Conclusion. Compared to slitlamp examination, Fourier-domain OCT of AC tube shunts provided more detailed anatomic information regarding the insertion level relative to SL, scar tissue between the tube and the corneal endothelium, and patency of the tube opening.

  13. Structure-function relationships using spectral-domain optical coherence tomography: comparison with scanning laser polarimetry.

    Science.gov (United States)

    Aptel, Florent; Sayous, Romain; Fortoul, Vincent; Beccat, Sylvain; Denis, Philippe

    2010-12-01

    To evaluate and compare the regional relationships between visual field sensitivity and retinal nerve fiber layer (RNFL) thickness as measured by spectral-domain optical coherence tomography (OCT) and scanning laser polarimetry. Prospective cross-sectional study. One hundred and twenty eyes of 120 patients (40 with healthy eyes, 40 with suspected glaucoma, and 40 with glaucoma) were tested on Cirrus-OCT, GDx VCC, and standard automated perimetry. Raw data on RNFL thickness were extracted for 256 peripapillary sectors of 1.40625 degrees each for the OCT measurement ellipse and 64 peripapillary sectors of 5.625 degrees each for the GDx VCC measurement ellipse. Correlations between peripapillary RNFL thickness in 6 sectors and visual field sensitivity in the 6 corresponding areas were evaluated using linear and logarithmic regression analysis. Receiver operating curve areas were calculated for each instrument. With spectral-domain OCT, the correlations (r(2)) between RNFL thickness and visual field sensitivity ranged from 0.082 (nasal RNFL and corresponding visual field area, linear regression) to 0.726 (supratemporal RNFL and corresponding visual field area, logarithmic regression). By comparison, with GDx-VCC, the correlations ranged from 0.062 (temporal RNFL and corresponding visual field area, linear regression) to 0.362 (supratemporal RNFL and corresponding visual field area, logarithmic regression). In pairwise comparisons, these structure-function correlations were generally stronger with spectral-domain OCT than with GDx VCC and with logarithmic regression than with linear regression. The largest areas under the receiver operating curve were seen for OCT superior thickness (0.963 ± 0.022; P polarimetry, and was better expressed logarithmically than linearly. Measurements with these 2 instruments should not be considered to be interchangeable. Copyright © 2010 Elsevier Inc. All rights reserved.

  14. Anterior Chamber Angle Measurements Using Schwalbe's Line with High Resolution Fourier-Domain Optical Coherence Tomography

    Science.gov (United States)

    Qin, Bing; Francis, Brian A.; Li, Yan; Tang, Maolong; Zhang, Xinbo; Jiang, Chunhui; Cleary, Catherine; Huang, David

    2012-01-01

    Purpose To use Fourier-domain optical coherence tomography (OCT) to measure the angle opening distance at Schwalbe's line (AOD-SL) and determine its value in anterior chamber angle assessment. Methods Horizontal scans of the nasal and temporal anterior chamber angles in glaucoma subjects were performed by 830 nm wavelength Fourier-domain OCT. Images were graded by two ophthalmologists who assessed the visibility of Schwalbe’s line (SL), anterior limbus (AL), scleral spur (SS), and angle recess (AR). AOD-SL was measured with computer calipers. SL was manually identified by the termination of the corneal endothelium. Gonioscopy was used to classify anterior chamber angles according to a modified Shaffer system. Spearman's rho analysis was performed to assess correlation between AOD-SL and modified Shaffer grade. A cut-off value of AOD-SL for diagnosing occludable angles (modified Shaffer grade ≤1) was determined by receiver operating characteristic (ROC) analyses. Results Thirty-five glaucoma subjects (65 eyes) were enrolled. SL, AL, AR, and SS were visible by OCT in 97.7%, 99.2%, 87.3%, and 80.8% of eyes, respectively. Nasal and temporal AOD-SLs were 322.6 ± 200.2 µm and 341.4 ± 197.4 µm, respectively. Correlation coefficients between AOD-SL and modified Shaffer grade were 0.80 (nasal) and 0.81 (temporal). The diagnostic cut-off value of AOD-SL for occludable angles was 290 µm. The areas under the ROC curve, sensitivity, specificity values were 0.90, 0.80, 0.87 (nasal) and 0.90, 0.85, 0.77 (temporal). Conclusions The measurement of AOD-SL by Fourier-domain OCT is highly correlated with gonioscopy and may be a useful noncontact method of assessing angle closure risk. PMID:22827999

  15. Automated 3-D method for the correction of axial artifacts in spectral-domain optical coherence tomography images

    NARCIS (Netherlands)

    B. Antony (Bhavna); M.D. Abràmoff (Michael); L. Tang (Li); W.D. Ramdas (Wishal); J.R. Vingerling (Hans); N.M. Jansonius (Nomdo); K. Lee (Kyungmoo); Y.H. Kwon (Young); M. Sonka (Milan); M.K. Garvin (Mona)

    2011-01-01

    textabstractThe 3-D spectral-domain optical coherence tomography (SD-OCT) images of the retina often do not reflect the true shape of the retina and are distorted differently along the x and y axes. In this paper, we propose a novel technique that uses thin-plate splines in two stages to estimate

  16. Automated 3-D method for the correction of axial artifacts in spectral-domain optical coherence tomography images

    NARCIS (Netherlands)

    Antony, Bhavna; Abramoff, Michael D.; Tang, Li; Ramdas, Wishal D.; Vingerling, Johannes R.; Jansonius, Nomdo M.; Lee, Kyungmoo; Kwon, Young H.; Sonka, Milan; Garvin, Mona K.

    2011-01-01

    The 3-D spectral-domain optical coherence tomography (SD-OCT) images of the retina often do not reflect the true shape of the retina and are distorted differently along the x and y axes. In this paper, we propose a novel technique that uses thin-plate splines in two stages to estimate and correct

  17. Infrared imaging and spectral-domain optical coherence tomography findings correlate with microperimetry in acute macular neuroretinopathy: a case report

    Directory of Open Access Journals (Sweden)

    Grover Sandeep

    2011-10-01

    Full Text Available Abstract Introduction Spectral-domain optical coherence tomography findings in a patient with acute macular neuroretinopathy, and correlation with functional defects on microperimetry, are presented. Case presentation A 25-year old Caucasian woman presented with bitemporal field defects following an upper respiratory tract infection. Her visual acuity was 20/20 in both eyes and a dilated fundus examination revealed bilateral hyperpigmentary changes in the papillomacular bundle. Our patient underwent further evaluation with spectral-domain optical coherence tomography, infrared and fundus autofluorescence imaging. Functional changes were assessed by microperimetry. Infrared imaging showed the classic wedge-shaped defects and spectral-domain optical coherence tomography exhibited changes at the inner segment-outer segment junction, with a thickened outer plexiform layer overlying these areas. Fluorescein and indocyanine green angiography did not demonstrate any perfusion defects or any other abnormality. Microperimetry demonstrated focal elevation in threshold correlating with the wedge-shaped defects in both eyes. Conclusion Spectral-domain optical coherence tomography findings provide new evidence of the involvement of the outer plexiform layer of the retina in acute macular neuroretinopathy.

  18. Fourier Domain Optical Coherence Tomography integrated into a slit lamp; a novel technique combining anterior and posterior segment OCT

    NARCIS (Netherlands)

    Stehouwer, M.; Verbraak, F. D.; de Vries, H.; Kok, P. H. B.; van Leeuwen, T. G.

    2010-01-01

    Purpose Fourier Domain Optical Coherence Tomography (FD-OCT) provides high resolution cross-sectional images of the retina and the anterior segment. It has become an important tool in ophthalmology in the examination, diagnosis, and treatment of important and common diseases. Present OCT imaging

  19. En Face Spectral-Domain Optical Coherence Tomography for the Monitoring of Lesion Area Progression in Stargardt Disease.

    Science.gov (United States)

    Melillo, Paolo; Testa, Francesco; Rossi, Settimio; Di Iorio, Valentina; Orrico, Ada; Auricchio, Alberto; Simonelli, Francesca

    2016-07-01

    We investigated the progression of Stargardt disease (STGD1) over a multiyear follow-up by evaluating the macular lesion area as computed by an automatic algorithm from spectral-domain optical coherence tomography (SD-OCT). We reviewed medical records of STGD1 patients, with a clinical and molecular diagnosis of STGD1 at a single institution, who underwent best-corrected visual acuity (BCVA), fundus photography, SD-OCT, full-field electroretinography, and, when available, fundus autofluorescence (FAF). Regression models were fitted on the selected clinical parameters; in particular, on the macular lesion area computed by SD-OCT, to evaluate the disease progression over a multiyear follow-up. The comparison between SD-OCT and FAF, available for 22 patients, showed that macular lesion area, assessed by SD-OCT, significantly correlated with the area of absent FAF (P disease, showing a significant progression over the follow-up. Our findings suggest that the evaluation of macular lesion area by en face SD-OCT, together with FAF, could drive the choice of the most amenable candidates and the most suitable area to be treated in gene therapy clinical trials.

  20. En Face Spectral-Domain Optical Coherence Tomography for the Monitoring of Lesion Area Progression in Stargardt Disease

    Science.gov (United States)

    Melillo, Paolo; Testa, Francesco; Rossi, Settimio; Di Iorio, Valentina; Orrico, Ada; Auricchio, Alberto; Simonelli, Francesca

    2016-01-01

    Purpose We investigated the progression of Stargardt disease (STGD1) over a multiyear follow-up by evaluating the macular lesion area as computed by an automatic algorithm from spectral-domain optical coherence tomography (SD-OCT). Methods We reviewed medical records of STGD1 patients, with a clinical and molecular diagnosis of STGD1 at a single institution, who underwent best-corrected visual acuity (BCVA), fundus photography, SD-OCT, full-field electroretinography, and, when available, fundus autofluorescence (FAF). Regression models were fitted on the selected clinical parameters; in particular, on the macular lesion area computed by SD-OCT, to evaluate the disease progression over a multiyear follow-up. Results The comparison between SD-OCT and FAF, available for 22 patients, showed that macular lesion area, assessed by SD-OCT, significantly correlated with the area of absent FAF (P disease, showing a significant progression over the follow-up. Our findings suggest that the evaluation of macular lesion area by en face SD-OCT, together with FAF, could drive the choice of the most amenable candidates and the most suitable area to be treated in gene therapy clinical trials. PMID:27409479

  1. One-, two- and three-photon spectroscopy of π-conjugated dendrimers: cooperative enhancement and coherent domains

    International Nuclear Information System (INIS)

    Drobizhev, M.; Rebane, A.; Suo, Z.; Spangler, C.W.

    2005-01-01

    We use wavelength tunable femtosecond pulses to measure intrinsic (simultaneous) two-photon absorption (2PA) and three-photon absorption (3PA) molecular cross section in two series of π-conjugated dendrimers built of identical 4,4'-bis(diphenylamino) stilbene (BDPAS) and 4,4'-bis(diphenylamino) distyrylbenzene (BDPADSB) repeat units. Record large 2PA cross sections, σ 2 =10 -46 cm 4 s are obtained for the largest second-generation BDPAS-based dendrimer, as well as zeroth-generation 4-arm BDPADSB-based dendrimer. In both series, maximum 2PA cross section increases nonlinearly with the number of π-electrons, whereas for higher generations this dependence turns to linear one. 3PA cross section also increases nonlinearly with the size of the system in the series of BDPAS-based molecules, amounting a record large value, σ 3 =10 -79 cm 6 s 2 , for the largest, second-generation dendrimer. We interpret these results in terms of direct inter-branch conjugation, which facilitates cooperative enhancement of the nonlinear-optical response. We propose a simple model which allows us to determine the effective size of coherent domains (extent of conjugation), which, in turn, determines the optimum dendrimer size for most efficient nonlinear response

  2. Molecular dynamics simulations of ferroelectric domain formation by oxygen vacancy

    Science.gov (United States)

    Zhu, Lin; You, Jeong Ho; Chen, Jinghong; Yeo, Changdong

    2018-05-01

    An oxygen vacancy, known to be detrimental to ferroelectric properties, has been investigated numerically for the potential uses to control ferroelectric domains in films using molecular dynamics simulations based on the first-principles effective Hamiltonian. As an electron donor, an oxygen vacancy generates inhomogeneous electrostatic and displacement fields which impose preferred polarization directions near the oxygen vacancy. When the oxygen vacancies are placed at the top and bottom interfaces, the out-of-plane polarizations are locally developed near the interfaces in the directions away from the interfaces. These polarizations from the interfaces are in opposite directions so that the overall out-of-plane polarization becomes significantly reduced. In the middle of the films, the in-plane domains are formed with containing 90° a 1/a 2 domain walls and the films are polarized along the [1 1 0] direction even when no electric field is applied. With oxygen vacancies placed at the top interface only, the films exhibit asymmetric hysteresis loops, confirming that the oxygen vacancies are one of the possible sources of ferroelectric imprint. It has been qualitatively demonstrated that the domain structures in the imprint films can be turned on and off by controlling an external field along the thickness direction. This study shows qualitatively that the oxygen vacancies can be utilized for tuning ferroelectric domain structures in films.

  3. Macular thickness and macular volume measurements using spectral domain optical coherence tomography in normal Nepalese eyes

    Directory of Open Access Journals (Sweden)

    Pokharel A

    2016-03-01

    Full Text Available Amrit Pokharel,1 Gauri Shankar Shrestha,2 Jyoti Baba Shrestha2 1Department of Ophthalmology, Kathmandu Medical College Teaching Hospital, 2B P Koirala Lions Centre for Ophthalmic Studies, Institute of Medicine, Kathmandu, Nepal Purpose: To record the normative values for macular thickness and macular volume in normal Nepalese eyes. Methods: In all, 126 eyes of 63 emmetropic subjects (mean age: 21.17±6.76 years; range: 10–37 years were assessed for macular thickness and macular volume, using spectral domain-optical coherence tomography over 6×6 mm2 in the posterior pole. A fast macular thickness protocol was employed. Statistics such as the mean, median, standard deviation, percentiles, and range were used, while a P-value was set at 0.05 to test significance. Results: Average macular thickness and total macular volume were larger in males compared to females. With each year of increasing age, these variables decreased by 0.556 µm and 0.0156 mm3 for average macular thickness and total macular volume, respectively. The macular thickness was greatest in the inner superior section and lowest at the center of the fovea. The volume was greatest in the outer nasal section and thinnest in the fovea. The central subfield thickness (r=-0.243, P=0.055 and foveal volume (r=0.216, P=0.09 did not correlate with age. Conclusion: Males and females differ significantly with regard to macular thickness and macular volume measurements. Reports by other studies that the increase in axial length reduced thickness and volume, were negated by this study which found a positive correlation among axial length, thickness, and volume. Keywords: macular thickness, macular volume, optical coherence tomography, Nepal

  4. EVALUATION OF DIABETIC MACULAR OEDEMA WITH SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY AND FUNDUS FLUORESCEIN ANGIOGRAPHY

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    Mallika Venkitasubramanian

    2017-02-01

    Full Text Available BACKGROUND Macular oedema is an important cause of visual morbidity in Diabetic Retinopathy. It can be assessed by both Fundus Fluorescein Angiography (FFA and Optical Coherence Tomography (OCT. The aims of this study were to evaluate the agreement between morphological features on spectral domain Optical Coherence Tomography and Fluorescein Angiographic leakage patterns in Diabetic Macular Oedema, and to study the correlation between the best corrected visual acuity and central foveal thickness measured by Optical Coherence Tomography. MATERIALS AND METHODS This was an observational study. All patients with Diabetic Macular Oedema underwent complete ophthalmic examination and subjected to FFA and OCT. Presence or absence of macular oedema by FFA and OCT was noted and agreement between two modalities of imaging was assessed. Sensitivity of these modalities were also found out using appropriate statistical methods. Best Corrected Visual Acuity (BCVA measured were converted to LogMAR scale and Central foveal thickness measured by OCT. Linear regression analysis was done with central foveal thickness and LogMAR visual acuity. RESULTS A total of 69 eyes of 39 patients were studied. OCT revealed Diabetic Macular Oedema in 97.5% of eyes. Fundus Fluorescein Angiography performed in these patients identified leakage in 95.6% of eyes. Sensitivity and specificity of FFA and OCT were calculated keeping one as the gold standard for sensitivity and specificity of the other. FFA and OCT had almost equal sensitivity (95.46 for OCT and 96.92 for FFA for detection of DME. Specificity of OCT was found to be slightly higher (33.33% compared to FFA (25%. Our results suggest that there is minimal agreement between these two imaging modalities in evaluating DME. Statistically, Kappa value was 0.248. Linear regression analysis showed that central foveal thickness had a significant correlation with visual acuity, with Pearson correlation coefficient r=0.442, p=0

  5. Imaging retinal degeneration in mice by combining Fourier domain optical coherence tomography and fluorescent scanning laser ophthalmoscopy

    Science.gov (United States)

    Hossein-Javaheri, Nima; Molday, Laurie L.; Xu, Jing; Molday, Robert S.; Sarunic, Marinko V.

    2009-02-01

    Visualization of the internal structures of the retina is critical for clinical diagnosis and monitoring of pathology as well as for medical research investigating the root causes of retinal degeneration. Optical Coherence Tomography (OCT) is emerging as the preferred technique for non-contact sub-surface depth-resolved imaging of the retina. The high resolution cross sectional images acquired in vivo by OCT can be compared to histology to visually delineate the retinal layers. The recent demonstration of the significant sensitivity increase obtained through use of Fourier domain (FD) detection with OCT has been used to facilitate high speed scanning for volumetric reconstruction of the retina in software. The images acquired by OCT are purely structural, relying on refractive index differences in the tissue for contrast, and do not provide information on the molecular content of the sample. We have constructed a FDOCT prototype and combined it with a fluorescent Scanning Laser Ophthalmoscope (fSLO) to permit real time alignment of the field of view on the retina. The alignment of the FDOCT system to the specimen is crucial for the registration of measurements taken throughout longitudinal studies. In addition, fluorescence detection has been integrated with the SLO to enable the en face localization of a molecular contrast signal, which is important for retinal angiography, and also for detection of autofluorescence associated with some forms of retinal degeneration, for example autofluorescence lipofuscin accumulations are associated with Stargardt's Macular Dystrophy. The integrated FD OCT/fSLO system was investigated for imaging the retina of the mice in vivo.

  6. Full molecular dynamics simulations of liquid water and carbon tetrachloride for two-dimensional Raman spectroscopy in the frequency domain

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Ju-Yeon, E-mail: ju8879@kuchem.kyoto-u.ac.jp; Ito, Hironobu, E-mail: h.ito@kuchem.kyoto-u.ac.jp; Tanimura, Yoshitaka, E-mail: tanimura@kuchem.kyoto-u.ac.jp

    2016-12-20

    Frequency-domain two-dimensional (2D) Raman signals, which are equivalent to coherent two-dimensional Raman scattering (COTRAS) signals, for liquid water and carbon tetrachloride were calculated using an equilibrium–nonequilibrium hybrid molecular dynamics (MD) simulation algorithm. An appropriate representation of the 2D Raman spectrum obtained from MD simulations provides an easy-to-understand depiction of structural and dynamical properties. We elucidate mechanisms governing the 2D signal profiles involving anharmonic mode–mode coupling and the nonlinearities of the polarizability for the intermolecular and intramolecular vibrational modes. The predicted signal profiles and intensities can be utilized to analyze recently developed single-beam 2D spectra, whose signals are generated from a coherently controlled pulse, allowing the single-beam measurement to be carried out more efficiently. Moreover, the MD simulation results allow us to visualize the molecular structure and dynamics by comparing the accurately calculated spectrum with experimental result.

  7. Equations describing coherent and partially coherent multilevel molecular excitation induced by pulsed Raman transitions: III

    International Nuclear Information System (INIS)

    Shore, B.W.; Sacks, R.; Karr, T.

    1987-01-01

    This memo discusses the equations of motion used to describe multilevel molecular excitation induced by Raman transitions. These equations are based upon the time-dependent Schroedinger equation expressed in a basis of molecular energy states. A partition of these states is made into two sets, those that are far from resonance (and hence unpopulated) and those that are close to resonance, either by one-photon transition or two-photon (Raman) processes. By adiabatic elimination an effective Schroedinger equation is obtained for the resonance states alone. The effective Hamiltonian is expressible in terms of a polarizibility operator

  8. Rotation commensurate echo of asymmetric molecules—Molecular fingerprints in the time domain

    Energy Technology Data Exchange (ETDEWEB)

    Chesnokov, E. N., E-mail: chesnok@kinetics.nsc.ru [Institute of Chemical Kinetics and Combustion, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, Novosibirsk 630090 (Russian Federation); Kubarev, V. V. [Budker Institute of Nuclear Physics, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, Novosibirsk 630090 (Russian Federation); Koshlyakov, P. V. [Institute of Chemical Kinetics and Combustion, Novosibirsk 630090 (Russian Federation)

    2014-12-29

    Using the pulses of terahertz free electron laser and ultra-fast Schottky diode detectors, we observed the coherent transients within a free induction decay of gaseous nitrogen dioxide NO{sub 2}. The laser excited different sub-bands of rotation spectra of NO{sub 2} containing about 50–70 lines. The free induction signal continued more than 30 ns and consisted of many echo-like bursts duration about 0.2 ns. Unlike the similar effect observed previously for linear and symmetric top molecules, the sequence of echo bursts is not periodic. The values for delay of individual echo are stable, and the set of these delays can be considered as a “molecular fingerprint” in the time domain.

  9. Investigations of soft and hard tissues in oral cavity by spectral domain optical coherence tomography

    Science.gov (United States)

    Madjarova, Violeta Dimitrova; Yasuno, Yoshiaki; Makita, Shuichi; Hori, Yasuaki; Voeffray, Jean-Baptiste; Itoh, Masahide; Yatagai, Toyohiko; Tamura, Masami; Nanbu, Toshiyuki

    2006-02-01

    Fourier Domain Optical Coherence Tomography (SD-OCT) systems for dental measurements are demonstrated. Two systems have been developed. The first system is fiber based Michelson interferometer with super luminescent diodes at 1310 nm and 100 nm FWHM as a light source. The sensitivity of the system was 106 dB with depth measurement range in air of 2.5 mm. The second systems is a fiber based Mach-Zehnder interferometer with wavelength scanning laser as light source at center wavelength of 1310 nm, wavelength range of 110 nm and scanning rate of 20 KHz. The sensitivity of the system is 112 dB and depth measurement range in air is 6 mm. Both systems can acquire real-time three dimensional (3-D) images in the range of several second. The systems were applied for early caries detection in tooth, for diagnostics of tooth condition after operational tooth treatment, and for diagnostics of the alveolar bone structure. In-vivo measurements were performed on two volunteers. The systems were able to detect discontinuities in tooth and resin filling after tooth treatment. In addition early carries lesion was detected in one of the volunteers. The 3-D profile of the alveolar bone was acquired for first time with non-contact method.

  10. Enhanced performance for differential detection in coherent Brillouin optical time-domain analysis sensors

    Science.gov (United States)

    Shao, Liyang; Zhang, Yunpeng; Li, Zonglei; Zhang, Zhiyong; Zou, Xihua; Luo, Bin; Pan, Wei; Yan, Lianshan

    2016-11-01

    Logarithmic detectors (LogDs) have been used in coherent Brillouin optical time-domain analysis (BOTDA) sensors to reduce the effect of phase fluctuation, demodulation complexities, and measurement time. However, because of the inherent properties of LogDs, a DC component at the level of hundreds of millivolts that prohibits high-gain signal amplification (SA) could be generated, resulting in unacceptable data acquisition (DAQ) inaccuracies and decoding errors in the process of prototype integration. By generating a reference light at a level similar to the probe light, differential detection can be applied to remove the DC component automatically using a differential amplifier before the DAQ process. Therefore, high-gain SA can be employed to reduce quantization errors. The signal-to-noise ratio of the weak Brillouin gain signal is improved from ˜11.5 to ˜21.8 dB. A BOTDA prototype is implemented based on the proposed scheme. The experimental results show that the measurement accuracy of the Brillouin frequency shift (BFS) is improved from ±1.9 to ±0.8 MHz at the end of a 40-km sensing fiber.

  11. Three dimensional tracking for volumetric spectral-domain optical coherence tomography.

    Science.gov (United States)

    Maguluri, Gopi; Mujat, Mircea; Park, B H; Kim, K H; Sun, Wei; Iftimia, N V; Ferguson, R D; Hammer, Daniel X; Chen, Teresa C; de Boer, Johannes F

    2007-12-10

    We present a three-dimensional (3D) tracker for a clinical ophthalmic spectral domain optical coherence tomography (SD-OCT) system that combines depth-tracking with lateral tracking, providing a stabilized reference frame for 3D data recording and post acquisition analysis. The depth-tracking system is implemented through a real-time dynamic feedback mechanism to compensate for motion artifact in the axial direction. Active monitoring of the retina and adapting the reference arm of the interferometer allowed the whole thickness of the retina to be stabilized to within +/-100 mum. We achieve a relatively constant SNR from image to image by stabilizing the image of the retina with respect to the depth dependent sensitivity of SD-OCT. The depth tracking range of our system is 5.2 mm in air and the depth is adjusted every frame.nhancement in the stability of the images with the depth-tracking algorithm is demonstrated on a healthy volunteer.

  12. Microvascular anastomosis in rodent model evaluated by Fourier domain Doppler optical coherence tomography

    Science.gov (United States)

    Huang, Yong; Tong, Dedi; Zhu, Shan; Wu, Lehao; Ibrahim, Zuhaib; Lee, WP Andrew; Brandacher, Gerald; Kang, Jin U.

    2014-03-01

    Vascular and microvascular anastomosis are critical components of reconstructive microsurgery, vascular surgery and transplant surgery. Imaging modality that provides immediate, real-time in-depth view and 3D structure and flow information of the surgical site can be a great valuable tool for the surgeon to evaluate surgical outcome following both conventional and innovative anastomosis techniques, thus potentially increase the surgical success rate. Microvascular anastomosis for vessels with outer diameter smaller than 1.0 mm is extremely challenging and effective evaluation of the outcome is very difficult if not impossible using computed tomography (CT) angiograms, magnetic resonance (MR) angiograms and ultrasound Doppler. Optical coherence tomography (OCT) is a non-invasive high-resolution (micron level), high-speed, 3D imaging modality that has been adopted widely in biomedical and clinical applications. Phaseresolved Doppler OCT that explores the phase information of OCT signals has been shown to be capable of characterizing dynamic blood flow clinically. In this work, we explore the capability of Fourier domain Doppler OCT as an evaluation tool to detect commonly encountered post-operative complications that will cause surgical failure and to confirm positive result with surgeon's observation. Both suture and cuff based techniques were evaluated on the femoral artery and vein in the rodent model.

  13. Intraretinal hyperreflective foci on spectral-domain optical coherence tomographic images of patients with retinitis pigmentosa

    Science.gov (United States)

    Kuroda, Masako; Hirami, Yasuhiko; Hata, Masayuki; Mandai, Michiko; Takahashi, Masayo; Kurimoto, Yasuo

    2014-01-01

    Background The purpose of this study was to observe the characteristic findings of spectral-domain optical coherence tomography (SD-OCT) images in the retinas of patients with retinitis pigmentosa and to evaluate their distribution patterns in the early and advanced stages of the disease. Methods A total of 184 patients (368 eyes) with retinitis pigmentosa were observed using SD-OCT. We studied the presence or absence of continuous inner/outer segment (IS/OS) lines, presence of thinning of the retinal pigment epithelium-Bruch’s membrane complex, and distribution patterns of hyperreflective foci in the inner and outer nuclear layers (INL and ONL). Results The IS/OS junction had partially disappeared in 275 eyes, which were at the early stage of retinitis pigmentosa (group X), whereas the junction had totally disappeared in 93, which were at the advanced stage of retinitis pigmentosa (group Y). Hyperreflective foci in the INL were observed in a significantly larger proportion of the eyes in group X than in group Y (90% versus 61%, Pretinitis pigmentosa and hyperreflective foci in the ONL were more frequently observed in the advanced stage. Hyperreflective foci may be indicative of changes in the retinal structure at each stage of retinitis pigmentosa. PMID:24591813

  14. Agreement between Gonioscopic Examination and Swept Source Fourier Domain Anterior Segment Optical Coherence Tomography Imaging

    Directory of Open Access Journals (Sweden)

    Mohammed Rigi

    2016-01-01

    Full Text Available Purpose. To evaluate interobserver, intervisit, and interinstrument agreements for gonioscopy and Fourier domain anterior segment optical coherence tomography (FD ASOCT for classifying open and narrow angle eyes. Methods. Eighty-six eyes with open or narrow anterior chamber angles were included. The superior angle was classified open or narrow by 2 of 5 glaucoma specialists using gonioscopy and imaged by FD ASOCT in the dark. The superior angle of each FD ASOCT image was graded as open or narrow by 2 masked readers. The same procedures were repeated within 6 months. Kappas for interobserver and intervisit agreements for each instrument and interinstrument agreements were calculated. Results. The mean age was 50.9 (±18.4 years. Interobserver agreements were moderate to good for both gonioscopy (0.57 and 0.69 and FD ASOCT (0.58 and 0.75. Intervisit agreements were moderate to excellent for both gonioscopy (0.53 to 0.86 and FD ASOCT (0.57 and 0.85. Interinstrument agreements were fair to good (0.34 to 0.63, with FD ASOCT classifying more angles as narrow than gonioscopy. Conclusions. Both gonioscopy and FD ASOCT examiners were internally consistent with similar interobserver and intervisit agreements for angle classification. Agreement between instruments was fair to good, with FD ASOCT classifying more angles as narrow than gonioscopy.

  15. Imaging of the iridocorneal angle with the RTVue spectral domain optical coherence tomography.

    Science.gov (United States)

    Perera, Shamira A; Ho, Ching Lin; Aung, Tin; Baskaran, Mani; Ho, Henrietta; Tun, Tin A; Lee, Tian Loon; Kumar, Rajesh S

    2012-04-02

    To determine the ability of the RTVue spectral domain optical coherence tomography (SDOCT) to image the anterior chamber angle (ACA). Consecutive subjects, recruited from glaucoma clinics, prospectively underwent ophthalmic evaluation including gonioscopy by an ophthalmologist and anterior chamber imaging with SDOCT, adapted with a corneal lens adapter (cornea anterior module-low magnification [CAM-L]) and anterior segment OCT (ASOCT), both performed by a technician. Two different ophthalmologists, masked to gonioscopy findings, assessed visualization of the scleral spur (SS), Schwalbe's line (SL), and trabecular meshwork (TM) by the two modalities. The ability to detect a closed angle was compared with gonioscopy. The average age (SD) of the 81 subjects enrolled was 64.1 (11.4) years; the majority were Chinese (91.4%) and female (61.7%). SDOCT images revealed the SS in 26.9% (56/324) of quadrants and the SL in 44.1% (143/324) of quadrants; in ASOCT images, the SS could be visualized in 69.1% (224/324) of quadrants (P gonioscopy. When analyzing the horizontal quadrants only, both modalities agreed well with gonioscopy, 0.75 and 0.74, respectively (AC1 statistics). The RTVue SDOCT allowed visualization of SL, TM, and SS. However, these landmarks were not detected in a large percentage of images.

  16. Agreement between Gonioscopic Examination and Swept Source Fourier Domain Anterior Segment Optical Coherence Tomography Imaging

    Science.gov (United States)

    Nguyen, Donna; Minnal, Vandana R.

    2016-01-01

    Purpose. To evaluate interobserver, intervisit, and interinstrument agreements for gonioscopy and Fourier domain anterior segment optical coherence tomography (FD ASOCT) for classifying open and narrow angle eyes. Methods. Eighty-six eyes with open or narrow anterior chamber angles were included. The superior angle was classified open or narrow by 2 of 5 glaucoma specialists using gonioscopy and imaged by FD ASOCT in the dark. The superior angle of each FD ASOCT image was graded as open or narrow by 2 masked readers. The same procedures were repeated within 6 months. Kappas for interobserver and intervisit agreements for each instrument and interinstrument agreements were calculated. Results. The mean age was 50.9 (±18.4) years. Interobserver agreements were moderate to good for both gonioscopy (0.57 and 0.69) and FD ASOCT (0.58 and 0.75). Intervisit agreements were moderate to excellent for both gonioscopy (0.53 to 0.86) and FD ASOCT (0.57 and 0.85). Interinstrument agreements were fair to good (0.34 to 0.63), with FD ASOCT classifying more angles as narrow than gonioscopy. Conclusions. Both gonioscopy and FD ASOCT examiners were internally consistent with similar interobserver and intervisit agreements for angle classification. Agreement between instruments was fair to good, with FD ASOCT classifying more angles as narrow than gonioscopy. PMID:27990300

  17. Agreement of Two Different Spectral Domain Optical Coherence Tomography Instruments for Retinal Nerve Fiber Layer Measurements

    Directory of Open Access Journals (Sweden)

    Hooshang Faghihi

    2014-01-01

    Full Text Available Purpose: To determine the agreement between Spectralis and Cirrus spectral domain optical coherence tomography (SD-OCT measurements of peripapillary retinal nerve fiber layer (RNFL thickness. Methods: Suspected or confirmed cases of glaucoma who met the inclusion criteria underwent peripapillary RNFL thickness measurement using both the Spectralis and Cirrus on the same day within a few minutes. Results: Measurements were performed on 103 eyes of 103 patients with mean age of 50.4±17.7 years. Mean RNFL thickness was 89.22±15.87 versus 84.54±13.68 μm using Spectralis and Cirrus, respectively. The difference between measurements and the average of paired measurements with the two devices showed a significant linear relationship. Bland-Altman plots demonstrated that Spectralis thickness values were systematically larger than that of Cirrus. Conclusion: Spectralis OCT generates higher peripapillary RNFL thickness readings as compared to Cirrus OCT; this should be kept in mind when values obtained with different instruments are compared during follow-up.

  18. Acute Retinal Pigment Epitheliitis: Spectral Domain Optical Coherence Tomography, Fluorescein Angiography, and Autofluorescence Findings

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    Tuğba Aydoğan

    2015-01-01

    Full Text Available A 17-year-old presented with central and paracentral scotomas in his right eye for one week. There was no remarkable medical or ocular history. Blood analyses were within normal range. At presentation both eyes’ best-corrected visual acuities were 20/20. Slit-lamp examination result was normal. Fundus examination revealed yellow-white hypopigmented areas in the macula. Fluorescein angiography (FA showed hypofluorescence surrounded by ring of hyperfluorescence. Fundus autofluorescence (FAF was slightly increased. Spectral domain optical coherence tomography (SD-OCT showed disruption of IS/OS junction with expansion of abnormal hyperreflectivity from retinal pigment epithelium to the outer nuclear layer (ONL. One month later fundus examination showed disappearance of the lesions. FA revealed transmission hyperfluorescence. FAF showed increased autofluorescence and pigment clumping. Hyperreflective band in SD-OCT disappeared. Loss of photoreceptor segment layers was observed in some of the macular lesions. The diagnosis of acute retinal pigment epitheliitis can be challenging after disappearance of fundus findings. FA, FAF, and SD-OCT are important tests for diagnosis after resolution of the disease.

  19. In vivo monitoring laser tissue interaction using high resolution Fourier-domain optical coherence tomography

    Science.gov (United States)

    Jo, Hang Chan; Shin, Dong Jun; Ahn, Jin-Chul; Chung, Phil-Sang; Kim, DaeYu

    2017-02-01

    Laser-induced therapies include laser ablation to remove or cut target tissue by irradiating high-power focused laser beam. These laser treatments are widely used tools for minimally invasive surgery and retinal surgical procedures in clinical settings. In this study, we demonstrate laser tissue interaction images of various sample tissues using high resolution Fourier-domain optical coherence tomography (Fd-OCT). We use a Q-switch diode-pumped Nd:YVO4 nanosecond laser (532nm central wavelength) with a 4W maximum output power at a 20 kHz repetition rate to ablate in vitro and in vivo samples including chicken breast and mouse ear tissues. The Fd-OCT system acquires time-series Bscan images at the same location during the tissue ablation experiments with 532nm laser irradiation. The real-time series of OCT cross-sectional (B-scan) images compare structural changes of 532nm laser ablation using same and different laser output powers. Laser tissue ablation is demonstrated by the width and the depth of the tissue ablation from the B-scan images.

  20. Use of Fourier-Domain Optical Coherence Tomography to Evaluate Anterior Stromal Opacities in Donor Corneas

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    Matthew R. Bald

    2013-01-01

    Full Text Available Purpose. To evaluate Fourier-domain optical coherence tomography (FD-OCT as an adjunct to traditional slit lamp examination of donor corneas with suspected Anterior Stromal Opacities. Methods. Seven corneas suspected of having anterior stromal opacities by slit lamp examination were evaluated with FD-OCT. Each cornea was evaluated to confirm the presence of opacity and, if present, the depth of opacity was measured. Results. The opacity depth ranged from 82 μm to 624 μm. The initial slit lamp impressions of five of the seven corneas were confirmed by OCT. In two corneas, the OCT findings were different from the initial slit lamp impressions. Slit lamp examination of the first cornea gave the impression of anterior stromal scarring, but OCT showed that the opacity was limited to the epithelium. Slit lamp examination of the second cornea suggested opacity limited to the epithelium, but OCT identified significant sub-Bowman's scarring. In all cases, the Eye Bank Technicians reported that the location and depth of corneal opacity were more sharply defined by OCT than by slit lamp. Conclusion. The high resolution of OCT makes it easier to determine the location of corneal opacities compared to slit lamp examinations. This enhanced visualization can improve decisions regarding transplant suitability of donor corneas.

  1. Fundus auto fluorescence and spectral domain ocular coherence tomography in the early detection of chloroquine retinopathy

    Directory of Open Access Journals (Sweden)

    Megan B. Goodman

    2015-08-01

    Full Text Available Purpose: To determine the sensitivity of spectral domain ocular coherence tomography (SD-OCT and fundus auto fluorescence (FAF images as a screening test to detect early changes in the retina prior to the onset of chloroquine retinopathy. Method: The study was conducted using patients taking chloroquine (CQ, referred by the Rheumatology Department to the Ophthalmology Department at Tygerberg Academic Hospital. Group A consisted of 59 patients on CQ for less than 5 years, and Group B consisted of 53 patients on CQ for more than 5 years. A 200 × 200 macula thickness map, 5-line raster SD-OCT on a Carl Zeiss Meditec Cirrus HD-OCT and FAF images on a Carl Zeiss Meditec Visucam 500 were recorded for 223 eyes. Images were reviewed independently, and then those of Groups A and B compared. Results: There were no statistically significant differences between Groups A and B. The criteria included the internal limiting membrane and the retinal pigment epithelium (ILM-RPE thickness, interdigitation zone integrity (p = 0.891, df = 1, χ² = 0.1876, ellipsoid zone integrity (p = 0.095, df = 2, χ² = 4.699 and FAF image irregularities (p = 0.479, df = 1, χ²= 4995978. Conclusion: The inclusion of SD-OCT and FAF as objective tests into the prescribed screening guidelines does not appear to simplify the detection of subclinical injury in patients on chloroquine treatment.

  2. Zero-guard-interval coherent optical OFDM with overlapped frequency-domain CD and PMD equalization.

    Science.gov (United States)

    Chen, Chen; Zhuge, Qunbi; Plant, David V

    2011-04-11

    This paper presents a new channel estimation/equalization algorithm for coherent OFDM (CO-OFDM) digital receivers, which enables the elimination of the cyclic prefix (CP) for OFDM transmission. We term this new system as the zero-guard-interval (ZGI)-CO-OFDM. ZGI-CO-OFDM employs an overlapped frequency-domain equalizer (OFDE) to compensate both chromatic dispersion (CD) and polarization mode dispersion (PMD) before the OFDM demodulation. Despite the zero CP overhead, ZGI-CO-OFDM demonstrates a superior PMD tolerance than the previous reduced-GI (RGI)-CO-OFDM, which is verified under several different PMD conditions. Additionally, ZGI-CO-OFDM can improve the channel estimation accuracy under high PMD conditions by using a larger intra-symbol frequency-averaging (ISFA) length as compared to RGI-CO-OFDM. ZGI-CO-OFDM also enables the use of ever smaller fast Fourier transform (FFT) sizes (i.e. OFDM. We show that ZGI-CO-OFDM requires reasonably small additional computation effort (~13.6%) compared to RGI-CO-OFDM for 112-Gb/s transmission over a 1600-km dispersion-uncompensated optical link. © 2011 Optical Society of America

  3. Reproducibility of Scleral Spur Identification and Angle Measurements Using Fourier Domain Anterior Segment Optical Coherence Tomography

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    Ricardo J. Cumba

    2012-01-01

    Full Text Available Purpose. To evaluate intraobserver and interobserver agreement in locating the scleral spur landmark (SSL and anterior chamber angle measurements obtained using Fourier Domain Anterior Segment Optical Coherence Tomography (ASOCT images. Methods. Two independent, masked observers (SR and AZC identified SSLs on ASOCT images from 31 eyes with open and nonopen angles. A third independent reader, NPB, adjudicated SSL placement if identifications differed by more than 80 μm. Nine months later, SR reidentified SSLs. Intraobserver and interobserver agreement in SSL placement, trabecular-iris space area (TISA750, and angle opening distance (AOD750 were calculated. Results. In 84% of quadrants, SR’s SSL placements during 2 sessions were within 80 μm in both the X- and Y-axes, and in 77% of quadrants, SR and AZC were within 80 μm in both axes. In adjudicated images, 90% of all quadrants were within 80 μm, 88% in nonopen-angle eyes, and 92% in open-angle eyes. The intraobserver and interobserver correlation coefficients (with and without adjudication were above 0.9 for TISA750 and AOD750 for all quadrants. Conclusions. Reproducible identification of the SSL from images obtained with FD-ASOCT is possible. The ability to identify the SSL allows reproducible measurement of the anterior chamber angle using TISA750 and AOD750.

  4. Spectral domain optical coherence tomography morphology in optic disc pit associated maculopathy

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    Janusz Michalewski

    2014-01-01

    Full Text Available Purpose: Our purpose was to study the clinical manifestation and course of optic pit maculopathy using Spectral Domain Optical Coherence Tomography (SD- OCT images. Materials and Methods: We used SD-OCT to examine 20 eyes of 19 patients with a macular detachment in combination with an optic. Results: We observed five different fovea appearances in regard to fluid localization. In five eyes, we recorded changes in the fluid distribution with SD-OCT. In 17/20 eyes, we noted a communication between the perineural and subretinal and/or intraretinal space at the margin of the optic disc. Conclusion: 3-dimensional SD-OCT (3D-SDOCT scans revealed a three-fold connection, between subretinal and intraretinal space, perineural space, and the vitreous cavity. Therefore, we suppose that intraretinal or subretinal fluid in optic pit maculopathy may have both a vitreous and cerebrospinal origin. A membrane, covering the optic nerve was noted in 14 cases. Even if it seems intact in some B-scans, it is not complete in others several micrometers apart. Additionally, we observed fluid accumulation below the margin of the optic disc and hyperreflective porous tissue in the optic disc excavation. Those findings do not influence the course of maculopathy.

  5. Fourier-domain angle-resolved low coherence interferometry for clinical detection of dysplasia

    Science.gov (United States)

    Terry, Neil G.; Zhu, Yizheng; Wax, Adam

    2010-02-01

    Improved methods for detecting dysplasia, or pre-cancerous growth are a current clinical need, particularly in the esophagus. The currently accepted method of random biopsy and histological analysis provides only a limited examination of tissue in question while being coupled with a long time delay for diagnosis. Light scattering spectroscopy, in contrast, allows for inspection of the cellular structure and organization of tissue in vivo. Fourier-domain angle-resolved low-coherence interferometry (a/LCI) is a novel light scattering spectroscopy technique that provides quantitative depth-resolved morphological measurements of the size and optical density of the examined cell nuclei, which are characteristic biomarkers of dysplasia. Previously, clinical viability of the a/LCI system was demonstrated through analysis of ex vivo human esophageal tissue in Barrett's esophagus patients using a portable a/LCI, as was the development of a clinical a/LCI system. Data indicating the feasibility of the technique in other organ sites (colon, oral cavity) will be presented. We present an adaptation of the a/LCI system that will be used to investigate the presence of dysplasia in vivo in Barrett's esophagus patients.

  6. Automated Fovea Detection in Spectral Domain Optical Coherence Tomography Scans of Exudative Macular Disease

    Directory of Open Access Journals (Sweden)

    Jing Wu

    2016-01-01

    Full Text Available In macular spectral domain optical coherence tomography (SD-OCT volumes, detection of the foveal center is required for accurate and reproducible follow-up studies, structure function correlation, and measurement grid positioning. However, disease can cause severe obscuring or deformation of the fovea, thus presenting a major challenge in automated detection. We propose a fully automated fovea detection algorithm to extract the fovea position in SD-OCT volumes of eyes with exudative maculopathy. The fovea is classified into 3 main appearances to both specify the detection algorithm used and reduce computational complexity. Based on foveal type classification, the fovea position is computed based on retinal nerve fiber layer thickness. Mean absolute distance between system and clinical expert annotated fovea positions from a dataset comprised of 240 SD-OCT volumes was 162.3 µm in cystoid macular edema and 262 µm in nAMD. The presented method has cross-vendor functionality, while demonstrating accurate and reliable performance close to typical expert interobserver agreement. The automatically detected fovea positions may be used as landmarks for intra- and cross-patient registration and to create a joint reference frame for extraction of spatiotemporal features in “big data.” Furthermore, reliable analyses of retinal thickness, as well as retinal structure function correlation, may be facilitated.

  7. From Computational Photobiology to the Design of Vibrationally Coherent Molecular Devices and Motors

    Science.gov (United States)

    Olivucci, Massimo

    2014-03-01

    In the past multi-configurational quantum chemical computations coupled with molecular mechanics force fields have been employed to investigate spectroscopic, thermal and photochemical properties of visual pigments. Here we show how the same computational technology can nowadays be used to design, characterize and ultimately, prepare light-driven molecular switches which mimics the photophysics of the visual pigment bovine rhodopsin (Rh). When embedded in the protein cavity the chromophore of Rh undergoes an ultrafast and coherent photoisomerization. In order to design a synthetic chromophore displaying similar properties in common solvents, we recently focused on indanylidene-pyrroline (NAIP) systems. We found that these systems display light-induced ground state coherent vibrational motion similar to the one detected in Rh. Semi-classical trajectories provide a mechanistic description of the structural changes associated to the observed coherent motion which is shown to be ultimately due to periodic changes in the π-conjugation.

  8. Spectral triangulation molecular contrast optical coherence tomography with indocyanine green as the contrast agent

    OpenAIRE

    Yang, Changhuei; McGuckin, Laura E. L.; Simon, John D.; Choma, Michael A.; Applegate, Brian E.; Izatt, Joseph A.

    2004-01-01

    We report a new molecular contrast optical coherence tomography (MCOCT) implementation that profiles the contrast agent distribution in a sample by measuring the agent's spectral differential absorption. The method, spectra triangulation MCOCT, can effectively suppress contributions from spectrally dependent scatterings from the sample without a priori knowledge of the scattering properties. We demonstrate molecular imaging with this new MCOCT modality by mapping the distribution of indocyani...

  9. Electron and phonon drag in thermoelectric transport through coherent molecular conductors

    DEFF Research Database (Denmark)

    Lü, Jing-Tao; Wang, Jian-Sheng; Hedegård, Per

    2016-01-01

    We study thermoelectric transport through a coherent molecular conductor connected to two electron and two phonon baths using the nonequilibrium Green's function method. We focus on the mutual drag between electron and phonon transport as a result of ‘momentum’ transfer, which happens only when...

  10. Atomic and molecular spectroscopy with optical-frequency-comb-referenced IR coherent sources

    International Nuclear Information System (INIS)

    Cancio, P.; Bartalini, S.; De Rosa, M.; Giusfredi, G.; Mazzotti, D.; Maddaloni, P.; Vitiello, M. S.; De Natale, P.

    2013-01-01

    We provide a review of progress in the development of metrological-grade measurements in atomic and molecular systems through the extension, in the mid-infrared and far-infrared range, of optical frequency combs (OFCs) and the introduction of new techniques and highly coherent sources. (authors)

  11. MEMS-based handheld fourier domain Doppler optical coherence tomography for intraoperative microvascular anastomosis imaging.

    Directory of Open Access Journals (Sweden)

    Yong Huang

    Full Text Available To demonstrate the feasibility of a miniature handheld optical coherence tomography (OCT imager for real time intraoperative vascular patency evaluation in the setting of super-microsurgical vessel anastomosis.A novel handheld imager Fourier domain Doppler optical coherence tomography based on a 1.3-µm central wavelength swept source for extravascular imaging was developed. The imager was minimized through the adoption of a 2.4-mm diameter microelectromechanical systems (MEMS scanning mirror, additionally a 12.7-mm diameter lens system was designed and combined with the MEMS mirror to achieve a small form factor that optimize functionality as a handheld extravascular OCT imager. To evaluate in-vivo applicability, super-microsurgical vessel anastomosis was performed in a mouse femoral vessel cut and repair model employing conventional interrupted suture technique as well as a novel non-suture cuff technique. Vascular anastomosis patency after clinically successful repair was evaluated using the novel handheld OCT imager.With an adjustable lateral image field of view up to 1.5 mm by 1.5 mm, high-resolution simultaneous structural and flow imaging of the blood vessels were successfully acquired for BALB/C mouse after orthotopic hind limb transplantation using a non-suture cuff technique and BALB/C mouse after femoral artery anastomosis using a suture technique. We experimentally quantify the axial and lateral resolution of the OCT to be 12.6 µm in air and 17.5 µm respectively. The OCT has a sensitivity of 84 dB and sensitivity roll-off of 5.7 dB/mm over an imaging range of 5 mm. Imaging with a frame rate of 36 Hz for an image size of 1000(lateral×512(axial pixels using a 50,000 A-lines per second swept source was achieved. Quantitative vessel lumen patency, lumen narrowing and thrombosis analysis were performed based on acquired structure and Doppler images.A miniature handheld OCT imager that can be used for intraoperative evaluation of

  12. Enhanced spectral domain optical coherence tomography for pathological and functional studies

    Science.gov (United States)

    Yuan, Zhijia

    Optical coherence tomography (OCT) is a novel technique that enables noninvasive or minimally invasive, cross-sectional imaging of biological tissue at sub-10mum spatial resolution and up to 2-3mm imaging depth. Numerous technological advances have emerged in recent years that have shown great potential to develop OCT into a powerful imaging and diagnostic tools. In particular, the implementation of Fourier-domain OCT (FDOCT) is a major step forward that leads to greatly improved imaging rate and image fidelity of OCT. This dissertation summarizes the work that focuses on enhancing the performances and functionalities of spectral radar based FDOCT (SDOCT) for pathological and functional applications. More specifically, chapters 1-4 emphasize on the development of SDOCT and its utility in pathological studies, including cancer diagnosis. The principle of SDOCT is first briefly outlined, followed by the design of our bench-top SDOCT systems with emphasis on spectral linear interpolation, calibration and system dispersion compensation. For ultrahigh-resolution SDOCT, time-lapse image registration and frame averaging is introduced to effectively reduce speckle noise and uncover subcellular details, showing great promise for enhancing the diagnosis of carcinoma in situ. To overcome the image depth limitation of OCT, a dual-modal imaging method combing SDOCT with high-frequency ultrasound is proposed and examined in animal cancer models to enhance the sensitivity and staging capabilities for bladder cancer diagnosis. Chapters 5-7 summarize the work on developing Doppler SDOCT for functional studies. Digital-frequency-ramping OCT (DFR-OCT) is developed in the study, which has demonstrated the ability to significantly improve the signal-to-noise ratio and thus sensitivity for retrieving subsurface blood flow imaging. New DFR algorithms and imaging processing methods are discussed to further enhance cortical CBF imaging. Applications of DFR-OCT for brain functional studies

  13. A coherent modified Redfield theory for excitation energy transfer in molecular aggregates

    Energy Technology Data Exchange (ETDEWEB)

    Hwang-Fu, Yu-Hsien; Chen, Wei; Cheng, Yuan-Chung, E-mail: yuanchung@ntu.edu.tw

    2015-02-02

    Highlights: • A CMRT method for coherent energy transfer in molecular aggregates was developed. • Applicability of the method was verified in two-site systems with various parameters. • CMRT accurately describes population dynamics in the FMO-complex. • The method is accurate in a large parameter space and computationally efficient. - Abstract: Excitation energy transfer (EET) is crucial in photosynthetic light harvesting, and quantum coherence has been recently proven to be a ubiquitous phenomenon in photosynthetic EET. In this work, we derive a coherent modified Redfield theory (CMRT) that generalizes the modified Redfield theory to treat coherence dynamics. We apply the CMRT method to simulate the EET in a dimer system and compare the results with those obtained from numerically exact path integral calculations. The comparison shows that CMRT provides excellent computational efficiency and accuracy within a large EET parameter space. Furthermore, we simulate the EET dynamics in the FMO complex at 77 K using CMRT. The results show pronounced non-Markovian effects and long-lasting coherences in the ultrafast EET, in excellent agreement with calculations using the hierarchy equation of motion approach. In summary, we have successfully developed a simple yet powerful framework for coherent EET dynamics in photosynthetic systems and organic materials.

  14. An application of coherence resonances in molecular transition identification

    International Nuclear Information System (INIS)

    Alekseev, V.A.; Salomaa, R.

    1978-01-01

    In Λ-type three level configurations having long lived lower levels extremely sharp two photon resonances occur. We want to draw attention to the use of these resonances for distinguishing the hyperfine splitting of lower and upper set of levels of molecular transitions. A new feature in the theoretical model is that the saturator and probe beams are coupled to both transitions rendering possible the appearance of interference between the resonances. (author)

  15. CLASSIFICATION AND QUANTITATIVE ANALYSIS OF GEOGRAPHIC ATROPHY JUNCTIONAL ZONE USING SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY.

    Science.gov (United States)

    Qu, Jinfeng; Velaga, Swetha Bindu; Hariri, Amir H; Nittala, Muneeswar Gupta; Sadda, Srinivas

    2017-08-22

    The junctional zone at the border of areas of geographic atrophy (GA) in eyes with nonneovascular age-related macular degeneration is an important target region for future therapeutic strategies. The goal of this study was to perform a detailed classification and quantitative characterization of the junctional zone using spectral domain optical coherence tomography. Spectral domain optical coherence tomography volume cube scans (Spectralis OCT, 1024 × 37, Automatic Real Time > 9) were obtained from 15 eyes of 11 patients with GA because of nonneovascular age-related macular degeneration. Volume optical coherence tomography data were imported into previously described validated grading software (3D-OCTOR), and manual segmentation of the retinal pigment epithelium (RPE) and photoreceptor layers was performed on all B-scans (total of 555). Retinal pigment epithelium and photoreceptor defect maps were produced for each case. The borders of the photoreceptor defect area and RPE defect area were delineated individually on separate annotation layers. The two outlines were then superimposed to compare the areas of overlap and nonoverlap. The perimeter of the RPE defect area was calculated by the software in pixels. The superimposed outline of the photoreceptor defect area and the RPE defect area was scrutinized to classify the overlap configuration of the junctional zone into one of three categories: Type 0, exact correspondence between the edge of the RPE defect and photoreceptor defect; Type 1, loss of photoreceptors outside and beyond the edge of the RPE defect; Type 2, preservation of photoreceptors beyond the edge of the RPE defect. The relative proportion of the various border configurations was expressed as a percentage of the perimeter of the RPE defect. Each configuration was then classified into four subgroups according to irregularity of the RPE band and the presence of debris. Fifteen eyes of 11 patients (mean age: 79.3 ± 4.3 years; range: 79-94 years) were

  16. Characteristics of time-domain optical coherence tomography profiles generated from blood-saline mixtures

    International Nuclear Information System (INIS)

    Popescu, Dan P; Sowa, Michael G

    2009-01-01

    Time-domain optical coherence tomography (OCT) employing a 1300 nm broadband source is used to study flowing blood-saline mixtures with blood concentration ranging from 20% to 100%. The study emphasizes the characteristics of the recorded OCT signal and its connection with the properties of the corresponding fluids. There are three regions with distinct properties along the compounded OCT profiles showing the signal dependence on depth. The recorded OCT signal increases for the first 80 μm into the fluid. The flow characteristics of the solution and the average spatial orientation of the blood cells can be extracted from this region of the OCT profile. In the second region, the OCT signal decreases with depth into the sample. An admixture of quasi-ballistic light detected after a single reflection and light recorded after undergoing multiple-scattering interactions with blood cells contributes to the signal recorded in this region. As a consequence, the attenuation of OCT signal with depth into the sample shows a weak dependence on the concentration of blood over this region. The third region starts at a depth of approximately 0.6 mm within all the studied blood-saline mixtures. OCT signal recorded from this region is dominated by light detected after multiple-scattering interactions with blood cells. This region of the OCT profile is characterized by a reduced rate of attenuation with depth compared to the rate recorded along the second region of the compounded profile. A geometrical method is used to estimate the contribution from multiple-scattered light to the OCT signal. The multiple-scattered component shows a parabolic dependence on blood concentration with a maximum contribution at a blood concentration of 55%.

  17. Adaptive optics parallel spectral domain optical coherence tomography for imaging the living retina

    Science.gov (United States)

    Zhang, Yan; Rha, Jungtae; Jonnal, Ravi S.; Miller, Donald T.

    2005-06-01

    Although optical coherence tomography (OCT) can axially resolve and detect reflections from individual cells, there are no reports of imaging cells in the living human retina using OCT. To supplement the axial resolution and sensitivity of OCT with the necessary lateral resolution and speed, we developed a novel spectral domain OCT (SD-OCT) camera based on a free-space parallel illumination architecture and equipped with adaptive optics (AO). Conventional flood illumination, also with AO, was integrated into the camera and provided confirmation of the focus position in the retina with an accuracy of ±10.3 μm. Short bursts of narrow B-scans (100x560 μm) of the living retina were subsequently acquired at 500 Hz during dynamic compensation (up to 14 Hz) that successfully corrected the most significant ocular aberrations across a dilated 6 mm pupil. Camera sensitivity (up to 94 dB) was sufficient for observing reflections from essentially all neural layers of the retina. Signal-to-noise of the detected reflection from the photoreceptor layer was highly sensitive to the level of cular aberrations and defocus with changes of 11.4 and 13.1 dB (single pass) observed when the ocular aberrations (astigmatism, 3rd order and higher) were corrected and when the focus was shifted by 200 μm (0.54 diopters) in the retina, respectively. The 3D resolution of the B-scans (3.0x3.0x5.7 μm) is the highest reported to date in the living human eye and was sufficient to observe the interface between the inner and outer segments of individual photoreceptor cells, resolved in both lateral and axial dimensions. However, high contrast speckle, which is intrinsic to OCT, was present throughout the AO parallel SD-OCT B-scans and obstructed correlating retinal reflections to cell-sized retinal structures.

  18. Comparison of two spectral domain optical coherence tomography devices for angle-closure assessment.

    Science.gov (United States)

    Quek, Desmond T; Narayanaswamy, Arun K; Tun, Tin A; Htoon, Hla M; Baskaran, Mani; Perera, Shamira A; Aung, Tin

    2012-08-03

    To compare two spectral domain optical coherence tomography (SD-OCT) devices for the identification of angle structures and the presence of angle closure. This was a prospective comparative study. Consecutive patients underwent gonioscopy and anterior segment imaging using two SD-OCT devices (iVue and Cirrus). Images were evaluated for the ability to detect angle structures such as Schwalbe's line (SL), trabecular meshwork (TM), Schlemm's canal (SC), and scleral spur (SS), and the presence of angle closure. Angle closure was defined as iris contact with the angle wall anterior to the SS on SD-OCT, and nonvisibility of the posterior TM on gonioscopy. Angle closure in an eye was defined as ≥two quadrants of closed angles. AC1 statistic was used to assess the agreement between devices. Of the 69 subjects studied (46.4% male, 84.1% Chinese, mean age 64.0 ± 10.5 years), 40 subjects (40 eyes, 58.0%) had angle closure on gonioscopy. The most identifiable structure on Cirrus SD-OCT was the SS (82.2%) and SL on iVue SD-OCT (74.5%). Angle closure was indeterminable in 14.5% and 50.7% of Cirrus and iVue scans (P gonioscopy was only fair (AC1 = 0.35 and 0.50 for Cirrus and iVue, respectively). It was more difficult to determine angle closure status with iVue compared with Cirrus SD-OCT. There was fair agreement between both devices with gonioscopy for identifying angle closure.

  19. En face spectral domain optical coherence tomography analysis of lamellar macular holes.

    Science.gov (United States)

    Clamp, Michael F; Wilkes, Geoff; Leis, Laura S; McDonald, H Richard; Johnson, Robert N; Jumper, J Michael; Fu, Arthur D; Cunningham, Emmett T; Stewart, Paul J; Haug, Sara J; Lujan, Brandon J

    2014-07-01

    To analyze the anatomical characteristics of lamellar macular holes using cross-sectional and en face spectral domain optical coherence tomography. Forty-two lamellar macular holes were retrospectively identified for analysis. The location, cross-sectional length, and area of lamellar holes were measured using B-scans and en face imaging. The presence of photoreceptor inner segment/outer segment disruption and the presence or absence of epiretinal membrane formation were recorded. Forty-two lamellar macular holes were identified. Intraretinal splitting occurred within the outer plexiform layer in 97.6% of eyes. The area of intraretinal splitting in lamellar holes did not correlate with visual acuity. Eyes with inner segment/outer segment disruption had significantly worse mean logMAR visual acuity (0.363 ± 0.169; Snellen = 20/46) than in eyes without inner segment/outer segment disruption (0.203 ± 0.124; Snellen = 20/32) (analysis of variance, P = 0.004). Epiretinal membrane was present in 34 of 42 eyes (81.0%). En face imaging allowed for consistent detection and quantification of intraretinal splitting within the outer plexiform layer in patients with lamellar macular holes, supporting the notion that an area of anatomical weakness exists within Henle's fiber layer, presumably at the synaptic connection of these fibers within the outer plexiform layer. However, the en face area of intraretinal splitting did not correlate with visual acuity, disruption of the inner segment/outer segment junction was associated with significantly worse visual acuity in patients with lamellar macular holes.

  20. Using spectral-domain optical coherence tomography to detect optic neuropathy in patients with craniosynostosis.

    Science.gov (United States)

    Dagi, Linda R; Tiedemann, Laura M; Heidary, Gena; Robson, Caroline D; Hall, Amber M; Zurakowski, David

    2014-12-01

    Detecting and monitoring optic neuropathy in patients with craniosynostosis is a clinical challenge due to limited cooperation, and subjective measures of visual function. The purpose of this study was to appraise the correlation of peripapillary retinal nerve fiber layer (RNFL) thickness measured by spectral-domain ocular coherence tomography (SD-OCT) with indication of optic neuropathy based on fundus examination. The medical records of all patients with craniosynostosis presenting for ophthalmic evaluation during 2013 were retrospectively reviewed. The following data were abstracted from the record: diagnosis, historical evidence of elevated intracranial pressure, current ophthalmic evaluation and visual field results, and current peripapillary RNFL thickness. A total of 54 patients were included (mean age, 10.6 years [range, 2.4-33.8 years]). Thirteen (24%) had evidence of optic neuropathy based on current fundus examination. Of these, 10 (77%) demonstrated either peripapillary RNFL elevation and papilledema or depression with optic atrophy. Sensitivity for detecting optic atrophy was 88%; for papilledema, 60%; and for either form of optic neuropathy, 77%. Specificity was 94%, 90%, and 83%, respectively. Kappa agreement was substantial for optic atrophy (κ = 0.73) and moderate for papilledema (κ = 0.39) and for either form of optic neuropathy (κ = 0.54). Logistic regression indicated that peripapillary RNFL thickness was predictive of optic neuropathy (P optic neuropathy than visual field testing (likelihood ratio = 10.02; P = 0.002). Sensitivity and specificity of logMAR visual acuity in detecting optic neuropathy were 15% and 95%, respectively. Peripapillary RNFL thickness measured by SD-OCT provides adjunctive evidence for identifying optic neuropathy in patients with craniosynostosis and appears more sensitive at detecting optic atrophy than papilledema. Copyright © 2014 American Association for Pediatric Ophthalmology and Strabismus. Published by

  1. Diabetic retinal pigment epitheliopathy: fundus autofluorescence and spectral-domain optical coherence tomography findings.

    Science.gov (United States)

    Kang, Eui Chun; Seo, Yuri; Byeon, Suk Ho

    2016-10-01

    To describe the characteristics of an unfamiliar disease entity, diabetic retinal pigment epitheliopathy (DRPE), using fundus autofluorescence (FAF) and spectral-domain optical coherence tomography (SD-OCT). This retrospective study included 17 eyes from 10 proliferative diabetic retinopathy (PDR) patients with granular hypo-autofluorescence and/or variable hyper-autofluorescence on FAF (DRPE group) and 17 eyes from 10 age- and sex-matched PDR patients without abnormal autofluorescence (PDR group). Eyes with diabetic macular edema were excluded. Visual acuity (VA), retinal thickness (RT), and choroidal thickness (CT) were compared between the groups. Eyes in the DRPE group had worse logMAR VA than eyes in the PDR group (0.369 ± 0.266 vs. 0.185 ± 0.119; P = 0.026). The thickness of the retinal pigment epithelium plus the inner segment/outer segment of the photoreceptors was reduced to a greater degree in the DRPE group than the PDR group (P retina showed no differences between the two groups. CT was significantly thicker in the DRPE group than in the PDR group (329.00 ± 33.76 vs. 225.62 ± 37.47 μm; P retina, and thicker choroid in comparison with eyes with PDR. Alterations of autofluorescence on FAF and changes in the outer retinal thickness and CT on SD-OCT can be helpful for differentiating DRPE in patients with PDR.

  2. Effect of ocular magnification on macular measurements made using spectral domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Mohana Kuppuswamy Parthasarathy

    2015-01-01

    Full Text Available Aim: The aim of the present study was to study the effect of ocular magnification on macular measurements made using spectral domain optical coherence tomography (OCT. Materials and Methods: One hundred and fifty-one subjects were included from the normative study of foveal morphology carried out at our hospital. Subjects underwent comprehensive eye examination and macular scanning using Cirrus high-definition OCT and axial length (AXL measurement. Macular cube 512 × 128 scan protocol was used for scanning the macula. Automated measurements of the fovea namely foveal diameter, foveal slope (lateral measurements and foveal depth (axial measurement were taken. A correction factor for ocular magnification was done using the formula t = p × q × s, where "t0" is the corrected measurement, "p" is the magnification of OCT, "q0" is the ocular magnification, and "s" is the measurement on OCT without correction. The difference between corrected and uncorrected measurements was evaluated for statistical significance. Results: Mean AXL was 22.95 ± 0.78 mm. Refractive error ranged from −3D to +4D. Mean difference between measured and corrected foveal diameter, slope and depth was 166.05 ± 95.37 ΅m (P < 0.001, 0.81° ± 0.53° (P < 0.001 and 0.05 ± 0.49 ΅m (P = 0.178 respectively. AXL lesser than the OCT calibrated value of 24.46 mm showed an increased foveal diameter (r = 0.961, P < 0.001 and a reduced foveal slope (r = −0.863, P < 0.001 than the corrected value. Conclusion: Lateral measurements made on OCT varied with AXL s other than the OCT calibrated value of 24.46 mm. Therefore, to estimate the actual dimensions of a retinal lesion using OCT, especially lateral dimensions, we recommend correction for the ocular magnification factor.

  3. The hand-hold polarization-sensitive spectral domain optical coherence and its applications

    Science.gov (United States)

    Liu, Hao; Gao, Wanrong

    2017-08-01

    The polarization-sensitive spectral domain optical coherence tomography (PSOCT) has the advantages of being able to measure the polarization properties of samples, such as phase-retardation, diattenuation, depolarization, and optical axis orientation, providing a contrast to identify the diseased area and normal area in tissues in PSOCT images. Conventionally, the sample arm of PSOCT is fixed on the stage where biomedical tissues or models is placed, and the OCT images is acquired by scanning with a galvanometer-based mirror. To be applied in the practical diagnosis, a promising way is to design a hand-held device. To this end, it is required that probe is assembled with a small volume to allow for comprehensively imaging large tissues areas at a microscopic scale, and is available to move on different samples to be acquired quickly with negligible motion artifacts. Meanwhile, the probe should be manufactured wih well stability to avoid system jitter error while it is used to detect the biological tissues in vivo. In this work, a design of a hand-hold fiber-based PSOCT is described. The device is of the size of 10 cm (length) × 8 cm (width) × 6 cm (height). Both the axial resolution and the imaging depth of the system are measured and were approximately 7 μm and 2.5 mm in air, respectively, which are in good agreement with the theoretical predictions. The A-scan rate of the system is 70 kHz. The structure is compact and all the components are fixed on the shell to reduce the motion artifact, resulting in a great stability on measuring the tissues in vivo. The cross sectional images of ex vivo chicken breast, ex vivo pork cartilage and in vivo forearm skin of human wolunteer are presented to demonstrate the capability of the system.

  4. Segmentation of the geographic atrophy in spectral-domain optical coherence tomography and fundus autofluorescence images.

    Science.gov (United States)

    Hu, Zhihong; Medioni, Gerard G; Hernandez, Matthias; Hariri, Amirhossein; Wu, Xiaodong; Sadda, Srinivas R

    2013-12-30

    Geographic atrophy (GA) is the atrophic late-stage manifestation of age-related macular degeneration (AMD), which may result in severe vision loss and blindness. The purpose of this study was to develop a reliable, effective approach for GA segmentation in both spectral-domain optical coherence tomography (SD-OCT) and fundus autofluorescence (FAF) images using a level set-based approach and to compare the segmentation performance in the two modalities. To identify GA regions in SD-OCT images, three retinal surfaces were first segmented in volumetric SD-OCT images using a double-surface graph search scheme. A two-dimensional (2-D) partial OCT projection image was created from the segmented choroid layer. A level set approach was applied to segment the GA in the partial OCT projection image. In addition, the algorithm was applied to FAF images for the GA segmentation. Twenty randomly chosen macular SD-OCT (Zeiss Cirrus) volumes and 20 corresponding FAF (Heidelberg Spectralis) images were obtained from 20 subjects with GA. The algorithm-defined GA region was compared with consensus manual delineation performed by certified graders. The mean Dice similarity coefficients (DSC) between the algorithm- and manually defined GA regions were 0.87 ± 0.09 in partial OCT projection images and 0.89 ± 0.07 in registered FAF images. The area correlations between them were 0.93 (P segment GA regions in both SD-OCT and FAF images. This approach demonstrated good agreement between the algorithm- and manually defined GA regions within each single modality. The GA segmentation in FAF images performed better than in partial OCT projection images. Across the two modalities, the GA segmentation presented reasonable agreement.

  5. Retinal ganglion cell complex changes using spectral domain optical coherence tomography in diabetic patients without retinopathy

    Directory of Open Access Journals (Sweden)

    Ahmed I. Hegazy

    2017-03-01

    Full Text Available AIM: To assess the ganglion cell complex (GCC thickness in diabetic eyes without retinopathy. METHODS: Two groups included 45 diabetic eyes without retinopathy and 21 non diabetic eyes. All subjects underwent full medical and ophthalmological history, full ophthalmological examination, measuring GCC thickness and central foveal thickness (CFT using the RTVue® spectral domain-optical coherence tomography (SD-OCT, and HbA1C level. RESULTS: GCC focal loss volume (FLV% was significantly more in diabetic eyes (22.2% below normal than normal eyes (P=0.024. No statistically significant difference was found between the diabetic group and the control group regarding GCC global loss volume (GLV% (P=0.160. CFT was positively correlated to the average, superior and inferior GCC (P=0.001, 0.000 and 0.001 respectively and negatively correlated to GLV% and FLV% (P=0.002 and 0.031 respectively in diabetic eyes. C/D ratio in diabetic eyes was negatively correlated to average, superior and inferior GCC (P=0.015, 0.007 and 0.017 respectively. The FLV% was negatively correlated to the refraction and level of HbA1c (P=0.019 and 0.013 respectively and positively correlated to the best corrected visual acuity (BCVA in logMAR in diabetic group (P=0.004. CONCLUSION: Significant GCC thinning in diabetes predates retinal vasculopathy, which is mainly focal rather than diffuse. It has no preference to either the superior or inferior halves of the macula. Increase of myopic error is significantly accompanied with increased focal GCC loss. GCC loss is accompanied with increased C/D ratio in diabetic eyes.

  6. Development of a low-cost, 11 µm spectral domain optical coherence tomography surface profilometry prototype

    Science.gov (United States)

    Suliali, Nyasha J.; Baricholo, Peter; Neethling, Pieter H.; Rohwer, Erich G.

    2017-06-01

    A spectral-domain Optical Coherence Tomography (OCT) surface profilometry prototype has been developed for the purpose of surface metrology of optical elements. The prototype consists of a light source, spectral interferometer, sample fixture and software currently running on Microsoft® Windows platforms. In this system, a broadband light emitting diode beam is focused into a Michelson interferometer with a plane mirror as its sample fixture. At the interferometer output, spectral interferograms of broadband sources were measured using a Czerny-Turner mount monochromator with a 2048-element complementary metal oxide semiconductor linear array as the detector. The software performs importation and interpolation of interferometer spectra to pre-condition the data for image computation. One dimensional axial OCT images were computed by Fourier transformation of the measured spectra. A first reflection surface profilometry (FRSP) algorithm was then formulated to perform imaging of step-function-surfaced samples. The algorithm re-constructs two dimensional colour-scaled slice images by concatenation of 21 and 13 axial scans to form a 10 mm and 3.0 mm slice respectively. Measured spectral interferograms, computed interference fringe signals and depth reflectivity profiles were comparable to simulations and correlated to displacements of a single reflector linearly translated about the arm null-mismatch point. Surface profile images of a double-step-function-surfaced sample, embedded with inclination and crack detail were plotted with an axial resolution of 11 μm. The surface shape, defects and misalignment relative to the incident beam were detected to the order of a micron, confirming high resolution of the developed system as compared to electro-mechanical surface profilometry techniques.

  7. Frequency doubling technique perimetry and spectral domain optical coherence tomography in patients with early glaucoma.

    Science.gov (United States)

    Horn, F K; Mardin, C Y; Bendschneider, D; Jünemann, A G; Adler, W; Tornow, R P

    2011-01-01

    To assess the combined diagnostic power of frequency-doubling technique (FDT)-perimetry and retinal nerve fibre layer (RNFL) thickness measurements with spectral domain optical coherence tomography (SDOCT). The study included 330 experienced participants in five age-related groups: 77 'preperimetric' open-angle glaucoma (OAG) patients, 52 'early' OAG, 50 'moderate' OAG, 54 ocular hypertensive patients, and 97 healthy subjects. For glaucoma assessment in all subjects conventional perimetry, evaluation of fundus photographs, FDT-perimetry and RNFL thickness measurement with SDOCT was done. Glaucomatous visual field defects were classified using the Glaucoma Staging System. FDT evaluation used a published method with casewise calculation of an 'FDT-score', including all missed localized probability levels. SDOCT evaluation used mean RNFL thickness and a new individual SDOCT-score considering normal confidence limits in 32 sectors of a peripapillary circular scan. To examine the joined value of both methods a combined score was introduced. Significance of the difference between Receiver-operating-characteristic (ROC) curves was calculated for a specificity of 96%. Sensitivity in the preperimetric glaucoma group was 44% for SDOCT-score, 25% for FDT-score, and 44% for combined score, in the early glaucoma group 83, 81, and 89%, respectively, and in the moderate glaucoma group 94, 94, and 98%, respectively, all at a specificity of 96%. ROC performance of the newly developed combined score is significantly above single ROC curves of FDT-score in preperimetric and early OAG and above RNFL thickness in moderate OAG. Combination of function and morphology by using the FDT-score and the SDOCT-score performs equal or even better than each single method alone.

  8. Reflectivity and thickness analysis of epiretinal membranes using spectral-domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Ajay E. Kuriyan

    2016-01-01

    Full Text Available AIM: To compare thickness and reflectivity spectral domain optical coherence tomography (SD-OCT findings in patients with idiopathic epiretinal membranes (ERMs, before and after ERM peeling surgery, with normal controls. METHODS: A retrospective study analyzed SD-OCTs of eyes with ERMs undergoing ERM peeling surgery by one surgeon from 2008 to 2010 and normal control eyes. SD-OCTs were analyzed using a customized algorithm to measure reflectivity and thickness. The relationship between the SD-OCT findings and best corrected visual acuity (BCVA outcomes was also studied. RESULTS: Thirty-four ERM eyes and 12 normal eyes were identified. Preoperative eyes had high reflectivity and thickness of the group of layers from the internal limiting membrane (ILM to the retinal pigment epithelium (RPE and the group of layers from the ILM to the external limiting membrane (ELM. The values of reflectivity of these two groups of layers decreased postoperatively, but were still higher than normal eyes. In contrast, preoperative eyes had lower reflectivity of two 10×15 pixel regions of interest (ROIs incorporating: 1 ELM + outer nuclear layer (ONL and 2 photoreceptor layer (PRL + RPE, compared to controls. The values of reflectivity of these ROIs increased postoperatively, but were still lower than normal controls. A larger improvement in BCVA postoperatively was correlated with a greater degree of abnormal preoperative reflectivity and thickness findings. CONCLUSION: Quantitative differences in reflectivity and thickness between preoperative, postoperative, and normal SD-OCTs allow assessment of changes in the retina secondary to ERM. Our study identified hyperreflective inner retina changes and hyporeflective outer retina changes in patients with ERMs. SD-OCT quantitative measures of reflectivity and/or thickness of specific groups of retinal layers and/or ROIs correlate with improvement in BCVA.

  9. Clinical manifestations of optic pit maculopathy as demonstrated by spectral domain optical coherence tomography.

    Science.gov (United States)

    Tzu, Jonathan H; Flynn, Harry W; Berrocal, Audina M; Smiddy, William E; Murray, Timothy G; Fisher, Yale L

    2013-01-01

    The purpose of this retrospective study was to evaluate the characteristic features, including spectral-domain optical coherence tomography (SD-OCT), clinical course, and outcome of treatment if given for patients with optic disc pit maculopathy. We investigated a consecutive series of patients with a diagnosis of optic pit maculopathy treated between 2001 and 2012 at the Bascom Palmer Eye Institute. Patients were divided into two main groups, ie, patients who were observed without surgery and patients who received surgical intervention. The main outcome measures were presenting and final visual acuity, and changes in SD-OCT imaging were recorded. Other data including age, gender, eye, age of onset, length of follow-up, location of optic pit, and location of fluid by OCT were also recorded. On OCT, 67% (12/18) of the eyes showed schisis-like cavities, 22% (4/18) had only subretinal fluid, and 17% (3/18) had only a schisis-like cavity without subretinal fluid. In the patients managed by observation, visual acuity was ≥20/200 in 6/8 eyes initially and 6/8 eyes at last follow-up. Ten of 18 patients received either focal laser, surgery or both. Six of 10 eyes undergoing surgery had initial visual acuity ≥ 20/200, and 8 of 10 eyes undergoing surgery had a visual acuity of ≥20/200 at last follow-up. In this study, many eyes were observed and remained stable during follow-up. In eyes with reduced vision, surgical intervention produced variable outcomes, and persistent intraretinal/subretinal fluid was a common occurrence.

  10. Transient Evolutional Dynamics of Quantum-Dot Molecular Phase Coherence for Sensitive Optical Switching

    Science.gov (United States)

    Shen, Jian Qi; Gu, Jing

    2018-04-01

    Atomic phase coherence (quantum interference) in a multilevel atomic gas exhibits a number of interesting phenomena. Such an atomic quantum coherence effect can be generalized to a quantum-dot molecular dielectric. Two quantum dots form a quantum-dot molecule, which can be described by a three-level Λ-configuration model { |0> ,|1> ,|2> } , i.e., the ground state of the molecule is the lower level |0> and the highly degenerate electronic states in the two quantum dots are the two upper levels |1> ,|2> . The electromagnetic characteristics due to the |0>-|1> transition can be controllably manipulated by a tunable gate voltage (control field) that drives the |2>-|1> transition. When the gate voltage is switched on, the quantum-dot molecular state can evolve from one steady state (i.e., |0>-|1> two-level dressed state) to another steady state (i.e., three-level coherent-population-trapping state). In this process, the electromagnetic characteristics of a quantum-dot molecular dielectric, which is modified by the gate voltage, will also evolve. In this study, the transient evolutional behavior of the susceptibility of a quantum-dot molecular thin film and its reflection spectrum are treated by using the density matrix formulation of the multilevel systems. The present field-tunable and frequency-sensitive electromagnetic characteristics of a quantum-dot molecular thin film, which are sensitive to the applied gate voltage, can be utilized to design optical switching devices.

  11. Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors.

    Science.gov (United States)

    Nishimura, Tamako; Morone, Nobuhiro; Suetsugu, Shiro

    2018-04-17

    Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  12. A domain specific language for performance portable molecular dynamics algorithms

    Science.gov (United States)

    Saunders, William Robert; Grant, James; Müller, Eike Hermann

    2018-03-01

    Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

  13. Automated retinal fovea type distinction in spectral-domain optical coherence tomography of retinal vein occlusion

    Science.gov (United States)

    Wu, Jing; Waldstein, Sebastian M.; Gerendas, Bianca S.; Langs, Georg; Simader, Christian; Schmidt-Erfurth, Ursula

    2015-03-01

    Spectral-domain Optical Coherence Tomography (SD-OCT) is a non-invasive modality for acquiring high- resolution, three-dimensional (3D) cross-sectional volumetric images of the retina and the subretinal layers. SD-OCT also allows the detailed imaging of retinal pathology, aiding clinicians in the diagnosis of sight degrading diseases such as age-related macular degeneration (AMD), glaucoma and retinal vein occlusion (RVO). Disease diagnosis, assessment, and treatment will require a patient to undergo multiple OCT scans, possibly using multiple scanners, to accurately and precisely gauge disease activity, progression and treatment success. However, cross-vendor imaging and patient movement may result in poor scan spatial correlation potentially leading to incorrect diagnosis or treatment analysis. The retinal fovea is the location of the highest visual acuity and is present in all patients, thus it is critical to vision and highly suitable for use as a primary landmark for cross-vendor/cross-patient registration for precise comparison of disease states. However, the location of the fovea in diseased eyes is extremely challenging to locate due to varying appearance and the presence of retinal layer destroying pathology. Thus categorising and detecting the fovea type is an important prior stage to automatically computing the fovea position. Presented here is an automated cross-vendor method for fovea distinction in 3D SD-OCT scans of patients suffering from RVO, categorising scans into three distinct types. OCT scans are preprocessed by motion correction and noise filing followed by segmentation using a kernel graph-cut approach. A statistically derived mask is applied to the resulting scan creating an ROI around the probable fovea location from which the uppermost retinal surface is delineated. For a normal appearance retina, minimisation to zero thickness is computed using the top two retinal surfaces. 3D local minima detection and layer thickness analysis are used

  14. Development of Fourier domain optical coherence tomography for applications in developmental biology

    Science.gov (United States)

    Davis, Anjul Maheshwari

    Developmental biology is a field in which explorations are made to answer how an organism transforms from a single cell to a complex system made up of trillions of highly organized and highly specified cells. This field, however, is not just for discovery, it is crucial for unlocking factors that lead to diseases, defects, or malformations. The one key ingredient that contributes to the success of studies in developmental biology is the technology that is available for use. Optical coherence tomography (OCT) is one such technology. OCT fills a niche between the high resolution of confocal microscopy and deep imaging penetration of ultrasound. Developmental studies of the chicken embryo heart are of great interest. Studies in mature hearts, zebrafish animal models, and to a more limited degree chicken embryos, indicate a relationship between blood flow and development. It is believed that at the earliest stages, when the heart is still a tube, the purpose of blood flow is not for convective transport of oxygen, nutrients and waster, bur rather to induce shear-related gene expressions to induce further development. Yet, to this date, the simple question of "what makes blood flow?" has not been answered. This is mainly due limited availability to adequate imaging and blood flow measurement tools. Earlier work has demonstrated the potential of OCT for use in studying chicken embryo heart development, however quantitative measurement techniques still needed to be developed. In this dissertation I present technological developments I have made towards building an OCT system to study chick embryo heart development. I will describe: (1) a swept-source OCT with extended imaging depth; (2) a spectral domain OCT system for non-invasive small animal imaging; (3) Doppler flow imaging and techniques for quantitative blood flow measurement in living chicken embryos; and (4) application of the OCT system that was developed in the Specific Aims 2-5 to test hypotheses generated by a

  15. Normative data for macular thickness by high-definition spectral-domain optical coherence tomography (spectralis).

    Science.gov (United States)

    Grover, Sandeep; Murthy, Ravi K; Brar, Vikram S; Chalam, Kakarla V

    2009-08-01

    To establish normative data for the macular thickness by spectral-domain optical coherence tomography (SD-OCT) in subjects with no known retinal disease. Prospective, observational study in an academic institutional setting. Fifty subjects (age range, 20 to 84 years) with no known retinal disease, best-corrected visual acuity 20/20, and normal intraocular pressure were enrolled. The subjects were divided into 3 age groups: group 1 included subjects 20 to 40 years of age; group 2 included subjects 41 to 60 years of age; and group 3 included subjects 61 years of age and older. All subjects underwent a complete ophthalmologic examination to rule out any retinal diseases or glaucoma. All the OCT scans were performed by a single operator, and data obtained from the right eyes were analyzed by default, unless the right eye did not meet the inclusion criteria, and then data from left eyes were analyzed (n = 4). Central point thickness (CPT) and retinal thickness (RT) in 9 Early Treatment Diabetic Retinopathy Study (ETDRS) subfields, including central subfield (CSF), were analyzed. Statistical analyses were carried out using the analysis of variance. Overall, the mean CPT was 227.3 +/- 23.2 microm, and mean CSF was 270.2 +/- 22.5 microm. Among the ETDRS subfields, the outer nasal quadrant had the maximum thickness (mean +/- standard deviation, 339.5 +/- 16.9 microm). The RT did not show significant difference with age (P = .62) or with gender (P = .1). However, there was a suggestion of significant difference in RT of Black subjects as compared with White subjects (P = .007) in the present study. Normative values for macular thickness in otherwise healthy eyes were measured to be 227.3 microm (CPT) and 270.2 microm (CSF) using commercially available Spectralis SD-OCT. Based on the data, the present study proposes the guidelines for normal CSF thickness to be 315 microm for future studies using macular thickness measurements with Spectralis SD-OCT (Heidelberg Engineering

  16. Three-dimensional mapping of peripapillary retinal layers using a spectral domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Hashmani N

    2017-12-01

    Full Text Available Nauman Hashmani, Sharif Hashmani Department of Ophthalmology, Hashmanis Hospital, Karachi, Pakistan Purpose: To map and view the effects of age, gender, and axial length on seven individual retinal layers around the optic nerve head (ONH.Methods: We scanned 242 healthy patients using the Spectralis spectral domain optical coherence tomography in an outpatient setting. The layers were observed on the Early Treatment Diabetic Retinopathy Study sectors using the standard Spectralis Family Acquisition Module 6.0.11.0. The center was the ONH, the inner circle (IC was 1–3 mm away, and the outer circle (OC was 3–6 mm away. The seven layers were retinal nerve fiber layer (RNFL, ganglion cell layer (GCL, inner plexiform layer (IPL, inner nuclear layer (INL, outer plexiform layer (OPL, outer nuclear layer (ONL, and retinal pigment epithelium (RPE. Additionally, we calculated the mean thickness of two combined layers: inner retinal layer (IRL and photoreceptor layer (PL. Finally, we measured the mean of the total retinal thickness (TRT.Results: The TRT was highest at the inferior end in the IC and at the nasal end in the OC. The RPE (p<0.001 and PL (p<0.001 were thicker in males; however, the IRL (p=0.015 was thicker in females. We found that the RNFL (p<0.001, r=0.139, GCL (p<0.001, r=0.116, IPL (p=0.016, r=0.059, INL (p<0.001, r=0.104, OPL (p=0.009, r=0.064, ONL (p<0.001, r=0.157, RPE (p=0.001, r=0.079, IRL (p<0.001, r=0.190, PL (p=0.030, r=0.053, and TRT (p<0.001, r=0.191 correlated negatively with age. The axial length significantly and negatively correlated at the GCL (p=0.003, r=0.093, IPL (p=0.020, r=0.072, INL (p=0.018, r=0.073, ONL (p<0.001, r=0.110, IRL (p=0.003, r=0.092, and TRT (p=0.003, r=0.094. We found poor reproducibility in the IC; however, this was excellent in the OC.Conclusion: We found significant differences in layers according to age, gender, and axial length. Additionally, reproducibility can be improved by altering the

  17. The Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Ferguson, Ken R. [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Department of Applied Physics, Stanford University, 348 Via Pueblo, Stanford, CA 94305 (United States); Bucher, Maximilian; Bozek, John D.; Carron, Sebastian; Castagna, Jean-Charles [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Coffee, Ryan [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Curiel, G. Ivan; Holmes, Michael; Krzywinski, Jacek; Messerschmidt, Marc; Minitti, Michael; Mitra, Ankush; Moeller, Stefan; Noonan, Peter; Osipov, Timur; Schorb, Sebastian; Swiggers, Michele; Wallace, Alexander; Yin, Jing [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Bostedt, Christoph, E-mail: bostedt@slac.stanford.edu [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States)

    2015-04-17

    A description of the Atomic, Molecular and Optical Sciences (AMO) instrument at the Linac Coherent Light Source is presented. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument. The Atomic, Molecular and Optical Science (AMO) instrument at the Linac Coherent Light Source (LCLS) provides a tight soft X-ray focus into one of three experimental endstations. The flexible instrument design is optimized for studying a wide variety of phenomena requiring peak intensity. There is a suite of spectrometers and two photon area detectors available. An optional mirror-based split-and-delay unit can be used for X-ray pump–probe experiments. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument.

  18. Coherent Rabi oscillations in a molecular system and sub-diffraction-limited pattern generation

    International Nuclear Information System (INIS)

    Liao, Zeyang; Al-Amri, M; Zubairy, M Suhail

    2015-01-01

    The resolution of a photolithography and optical imaging system is restricted by the diffraction limit. Coherent Rabi oscillations have been shown to be able to overcome the diffraction limit in a simple two-level atomic system (Z Liao, M Al-amri, and M S Zubairy 2010 Phys. Rev. Lett. 105 183601). In this paper, we numerically calculate the wave packet dynamics of a molecular system interacting with an ultrashort laser pulse and show that coherent Rabi oscillations in a molecular system are also possible. Moreover, a sub-diffraction-limited pattern can be generated in this system by introducing spatially modulated Rabi oscillations. We also discuss several techniques to improve the visibility of the sub-diffraction-limited pattern. Our result may have important applications in super-resolution optical lithography and optical imaging. (paper)

  19. Precise Control of Molecular Dynamics with a Femtosecond Frequency Comb - A Weak Field Route to Strong Field Coherent Control

    OpenAIRE

    Pe'er, Avi; Shapiro, Evgeny A.; Stowe, Matthew C.; Shapiro, Moshe; Ye, Jun

    2006-01-01

    We present a general and highly efficient scheme for performing narrow-band Raman transitions between molecular vibrational levels using a coherent train of weak pump-dump pairs of shaped ultrashort pulses. The use of weak pulses permits an analytic description within the framework of coherent control in the perturbative regime, while coherent accumulation of many pulse pairs enables near unity transfer efficiency with a high spectral selectivity, thus forming a powerful combination of pump-d...

  20. Biodiversity: molecular biological domains, symbiosis and kingdom origins

    Science.gov (United States)

    Margulis, L.

    1992-01-01

    The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still

  1. Molecular Insights into the Transmembrane Domain of the Thyrotropin Receptor.

    Directory of Open Access Journals (Sweden)

    Vanessa Chantreau

    Full Text Available The thyrotropin receptor (TSHR is a G protein-coupled receptor (GPCR that is member of the leucine-rich repeat subfamily (LGR. In the absence of crystal structure, the success of rational design of ligands targeting the receptor internal cavity depends on the quality of the TSHR models built. In this subfamily, transmembrane helices (TM 2 and 5 are characterized by the absence of proline compared to most receptors, raising the question of the structural conformation of these helices. To gain insight into the structural properties of these helices, we carried out bioinformatics and experimental studies. Evolutionary analysis of the LGR family revealed a deletion in TM5 but provided no information on TM2. Wild type residues at positions 2.58, 2.59 or 2.60 in TM2 and/or at position 5.50 in TM5 were substituted to proline. Depending on the position of the proline substitution, different effects were observed on membrane expression, glycosylation, constitutive cAMP activity and responses to thyrotropin. Only proline substitution at position 2.59 maintained complex glycosylation and high membrane expression, supporting occurrence of a bulged TM2. The TSHR transmembrane domain was modeled by homology with the orexin 2 receptor, using a protocol that forced the deletion of one residue in the TM5 bulge of the template. The stability of the model was assessed by molecular dynamics simulations. TM5 straightened during the equilibration phase and was stable for the remainder of the simulations. Our data support a structural model of the TSHR transmembrane domain with a bulged TM2 and a straight TM5 that is specific of glycoprotein hormone receptors.

  2. PREVALENCE OF FOVEOLAR LUCENCY WITH DIFFERENT GAS TAMPONADES IN SURGICALLY CLOSED MACULAR HOLES ASSESSED BY SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY.

    Science.gov (United States)

    Zarranz-Ventura, Javier; Ellabban, Abdallah A; Sim, Dawn A; Keane, Pearse A; Kirkpatrick, James N; Sallam, Ahmed A B

    2017-07-07

    To evaluate the prevalence of foveolar lucency (FL) in surgically closed macular holes by spectral domain optical coherence tomography. One hundred forty-two eyes of 132 patients underwent pars plana vitrectomy, internal limiting membrane peeling, and gas tamponade in a 60-month time frame. Anatomical success and FL rates assessed by spectral domain optical coherence tomography, mean preoperative, and postoperative best-measured visual acuity and surgical details were retrospectively analyzed. Spectral domain optical coherence tomography confirmed closed holes with FL in 33.7% (34/101) of eyes at 1 month, 7.3% (9/123) at 3 months, 4.6% (6/129) at 6 months, and 3% (4/133) at 12 months. Prevalence of FL in closed holes at Month 1 was lower in C3F8-treated eyes (9.5%, 2/21) compared with C2F6 (40.9%, 18/44, P = 0.03) and SF6-treated eyes (38.9%, 14/36, P = 0.05). No differences were observed at Month 3. No differences in best-measured visual acuity change were observed between closed holes with or without FL at Month 1 (-0.14 ± 0.19 vs. -0.11 ± 0.23, P = 0.48) or any of the other time points. Temporary FL is a highly prevalent feature in successfully closed macular holes. Eyes treated with C3F8 gas had lower rates of FL at Month 1 than C2F6 and SF6-treated eyes. The presence of FL in closed holes does not seem to have any effect on the visual outcomes.

  3. Towards spectral-domain optical coherence tomography on a silicon chip

    NARCIS (Netherlands)

    Akça, B.I.; Worhoff, Kerstin; Nguyen, V.D.; Kalkman, J.; van Leeuwen, Ton; de Ridder, R.M.; Pollnau, Markus

    Optical coherence tomography (OCT) is a widely used optical imaging technology, particularly in the medical field, since it can provide non-invasive, sub-micrometer resolution diagnostic images of tissue. Current OCT systems contain optical fibers and free-space optical components which make these

  4. Effects of absorption on coherence domain path length resolved dynamic light scattering in the diffuse regime

    NARCIS (Netherlands)

    Petoukhova, A. L.; Steenbergen, W.; van Leeuwen, T. G.; de Mul, F. F. M.

    2002-01-01

    A low coherence Mach-Zehnder interferometer is developed for path length resolved dynamic light scattering in highly turbid media. The path length distribution of multiply scattered photons in Intralipid is changed by the addition of absorbing dyes. Path length distributions obtained for various

  5. Effects of absorption on coherence domain path length resolved dynamic light scattering in the diffuse regime

    NARCIS (Netherlands)

    Petoukhova, Anna; Steenbergen, Wiendelt; van Leeuwen, Ton; de Mul, F.F.M.

    2002-01-01

    A low coherence Mach–Zehnder interferometer is developed for path length resolved dynamic light scattering in highly turbid media. The path length distribution of multiply scatteredphotons in Intralipid is changed by the addition of absorbing dyes. Path length distributions obtained for various

  6. Enhancement of phase-conjugate reflectivity using Zeeman coherence in highly degenerate molecular systems

    International Nuclear Information System (INIS)

    Mukherjee, Nandini

    2010-01-01

    A comprehensive theoretical analysis is developed for the vectorial phase conjugation using resonant four-wave mixing (FWM) in a highly degenerate rotational vibrational molecular system. The dynamic Stark shifts, saturation, and Doppler broadening are included for a realistic analysis. It is shown that the electromagnetically induced multilevel coherence controls the nonlinear wave mixing yielding interesting results for the phase conjugate (PC) reflectivity. It turns out that the efficiency of the PC reflectivity is decided by the relative phase of the Zeeman coherence and the population grating. When these two contributions are aligned in phase by a small detuning of the pump frequency, a large PC reflectivity (∼20%) is obtained with moderate pump intensity (∼500 mW/cm 2 ).

  7. Nanometer-size magnetic domains and coherent magnetization reversal in a giant exchange-bias system

    DEFF Research Database (Denmark)

    Dufour, C.; Fitzsimmons, M. R.; Borchers, J. A.

    2011-01-01

    The role of magnetic domains and domain walls in exchange bias has stimulated much contemporary deliberation. Here we present compelling evidence obtained with small-angle scattering of unpolarized- and polarized-neutron beams that magnetization reversal occurs via formation of 10-100s nm-sized m...... to that of structural defects at the seed-layer-superlattice interface....

  8. Development of an polarization sensitive Fourier domain optical coherence tomography and it utilization on the Mueller matrix determination

    International Nuclear Information System (INIS)

    Raele, Marcus Paulo

    2009-01-01

    This study approached theoretical and experimental aspects related with the development of a polarization sensitive, Fourier domain, optical coherence tomography system (PS-FD-OCT) and its utilization on the Mueller Matrix determination. This work began with a bibliographic revision, which describes since the early studies to the actual state of the art of the technique. The mathematical formalism of Fourier domain low coherence interferometry and light polarization was performed as well. Studies based on numerical simulations, of three different algorithm types, responsible to recover the scattering profile, were done. The implemented algorithms were: Direct Fourier Transform, Interpolation and zero-filling. By the end of the simulation study, was possible to conclude that the algorithm zero-filling 2N presented better characteristics when compared with the others. In the experimental part, firstly different OCT setups were assembled and measurements were done in order to verify aspects related with the theory. Then, using a polymeric sample, birefringence images were performed, which allowed determining the sample birefringence quantitatively. Finally, images taken of different polarization states were collected, and through then images related with the Mueller Matrix elements were calculated, which were analyzed individually. (author)

  9. WIDEFIELD SPECTRAL-DOMAIN OPTICAL COHERENCE TOMOGRAPHY IMAGING OF PERIPHERAL ROUND RETINAL HOLES WITH OR WITHOUT RETINAL DETACHMENT.

    Science.gov (United States)

    Casswell, Edward J; Abou Ltaif, Sleiman; Carr, Thomas; Keane, Pearse A; Charteris, David G; Wickham, Louisa

    2018-03-02

    To describe the widefield spectral-domain optical coherence tomography features of peripheral round retinal holes, with or without associated retinal detachment (RD). Retrospective, observational study of 28 eyes with peripheral round retinal holes, with and without RD. Patients underwent imaging with a widefield 50-degree spectral-domain optical coherence tomography (Heidelberg Engineering, Germany) and Optos ultra-widefield imaging systems (Optos, United Kingdom). Vitreous attachment at the site of the retinal hole was detected in 27/28 (96.4%) cases. Cases were split into three groups: RHs with RD (n = 12); RHs with subretinal fluid (n = 5), and flat RHs (n = 11), with minimal or no subretinal fluid. 91.6% retinal holes associated with subretinal fluid or RD had vitreous attachment at the site of the hole. Eighty percent had vitreous attachment at both edges of the retinal hole, in a U-shape configuration, which appeared to exert traction. By contrast, flat retinal holes had visible vitreous attachment only at one edge of the retinal hole in 45.4%. Vitreous attachment was commonly seen at the site of round retinal holes. Vitreous attachment at both edges of the retinal hole in a U-shape configuration was more commonly seen at holes associated with subretinal fluid or RD.

  10. A joint estimation detection of Glaucoma progression in 3D spectral domain optical coherence tomography optic nerve head images

    Science.gov (United States)

    Belghith, Akram; Bowd, Christopher; Weinreb, Robert N.; Zangwill, Linda M.

    2014-03-01

    Glaucoma is an ocular disease characterized by distinctive changes in the optic nerve head (ONH) and visual field. Glaucoma can strike without symptoms and causes blindness if it remains without treatment. Therefore, early disease detection is important so that treatment can be initiated and blindness prevented. In this context, important advances in technology for non-invasive imaging of the eye have been made providing quantitative tools to measure structural changes in ONH topography, an essential element for glaucoma detection and monitoring. 3D spectral domain optical coherence tomography (SD-OCT), an optical imaging technique, has been commonly used to discriminate glaucomatous from healthy subjects. In this paper, we present a new framework for detection of glaucoma progression using 3D SD-OCT images. In contrast to previous works that the retinal nerve fiber layer (RNFL) thickness measurement provided by commercially available spectral-domain optical coherence tomograph, we consider the whole 3D volume for change detection. To integrate a priori knowledge and in particular the spatial voxel dependency in the change detection map, we propose the use of the Markov Random Field to handle a such dependency. To accommodate the presence of false positive detection, the estimated change detection map is then used to classify a 3D SDOCT image into the "non-progressing" and "progressing" glaucoma classes, based on a fuzzy logic classifier. We compared the diagnostic performance of the proposed framework to existing methods of progression detection.

  11. Microscope Integrated Intraoperative Spectral Domain Optical Coherence Tomography for Cataract Surgery: Uses and Applications.

    Science.gov (United States)

    Das, Sudeep; Kummelil, Mathew Kurian; Kharbanda, Varun; Arora, Vishal; Nagappa, Somshekar; Shetty, Rohit; Shetty, Bhujang K

    2016-05-01

    To demonstrate the uses and applications of a microscope integrated intraoperative Optical Coherence Tomography in Micro Incision Cataract Surgery (MICS) and Femtosecond Laser Assisted Cataract Surgery (FLACS). Intraoperative real time imaging using the RESCAN™ 700 (Carl Zeiss Meditec, Oberkochen, Germany) was done for patients undergoing MICS as well as FLACS. The OCT videos were reviewed at each step of the procedure and the findings were noted and analyzed. Microscope Integrated Intraoperative Optical Coherence Tomography was found to be beneficial during all the critical steps of cataract surgery. We were able to qualitatively assess wound morphology in clear corneal incisions, in terms of subclinical Descemet's detachments, tears in the inner or outer wound lips, wound gaping at the end of surgery and in identifying the adequacy of stromal hydration, for both FLACS as well as MICS. It also enabled us to segregate true posterior polar cataracts from suspected cases intraoperatively. Deciding the adequate depth of trenching was made simpler with direct visualization. The final position of the intraocular lens in the capsular bag and the lack of bioadhesivity of hydrophobic acrylic lenses were also observed. Even though Microscope Integrated Intraoperative Optical Coherence Tomography is in its early stages for its application in cataract surgery, this initial assessment does show a very promising role for this technology in the future for cataract surgery both in intraoperative decision making as well as for training purposes.

  12. Nonlinear Optical Spectroscopy in the Time Domain: Studies of Ultrafast Molecular Processes in the Condensed Phase.

    Science.gov (United States)

    Joo, Taiha

    Ultrafast molecular processes in the condensed phase at room temperature are studied in the time domain by four wave mixing spectroscopy. The structure/dynamics of various quantum states can be studied by varying the time ordering of the incident fields, their polarization, their colors, etc. In one, time-resolved coherent Stokes Raman spectroscopy of benzene is investigated at room temperature. The reorientational correlation time of benzene as well as the T_2 time of the nu _1 ring-breathing mode have been measured by using two different polarization geometries. Bohr frequency difference beats have also been resolved between the nu_1 modes of ^ {12}C_6H_6 and ^{12}C_5^{13 }CH_6.. The dephasing dynamics of the nu _1 ring-breathing mode of neat benzene is studied by time-resolved coherent anti-Stokes Raman scattering. Ultrafast time resolution reveals deviation from the conventional exponential decay. The correlation time, tau _{rm c}, and the rms magnitude, Delta, of the Bohr frequency modulation are determined for the process responsible for the vibrational dephasing by Kubo dephasing function analysis. The electronic dephasing of two oxazine dyes in ethylene glycol at room temperature is investigated by photon echo experiments. It was found that at least two stochastic processes are responsible for the observed electronic dephasing. Both fast (homogeneous) and slow (inhomogeneous) dynamics are recovered using Kubo line shape analysis. Moreover, the slow dynamics is found to spectrally diffuse over the inhomogeneous distribution on the time scale around a picosecond. Time-resolved degenerate four wave mixing signal of dyes in a population measurement geometry is reported. The vibrational coherences both in the ground and excited electronic states produced strong oscillations in the signal together with the usual population decay from the excited electronic state. Absolute frequencies and their dephasing times of the vibrational modes at ~590 cm^{-1} are obtained

  13. Preparation and coherent manipulation of pure quantum states of a single molecular ion

    Science.gov (United States)

    Chou, Chin-Wen; Kurz, Christoph; Hume, David B.; Plessow, Philipp N.; Leibrandt, David R.; Leibfried, Dietrich

    2017-05-01

    Laser cooling and trapping of atoms and atomic ions has led to advances including the observation of exotic phases of matter, the development of precision sensors and state-of-the-art atomic clocks. The same level of control in molecules could also lead to important developments such as controlled chemical reactions and sensitive probes of fundamental theories, but the vibrational and rotational degrees of freedom in molecules pose a challenge for controlling their quantum mechanical states. Here we use quantum-logic spectroscopy, which maps quantum information between two ion species, to prepare and non-destructively detect quantum mechanical states in molecular ions. We develop a general technique for optical pumping and preparation of the molecule into a pure initial state. This enables us to observe high-resolution spectra in a single ion (CaH+) and coherent phenomena such as Rabi flopping and Ramsey fringes. The protocol requires a single, far-off-resonant laser that is not specific to the molecule, so many other molecular ions, including polyatomic species, could be treated using the same methods in the same apparatus by changing the molecular source. Combined with the long interrogation times afforded by ion traps, a broad range of molecular ions could be studied with unprecedented control and precision. Our technique thus represents a critical step towards applications such as precision molecular spectroscopy, stringent tests of fundamental physics, quantum computing and precision control of molecular dynamics.

  14. Spectral domain optical coherence tomography as an effective screening test for hydroxychloroquine retinopathy (the “flying saucer” sign

    Directory of Open Access Journals (Sweden)

    Eric Chen

    2010-10-01

    Full Text Available Eric Chen, David M Brown, Matthew S Benz, Richard H Fish, Tien P Wong, Rosa Y Kim, James C MajorRetina Consultants of Houston, The Methodist Hospital, Houston, Texas, USAPurpose: While the long-term incidence of hydroxychloroquine (HCQ retinopathy is low, there remains no definitive clinical screening test to recognize HCQ toxicity before ophthalmoscopic fundus changes or visual symptoms. Patients receiving HCQ were evaluated with spectral domain optical coherence tomography (SD OCT to assess the feasibility of identifying HCQ retinopathy at an early stage.Methods: Twenty-five patients referred for the evaluation of hydroxychloroquine toxicity underwent a comprehensive ocular examination, Humphrey visual field (HVF perimetry, time domain OCT, and SD OCT. Some patients with screening abnormalities also underwent further diagnostic testing at the discretion of the treating providers.Results: Five patients were found to have SD OCT findings corresponding to HCQ toxicity and retinal damage as seen by clinical exam and/or HVF perimetry. Two patients with advanced toxicity were found to have significant outer retina disruption in the macula on SD OCT. Three patients with early HCQ toxicity and HVF 10-2 perifoveal defects were found to have loss of the perifoveal photoreceptor inner segment/outer segment (IS/OS junction with intact outer retina directly under the fovea, creating the “flying saucer” sign. While two of these three patients had early ophthalmoscopic fundus changes, one had none.Conclusion: Outer retinal abnormalities including perifoveal photoreceptor IS/OS junction disruption can be identified by SD OCT in early HCQ toxicity, sometimes even before ophthalmoscopic fundus changes are apparent. SD OCT may have a potential complementary role in screening for HCQ retinopathy due to its quick acquisition and because it is more objective than automated perimetry.Keywords: drug toxicity, hydroxychloroquine, photoreceptors, screening test

  15. Agreement of Anterior Segment Parameters Obtained From Swept-Source Fourier-Domain and Time-Domain Anterior Segment Optical Coherence Tomography.

    Science.gov (United States)

    Chansangpetch, Sunee; Nguyen, Anwell; Mora, Marta; Badr, Mai; He, Mingguang; Porco, Travis C; Lin, Shan C

    2018-03-01

    To assess the interdevice agreement between swept-source Fourier-domain and time-domain anterior segment optical coherence tomography (AS-OCT). Fifty-three eyes from 41 subjects underwent CASIA2 and Visante OCT imaging. One hundred eighty-degree axis images were measured with the built-in two-dimensional analysis software for the swept-source Fourier-domain AS-OCT (CASIA2) and a customized program for the time-domain AS-OCT (Visante OCT). In both devices, we examined the angle opening distance (AOD), trabecular iris space area (TISA), angle recess area (ARA), anterior chamber depth (ACD), anterior chamber width (ACW), and lens vault (LV). Bland-Altman plots and intraclass correlation (ICC) were performed. Orthogonal linear regression assessed any proportional bias. ICC showed strong correlation for LV (0.925) and ACD (0.992) and moderate agreement for ACW (0.801). ICC suggested good agreement for all angle parameters (0.771-0.878) except temporal AOD500 (0.743) and ARA750 (nasal 0.481; temporal 0.481). There was a proportional bias in nasal ARA750 (slope 2.44, 95% confidence interval [CI]: 1.95-3.18), temporal ARA750 (slope 2.57, 95% CI: 2.04-3.40), and nasal TISA500 (slope 1.30, 95% CI: 1.12-1.54). Bland-Altman plots demonstrated in all measured parameters a minimal mean difference between the two devices (-0.089 to 0.063); however, evidence of constant bias was found in nasal AOD250, nasal AOD500, nasal AOD750, nasal ARA750, temporal AOD500, temporal AOD750, temporal ARA750, and ACD. Among the parameters with constant biases, CASIA2 tends to give the larger numbers. Both devices had generally good agreement. However, there were proportional and constant biases in most angle parameters. Thus, it is not recommended that values be used interchangeably.

  16. Photoswitchable molecular dipole antennas with tailored coherent coupling in glassy composite

    DEFF Research Database (Denmark)

    Elbahri, Mady; Zillohu, Ahnaf Usman; Gothe, Bastian

    2015-01-01

    . We also introduce the concept of 'tailored molecular photonic coupling' while highlighting the role of interferences for the design of optically active media by adjusting the photonic response of the medium with the real and imaginary refractive index of photoswitchable molecules in the 'ON' state...... alteration of photochromic molecular dipole antennas. We successfully demonstrate the concept of Brewster wavelength, which is based on the dipolar interaction between radiating dipoles and the surrounding matrix possessing a net dipole moment, as a key tool for highly localized sensing of matrix polarity....... Our results enhance our fundamental understanding of coherent dipole radiation and open a new vein of research based on glassy disordered dipolar composites that act as macroscopic antenna with cooperative action; furthermore, these results have important implications for new design rules of tailored...

  17. Quantification of retinal nerve fiber layer thickness using spectral domain optical coherence tomography in normal Indian population

    Directory of Open Access Journals (Sweden)

    Tarannum Mansoori

    2012-01-01

    Full Text Available The purpose of this study was to measure peripapillary retinal nerve fiber layer thickness (RNFLT using spectral domain optical coherence tomography (SD-OCT in normal Indian eyes, for which, 210 normal volunteers were recruited. One eye of each subject underwent RNFL scanning at 3.4 mm circle diameter around optic nerve using SD OCT. The data were analyzed to determine RNFLT in the sample population and its variation with age and gender. The average peripapillary RNFLT was 114.03 ± 9.59 μm. There was no effect of gender on RNFLT parameters. Age had significant negative correlation with average (P = 0.005, superior (P = 0.04, temporal (P = 0.049, and nasal quadrants (P = 0.01 RNFLT. Inferior quadrant RNFLT also had a negative correlation with age, but it was not statistically significant (P = 0.15.

  18. Common-path Fourier domain optical coherence tomography of irradiated human skin and ventilated isolated rabbit lungs

    Science.gov (United States)

    Popp, A.; Wendel, M.; Knels, L.; Knuschke, P.; Mehner, M.; Koch, T.; Boller, D.; Koch, P.; Koch, E.

    2005-08-01

    A compact common path Fourier domain optical coherence tomography (FD-OCT) system based on a broadband superluminescence diode is used for biomedical imaging. The epidermal thickening of human skin after exposure to ultraviolet radiation is measured to proof the feasibility of FD-OCT for future substitution of invasive biopsies in a long term study on natural UV skin protection. The FD-OCT system is also used for imaging lung parenchyma. FD-OCT images of a formalin fixated lung show the same alveolar structure as scanning electron microscopy images. In the ventilated and blood-free perfused isolated rabbit lung FD-OCT is used for real-time cross-sectional image capture of alveolar mechanics throughout tidal ventilation. The alveolar mechanics changing from alternating recruitment-derecruitment at zero positive end-expiratory pressure (PEEP) to persistent recruitment after applying a PEEP of 5 cm H2O is observed in the OCT images.

  19. Assessment of Corneal and Tear Film Parameters in Rheumatoid Arthritis Patients Using Anterior Segment Spectral Domain Optical Coherence Tomography.

    Science.gov (United States)

    El-Fayoumi, Dina; Youssef, Maha Mohamed; Khafagy, Mohamed Mahmoud; Badr El Dine, Nashwa; Gaber, Wafaa

    2018-01-01

    To study the corneal changes in rheumatoid arthritis (RA) patients in vivo, using spectral domain anterior segment optical coherence tomography (AS-OCT). A case-control study was done on 43 RA patients and 40 controls. The disease activity score (DAS28-ESR) was calculated and all participants had lower tear meniscus, corneal thickness, and epithelial thickness evaluation using AS-OCT. The lower tear meniscus height (LTMH) and the lower tear meniscus area (LTMA) were significantly lower in the RA patients than in controls (p < 0.001). RA patients also had a significantly thinner central corneal thickness (p = 0.02) and their epithelium was found to be thinner in the superotemporal peripheral sector. The LTMH and LTMA are significantly reduced in RA patients, despite the absence of clinical diagnosis of dry eye. RA patients have thinner corneal thickness and epithelial thickness than controls, which did not correlate with either disease duration or activity.

  20. Tomographic reconstruction of melanin structures of optical coherence tomography via the finite-difference time-domain simulation

    Science.gov (United States)

    Huang, Shi-Hao; Wang, Shiang-Jiu; Tseng, Snow H.

    2015-03-01

    Optical coherence tomography (OCT) provides high resolution, cross-sectional image of internal microstructure of biological tissue. We use the Finite-Difference Time-Domain method (FDTD) to analyze the data acquired by OCT, which can help us reconstruct the refractive index of the biological tissue. We calculate the refractive index tomography and try to match the simulation with the data acquired by OCT. Specifically, we try to reconstruct the structure of melanin, which has complex refractive indices and is the key component of human pigment system. The results indicate that better reconstruction can be achieved for homogenous sample, whereas the reconstruction is degraded for samples with fine structure or with complex interface. Simulation reconstruction shows structures of the Melanin that may be useful for biomedical optics applications.

  1. Fourier domain optical coherence tomography achieves full range complex imaging in vivo by introducing a carrier frequency during scanning

    International Nuclear Information System (INIS)

    Wang, Ruikang K

    2007-01-01

    The author describes a Fourier domain optical coherence tomography (FDOCT) system that is capable of full range complex imaging in vivo. This is achieved by introducing a constant carrier frequency into the OCT spectral interferograms at the time when imaging is performed. The complex functions of the spatial interferograms formed by each single wavelength are constructed before performing the Fourier transformation to localize the scatters within a sample. Two algorithms, based on Fourier filtering and Hilbert transformation, respectively, are described to achieve the full range complex FDOCT imaging. It is shown that the Hilbert transformation approach delivers better performance than the Fourier filtering method does in terms of tolerating the sample movement in vivo. The author finally demonstrates experimentally the system and algorithms for true in vivo imaging at a rate of 20 000 axial scans per second

  2. Quantitative Fourier Domain Optical Coherence Tomography Imaging of the Ocular Anterior Segment

    Science.gov (United States)

    McNabb, Ryan Palmer

    Clinical imaging within ophthalmology has had transformative effects on ocular health over the last century. Imaging has guided clinicians in their pharmaceutical and surgical treatments of macular degeneration, glaucoma, cataracts and numerous other pathologies. Many of the imaging techniques currently used are photography based and are limited to imaging the surface of ocular structures. This limitation forces clinicians to make assumptions about the underlying tissue which may reduce the efficacy of their diagnoses. Optical coherence tomography (OCT) is a non-invasive, non-ionizing imaging modality that has been widely adopted within the field of ophthalmology in the last 15 years. As an optical imaging technique, OCT utilizes low-coherence interferometry to produce micron-scale three-dimensional datasets of a tissue's structure. Much of the human body consists of tissues that significantly scatter and attenuate optical signals limiting the imaging depth of OCT in those tissues to only 1-2mm. However, the ocular anterior segment is unique among human tissue in that it is primarily transparent or translucent. This allows for relatively deep imaging of tissue structure with OCT and is no longer limited by the optical scattering properties of the tissue. This goal of this work is to develop methods utilizing OCT that offer the potential to reduce the assumptions made by clinicians in their evaluations of their patients' ocular anterior segments. We achieved this by first developing a method to reduce the effects of patient motion during OCT volume acquisitions allowing for accurate, three dimensional measurements of corneal shape. Having accurate corneal shape measurements then allowed us to determine corneal spherical and astigmatic refractive contribution in a given individual. This was then validated in a clinical study that showed OCT better measured refractive change due to surgery than other clinical devices. Additionally, a method was developed to combine

  3. Within-trait heterogeneity in age group differences in personality domains and facets: implications for the development and coherence of personality traits.

    Science.gov (United States)

    Mõttus, René; Realo, Anu; Allik, Jüri; Esko, Tõnu; Metspalu, Andres; Johnson, Wendy

    2015-01-01

    The study investigated differences in the Five-Factor Model (FFM) domains and facets across adulthood. The main questions were whether personality scales reflected coherent units of trait development and thereby coherent personality traits more generally. These questions were addressed by testing if the components of the trait scales (items for facet scales and facets for domain scales) showed consistent age group differences. For this, measurement invariance (MI) framework was used. In a sample of 2,711 Estonians who had completed the NEO Personality Inventory 3 (NEO PI-3), more than half of the facet scales and one domain scale did not meet the criterion for weak MI (factor loading equality) across 12 age groups spanning ages from 18 to 91 years. Furthermore, none of the facet and domain scales met the criterion for strong MI (intercept equality), suggesting that items of the same facets and facets of the same domains varied in age group differences. When items were residualized for their respective facets, 46% of them had significant (p < 0.0002) residual age-correlations. When facets were residualized for their domain scores, a majority had significant (p < 0.002) residual age-correlations. For each domain, a series of latent factors were specified using random quarters of their items: scores of such latent factors varied notably (within domains) in correlations with age. We argue that manifestations of aetiologically coherent traits should show similar age group differences. Given this, the FFM domains and facets as embodied in the NEO PI-3 do not reflect aetiologically coherent traits.

  4. Relationship Between Optic Nerve Appearance and Retinal Nerve Fiber Layer Thickness as Explored with Spectral Domain Optical Coherence Tomography

    Science.gov (United States)

    Aleman, Tomas S.; Huang, Jiayan; Garrity, Sean T.; Carter, Stuart B.; Aleman, Wendy D.; Ying, Gui-shuang; Tamhankar, Madhura A.

    2014-01-01

    Purpose To study the relationship between the appearance of the optic nerve and the retinal nerve fiber layer (RNFL) thickness determined by spectral domain optical coherence tomography (OCT). Methods Records from patients with spectral domain-OCT imaging in a neuro-ophthalmology practice were reviewed. Eyes with glaucoma/glaucoma suspicion, macular/optic nerve edema, pseudophakia, and with refractive errors > 6D were excluded. Optic nerve appearance by slit lamp biomicroscopy was related to the RNFL thickness by spectral domain-OCT and to visual field results. Results Ninety-one patients (176 eyes; mean age: 49 ± 15 years) were included. Eighty-three eyes (47%) showed optic nerve pallor; 89 eyes (50.6%) showed RNFL thinning (sectoral or average peripapillary). Average peripapillary RNFL thickness in eyes with pallor (mean ± SD = 76 ± 17 μm) was thinner compared to eyes without pallor (91 ± 14 μm, P < 0.001). Optic nerve pallor predicted RNFL thinning with a sensitivity of 69% and a specificity of 75%. Optic nerve appearance predicted RNFL thinning (with a sensitivity and specificity of 81%) when RNFL had thinned by ∼ 40%. Most patients with pallor had RNFL thinning with (66%) or without (25%) visual field loss; the remainder had normal RNFL and fields (5%) or with visual field abnormalities (4%). Conclusions Optic nerve pallor as a predictor of RNFL thinning showed fair sensitivity and specificity, although it is optimally sensitive/specific only when substantial RNFL loss has occurred. Translational Relevance Finding an acceptable relationship between the optic nerve appearance by ophthalmoscopy and spectral domain-OCT RNFL measures will help the clinician's interpretation of the information provided by this technology, which is gaining momentum in neuro-ophthalmic research. PMID:25374773

  5. Comparison of retina specialist preferences regarding spectral-domain and swept-source optical coherence tomography angiography

    Directory of Open Access Journals (Sweden)

    Su GL

    2017-05-01

    Full Text Available Grace L Su,1 Douglas M Baughman,2 Qinqin Zhang,3 Kasra Rezaei,2 Aaron Y Lee,2 Cecilia S Lee2 1Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 2Department of Ophthalmology, 3Department of Bioengineering, University of Washington, Seattle, WA, USA Purpose: The aim of this study was to compare physician preferences regarding the commercially available spectral-domain (SD optical coherence tomography angiography (OCTA and swept-source (SS OCTA prototype device.Design: Comparative analysis of diagnostic instruments was performed.Patients and methods: Subjects at the University of Washington Eye Institute and Harborview Medical Center were prospectively recruited and imaged with the Zeiss SD OCTA (HD-5000, Angioplex and Zeiss SS OCTA (Plex Elite, Everest devices on the same day. The study included 10 eyes from 10 subjects diagnosed with a retinal/choroidal disease. Deidentified images were compiled into a survey and sent to retina specialists in various countries. The survey presented masked SD and SS images of each eye for each retinal sublayer side by side. Respondents were asked about their image preference and impact on clinical management. A priori and post hoc preferences for SD vs SS were collected.Results: Fifty-four retina specialists responded to the survey. Median years in practice was 3.00 (interquartile range [IQR] 1.50–17.00. At baseline, 23 (48% physicians owned an OCTA machine. The majority of physician responses showed a preference for the SS over SD OCTA, independent of the retinal pathology shown (n=454 overall responses, 74%. Nevertheless, the majority indicated that both SD and SS would be equally valuable in informing clinical decisions (n=374 overall responses, 61%.Conclusion: These findings indicate that the majority of retina specialists surveyed prefer SS over SD OCTA based on image quality, regardless of the retinal pathology shown. Regarding the clinical utility of each modality, the majority of

  6. Spectral-domain optical coherence phase microscopy for label-free multiplexed protein microarray assay

    NARCIS (Netherlands)

    Joo, C.; Ozkumur, E.; Unlu, B.; de Boer, J.F.

    2009-01-01

    Quantitative measurement of affinities and kinetics of various biomolecular interactions such as protein-protein, protein-DNA and receptor-ligand is central to our understanding of basic molecular and cellular functions and is useful for therapeutic evaluation. Here, we describe a laser-scanning

  7. Molecular cloning and characterization of a putative OGG_N domain ...

    African Journals Online (AJOL)

    Molecular cloning and characterization of a putative OGG_N domain from the camel, Camelus dromedarius. Farid Shokry Ataya, Mohammad Saud Alanazi, Dalia Fouad, Hehsam Mahmoud Saeed, Mohammad Bazzi ...

  8. Nondestructive analysis of automotive paints with spectral domain optical coherence tomography.

    Science.gov (United States)

    Dong, Yue; Lawman, Samuel; Zheng, Yalin; Williams, Dominic; Zhang, Jinke; Shen, Yao-Chun

    2016-05-01

    We have demonstrated for the first time, to our knowledge, the use of optical coherence tomography (OCT) as an analytical tool for nondestructively characterizing the individual paint layer thickness of multiple layered automotive paints. A graph-based segmentation method was used for automatic analysis of the thickness distribution for the top layers of solid color paints. The thicknesses measured with OCT were in good agreement with the optical microscope and ultrasonic techniques that are the current standard in the automobile industry. Because of its high axial resolution (5.5 μm), the OCT technique was shown to be able to resolve the thickness of individual paint layers down to 11 μm. With its high lateral resolution (12.4 μm), the OCT system was also able to measure the cross-sectional area of the aluminum flakes in a metallic automotive paint. The range of values measured was 300-1850  μm2. In summary, the proposed OCT is a noncontact, high-resolution technique that has the potential for inclusion as part of the quality assurance process in automobile coating.

  9. Multi-second magnetic coherence in a single domain spinor Bose–Einstein condensate

    Science.gov (United States)

    Palacios, Silvana; Coop, Simon; Gomez, Pau; Vanderbruggen, Thomas; Natali Martinez de Escobar, Y.; Jasperse, Martijn; Mitchell, Morgan W.

    2018-05-01

    We describe a compact, robust and versatile system for studying the macroscopic spin dynamics in a spinor Bose–Einstein condensate. Condensates of {}87{Rb} are produced by all-optical evaporation in a 1560 nm optical dipole trap, using a non-standard loading sequence that employs an ancillary 1529 nm beam for partial compensation of the strong differential light-shift induced by the dipole trap itself. We use near-resonant Faraday rotation probing to non-destructively track the condensate magnetization, and demonstrate few-Larmor-cycle tracking with no detectable degradation of the spin polarization. In the ferromagnetic F = 1 ground state, we observe the spin orientation between atoms in the condensate is preserved, such that they precess all together like one large spin in the presence of a magnetic field. We characterize this dynamics in terms of the single-shot magnetic coherence times {{ \\mathcal T }}1 and {{ \\mathcal T }}2* , and observe them to be of several seconds, limited only by the residence time of the atoms in the trap. At the densities used, this residence is restricted only by one-body losses set by the vacuum conditions.

  10. Molecular Cloning And Sequencing Of Disintegrin Like Domain ...

    African Journals Online (AJOL)

    Disintegrin-like domain was cloned and sequenced from Cerastes cerastes venom gland tissue. Nested RT-PCR was performed using initial primers designed based on the homology of disintegrins from Trimeresurus flavoviridis, Glodius halys , Agkistrodon halys and Trimeresurus macrosquamatus. The homology was ...

  11. Insight into molecular interactions between two PB1 domains

    NARCIS (Netherlands)

    van Drogen-Petit, A.; Zwahlen, C.; Peter, M.; Bonvin, A.M.J.J.

    2004-01-01

    Specific protein–protein interactions play crucial roles in the regulation of any biological process. Recently, a new protein–protein interaction domain termed PB1 (Phox and Bem1) was identified, which is conserved throughout evolution and present in diverse proteins functioning in signal

  12. Choroidal thickness changes after dynamic exercise as measured by spectral-domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Nihat Sayin

    2015-01-01

    Full Text Available Purpose: To measure the choroidal thickness (CT after dynamic exercise by using enhanced depth imaging optical coherence tomography (EDI-OCT. Materials and Methods: A total of 19 healthy participants performed 10 min of low-impact, moderate-intensity exercise (i.e., riding a bicycle ergometer and were examined with EDI-OCT. Each participant was scanned before exercise and afterward at 5 min and 15 min. CT measurement was taken at the fovea and 1000 μ away from the fovea in the nasal, temporal, superior, and inferior regions. Retinal thickness, intraocular pressure, ocular perfusion pressure (OPP, heart rate, and mean blood pressure (mBP were also measured. Results: A significant increase occurred in OPP and mBP at 5 min and 15 min following exercise (P ˂ 0.05. The mean subfoveal CT at baseline was 344.00 ± 64.71 μm compared to 370.63 ± 66.87 μm at 5 min and 345.31 ± 63.58 μm at 15 min after exercise. CT measurements at all locations significantly increased at 5 min following exercise compared to the baseline (P ˂ 0.001, while measurements at 15 min following exercise did not significant differ compared to the baseline (P ˃ 0.05. There was no significant difference in retinal thickness at any location before and at 5 min and 15 min following exercise (P ˃ 0.05. Conclusion: Findings revealed that dynamic exercise causes a significant increase in CT for at least 5 min following exercise.

  13. Retinal ganglion cell complex changes using spectral domain optical coherence tomography in diabetic patients without retinopathy

    Institute of Scientific and Technical Information of China (English)

    Ahmed; I.Hegazy; Rasha; H.Zedan; Tamer; A.Macky; Soheir; M.Esmat

    2017-01-01

    AIM:To assess the ganglion cell complex(GCC)thickness in diabetic eyes without retinopathy. METHODS:Two groups included 45 diabetic eyes without retinopathy and 21 non diabetic eyes. All subjects underwent full medical and ophthalmological history,full ophthalmological examination,measuring GCC thickness and central foveal thickness(CFT)using the RTVue~? spectral domainoptical coherence tomography(SD-OCT),and HbA1C level.RESULTS:GCC focal loss volume(FLV%)was significantly more in diabetic eyes(22.2% below normal)than normal eyes(P=0.024). No statistically significant difference was found between the diabetic group and the control group regarding GCC global loss volume(GLV%)(P=0.160). CFT was positively correlated to the average,superior and inferior GCC(P=0.001,0.000 and 0.001 respectively)and negatively correlated to GLV% and FLV%(P=0.002 and0.031 respectively)in diabetic eyes. C/D ratio in diabetic eyes was negatively correlated to average,superior and inferior GCC(P=0.015,0.007 and 0.017 respectively). The FLV% was negatively correlated to the refraction and level of Hb A1c(P=0.019 and 0.013 respectively)and positively correlated to the best corrected visual acuity(BCVA)in log MAR in diabetic group(P=0.004).CONCLUSION:Significant GCC thinning in diabetes predates retinal vasculopathy,which is mainly focal rather than diffuse. It has no preference to either the superior or inferior halves of the macula. Increase of myopic error is significantly accompanied with increased focal GCC loss. GCC loss is accompanied with increased C/D ratio in diabetic eyes.

  14. Macular hole: 10 and 20-MHz ultrasound and spectral-domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Juliana Mantovani Bottós

    2012-12-01

    Full Text Available PURPOSE: Optical coherence tomography (OCT is valuable for macula evaluation. However, as this technique relies on light energy it cannot be performed in the presence of opaque media. In such cases, the ultrasound (US may predict some macular features. The aim of this study was to characterize images obtained by ultrasound with 10 and 20-MHz transducers comparing to OCT, as well as to analyze the relationship between the vitreous and retina in eyes with macular hole (MH. METHODS: 29 eyes of 22 patients with biomicroscopic evidence of MH at different stages were included. All patients were evaluated using ultrasonography with 10 and 20-MHz transducers and OCT. RESULTS: OCT identified signs of MH in 25 of 29 eyes. The remaining 4 cases not identified by US were pseudoholes caused by epiretinal membranes. In MH stages I (2 eyes and II (1 eye, both transducers were not useful to analyze the macular thickening, but suggestive findings as macular irregularity, operculum or partial posterior vitreous detachment (PVD were highlighted. In stages III (14 eyes and IV (5 eyes, both transducers identified the double hump irregularity and thickening. US could measure the macular thickness and other suggestive findings for MH: operculum, vitreomacular traction and partial or complete PVD. In cases of pseudoholes, US identified irregularities macular contour and a discrete depression. CONCLUSION: 10-MHz US was useful for an overall assessment of the vitreous body as well as its relationship to the retina. The 20-MHz transducer allowed valuable information on the vitreomacular interface and macular contour. OCT provides superior quality for fine morphological study of macular area, except in cases of opaque media. In these cases, and even if OCT is not available, the combined US study is able to provide a valid evaluation of the macular area improving therapeutic approach.

  15. Precision of high definition spectral-domain optical coherence tomography for measuring central corneal thickness.

    Science.gov (United States)

    Correa-Pérez, María E; López-Miguel, Alberto; Miranda-Anta, Silvia; Iglesias-Cortiñas, Darío; Alió, Jorge L; Maldonado, Miguel J

    2012-04-06

    This study was intended to assess the reliability of central corneal thickness (CCT) measurements using Cirrus high-definition optical coherence tomography (HD-OCT) in healthy subjects and its accuracy compared with ultrasonic pachymetry. Seventy-seven consecutive subjects were recruited for evaluating repeatability, and agreement between two examiners. To analyze repeatability, one examiner measured 77 eyes four times in succession. To study agreement between two observers, a second independently trained examiner obtained another CCT measurement. We also measured eyes in a subgroup of 20 patients using standard ultrasonic pachymetry. Within-subject standard deviation (S(w)), coefficient of variation (CV), limits of agreement (LoA), and intraclass correlation coefficient (ICC) data were obtained. For repeatability, the S(w) and precision (1.96 × S(w)) were 4.86 and 9.52 μm, respectively. Intraobserver CV was 0.89% and the ICC was 0.98 (95% confidence interval [CI], 0.97-0.99). For agreement between two examiners, the S(w) and precision were 7.58 and 14.85 μm, respectively; the CV was 1.40%. The mean difference between observers was -0.13 μm (95% CI, -1.85 to 1.58; P = 0.87). The width of the LoA was 29.64 μm. Median difference between Cirrus HD-OCT and ultrasound CCT measurements was -4.5 μm (interquartile range, -7.0-0.0; P = 0.04). Cirrus HD-OCT provides repeatable CCT measurements, good agreement between two independently trained examiners, and its systematic bias compared to ultrasonic pachymetry is clinically negligible. Therefore, research laboratories and eye clinics using Cirrus HD-OCT as a diagnostic imaging method, can also benefit from a reliable noncontact pachymeter when counseling patients with glaucoma and those undergoing corneal and refractive surgeries.

  16. Molecular Evolution of the Oxygen-Binding Hemerythrin Domain.

    Directory of Open Access Journals (Sweden)

    Claudia Alvarez-Carreño

    Full Text Available The evolution of oxygenic photosynthesis during Precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. Four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in marine invertebrates but further research has made it clear that it is present in the three domains of life, strongly suggesting that its origin predated the emergence of eukaryotes.Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histidine, histidine, glutamic acid cation-binding domain. Oxygen-binding hemerythrin homologs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 eukaryotic genomes. Overall, oxygen-binding hemerythrin homologues were found in the same proportion as single-domain and as long protein sequences. The associated functions of protein domains in long hemerythrin sequences can be classified in three major groups: signal transduction, phosphorelay response regulation, and protein binding. This suggests that in many organisms the reversible oxygen-binding capacity was incorporated in signaling pathways. A maximum-likelihood tree of oxygen-binding hemerythrin homologues revealed a complex evolutionary history in which lateral gene transfer, duplications and gene losses appear to have played an important role.Hemerythrin is an ancient protein domain with a complex evolutionary history. The distinctive iron-binding coordination site of oxygen-binding hemerythrins evolved first in prokaryotes, very likely prior to the divergence of Firmicutes and Proteobacteria, and spread into many bacterial, archaeal and eukaryotic species. The later evolution of the

  17. Within-Trait Heterogeneity in Age Group Differences in Personality Domains and Facets: Implications for the Development and Coherence of Personality Traits

    Science.gov (United States)

    Mõttus, René; Realo, Anu; Allik, Jüri; Esko, Tõnu; Metspalu, Andres; Johnson, Wendy

    2015-01-01

    The study investigated differences in the Five-Factor Model (FFM) domains and facets across adulthood. The main questions were whether personality scales reflected coherent units of trait development and thereby coherent personality traits more generally. These questions were addressed by testing if the components of the trait scales (items for facet scales and facets for domain scales) showed consistent age group differences. For this, measurement invariance (MI) framework was used. In a sample of 2,711 Estonians who had completed the NEO Personality Inventory 3 (NEO PI-3), more than half of the facet scales and one domain scale did not meet the criterion for weak MI (factor loading equality) across 12 age groups spanning ages from 18 to 91 years. Furthermore, none of the facet and domain scales met the criterion for strong MI (intercept equality), suggesting that items of the same facets and facets of the same domains varied in age group differences. When items were residualized for their respective facets, 46% of them had significant (p traits should show similar age group differences. Given this, the FFM domains and facets as embodied in the NEO PI-3 do not reflect aetiologically coherent traits. PMID:25751273

  18. Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

    NARCIS (Netherlands)

    Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.

    2007-01-01

    A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which

  19. Fundus autofluorescence in central serous chorioretinopathy:association with spectral-domain optical coherence tomography and fluorescein angiography

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    Peng Zhang

    2015-10-01

    Full Text Available AIM: To evaluate the correlation among changes in fundus autofluorescence (AF measured using infrared fundus AF (IR-AF and short-wave length fundus AF (SW-AF with changes in spectral-domain optical coherence tomography (SD-OCT and fluorescein angiography (FA in central serous chorioretinopathy (CSC.METHODS:Two hundred and twenty consecutive patients with CSC were included. In addition to AF, patients were assessed by means of SD-OCT and FA. Abnormalities in images of IR-AF, SW-AF, FA were analyzed and correlated with the corresponding outer retinal alterations in SD-OCT findings.RESULTS:Eyes with abnormalities on either IR-AF or SW-AF were found in 256 eyes (58.18%, among them 256 eyes (100% showed abnormal IR-AF, but SW-AF abnormalities were present only in 213 eyes (83.20%. The hypo-IR-AF corresponded to accumulation of sub-retinal liquid, collapse of retinal pigment epithelium (RPE or detachment of RPE with or without RPE leakage point in the corresponding area. The hyper-IR-AF corresponded to the area with loss of the ellipsoid portion of the inner segments and sub-sensory retinal deposits or focal melanogenesis under sensory retina. The hypo-SW-AF corresponded to accumulation of sub-retinal liquid or atrophy of RPE. The hyper-SW-AF associated with sub-sensory retinal deposits, detachment of RPE and focal melanogenesis.CONCLUSION:IR-AF was more sensitive than SW-AF and FA for identifying pathological abnormalities in CSC. The characteristics of IR-AF in CSC were attributable to the modification of melanin in the RPE. IR-AF should be used as a common diagnostic tool for identifying pathological lesion in CSC.KEYWORDS:central serous chorioretinopathy; fluorescein angiography; fundus autofluorescence; optical coherence tomography

  20. Influence of age-related macular degeneration on macular thickness measurement made with fourier-domain optical coherence tomography.

    Science.gov (United States)

    Garas, Anita; Papp, András; Holló, Gábor

    2013-03-01

    To evaluate the influence of age-related macular degeneration (AMD) on macular thickness measurement made with Fourier-domain optical coherence tomography (RTVue-OCT) to detect glaucoma. : One nonglaucomatous eye of 79 white persons was imaged. This comprised 25 healthy eyes, 19 eyes with early/intermediate AMD (geographic atrophy excluded), 16 eyes with subfoveal choroidal neovascularization (CNV), and 19 CNV eyes after intravitreal antiangiogenic treatment [CNV-antivascular endothelial growth factor (VEGF)]. Compared with the age-matched controls, no difference in any nerve fiber layer and optic disc parameter was seen for any AMD group. No macular retinal segmentation error was detected in the control group. Localized inner retinal image segmentation errors topographically related to AMD were detected in 8 eyes with drusen (42.1%), all 16 CNV eyes (100%) and 17 eyes in the CNV-anti-VEGF group (89.5%; χ test, P0.05). In contrast, all pattern-based ganglion cell complex (GCC) parameters were significantly higher (more abnormal) in the CNV and CNV-anti-VEGF group than in the control eyes (Mann-Whitney test, Bonferroni correction, P<0.001). For GCC focal loss volume, the only pattern-based parameter classified by the software, the frequency of "borderline" and "outside normal limits" classifications was significantly greater in each AMD group than in the control group (χ test, Bonferroni correction, P ≤0.03). In nonglaucomatous eyes, AMD significantly influences the pattern-based inner macular thickness parameters of the RTVue optical coherence tomograph and the software-provided classification of GCC focal loss volume, for detection of glaucoma.

  1. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics

    DEFF Research Database (Denmark)

    Quaiser, Achim; Ochsenreiter, Torsten; Lanz, Christa

    2003-01-01

    fragments differed between 2.3% and 19.9% and were placed into two different subgroups of Acidobacteria (groups III and V). Although partial co-linearity was found between genomic fragments, the gene content around the rRNA operons was generally not conserved. Phylogenetic reconstructions with orthologues......Acidobacteria have been established as a novel phylum of Bacteria that is consistently detected in many different habitats around the globe by 16S rDNA-based molecular surveys. The phylogenetic diversity, ubiquity and abundance of this group, particularly in soil habitats, suggest an important...... palustris and Bradyrhizobium japonicum, including a conserved two-component system. Phylogenetic analysis of the putative response regulator confirmed that this similarity between Rhizobiales and Acidobacteria might be due to a horizontal gene transfer. In total, our data give first insight into the genome...

  2. COPRED: prediction of fold, GO molecular function and functional residues at the domain level.

    Science.gov (United States)

    López, Daniel; Pazos, Florencio

    2013-07-15

    Only recently the first resources devoted to the functional annotation of proteins at the domain level started to appear. The next step is to develop specific methodologies for predicting function at the domain level based on these resources, and to implement them in web servers to be used by the community. In this work, we present COPRED, a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked. COPRED can be freely accessed at http://csbg.cnb.csic.es/copred. The interface works in all standard web browsers. WebGL (natively supported by most browsers) is required for the in-line preview and manipulation of protein 3D structures. The website includes a detailed help section and usage examples. pazos@cnb.csic.es.

  3. Assessment of ischemia in acute central retinal vein occlusion from inner retinal reflectivity on spectral domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Browning DJ

    2016-12-01

    Full Text Available David J Browning, Omar S Punjabi, Chong Lee Department of Ophthalmology, Charlotte Eye, Ear, Nose and Throat Associates, P.A., Charlotte, NC, USA Purpose: To determine the relationship between different spectral domain optical coherence tomography (SD-OCT signs of retinal ischemia in acute central retinal vein occlusion (CRVO and whether they predict anterior segment neovascularization (ASNV.Design: Retrospective, observational study.Subjects: Thirty-nine consecutive patients with acute CRVO and 12 months of follow-up.Methods: We graded baseline SD-OCTs for increased reflectivity of the inner retina, loss of definition of inner retinal layers, presence of a prominent middle-limiting membrane (p-MLM sign, and presence of paracentral acute middle maculopathy (PAMM. Graders were masked with respect to all clinical information.Results: The intraclass correlation coefficients (ICCs of grading–regrading by graders 1 and 2 were 0.8104, 95% confidence interval (CI (0.6686, 0.8956, and 0.7986, 95% CI (0.6475, 0.8892, respectively. The intragrader coefficients of repeatability (COR for graders 1 and 2 were 0.94 and 0.92, respectively. The ICC of graders 1 compared with 2 was 0.8039, 95% CI (0.6544, 0.8916. The intergrader COR was 0.80. SD-OCT grades of baseline ischemia were not associated with baseline visual acuity (VA, central subfield mean thickness (CSMT, or relative afferent pupillary defect; 12-month VA, CSMT, change in VA, change in CSMT, number of antivascular endothelial growth factor injections or corticosteroid injections, or proportion of eyes developing ASNV. SD-OCT grades of ischemia did not correlate with the proportion of eyes having the p-MLM sign or PAMM. PAMM and p-MLM are milder signs of ischemia than increased reflectivity of the inner retinal layers. Eyes with PAMM can evolve, losing PAMM and gaining the p-MLM sign.Conclusion: Grading of ischemia from SD-OCT in acute CRVO was repeatable within graders and reproducible across

  4. Influence of the Chemical Design on the Coherent Photoisomerization of Biomimetic Molecular Switches

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    Olivucci Massimo

    2013-03-01

    Full Text Available Ultrafast transient absorption spectroscopy reveals the effect of chemical substitutions on the photoreaction kinetics of biomimetic photoswitches displaying coherent dynamics. Ground state vibrational coherences are no longer observed when the excited state lifetime exceeds 300fs.

  5. Spectral-domain optical coherence tomography study on dynamic changes of human tears after instillation of artificial tears.

    Science.gov (United States)

    Napoli, Pietro Emanuele; Satta, Giovanni Maria; Coronella, Franco; Fossarello, Maurizio

    2014-07-01

    To analyze in vivo the dynamic changes induced by different artificial tears (ATs) in the precorneal tear film (PCTF) and lower tear meniscus (LTM) by using spectral-domain (SD) anterior segment optical coherence tomography (OCT). We prospectively examined 42 normal human eyes by using SD-OCT imaging. On the day before OCT imaging, all enrolled subjects were evaluated for abnormalities of ocular surface. All tear film images were obtained before and after instillation of three different types of ATs (mucomimetic, lipid-based, and saline) in five serial scans: immediately (within 30 seconds), at the first, fifth, 10th, and 20th minute. Subjects received a drop of 35 μL in one randomly selected eye. All examinations were conducted in the same conditions of temperature, brightness, humidity, and time of day. Changes in the morphological pattern of both LTM and PCTF were associated with the type of artificial tear instilled on the ocular surface. Similarly, the radius of curvature (rc), the height (h), and the depth (d) showed dynamic variations depending on treatment. Although by the 20th minute, both h and d returned to baseline values in all groups, a significant difference in rc (compared with baseline) was detected for mucomimetic ATs (P = 0.04) and lipid ATs (P = 0.02). Spectral-domain OCT imaging has preliminarily proved to be a noninvasive tool to evaluate, in real time, the different changes induced by ATs instillation. An important stride in understanding the clinical response to various tear substitutes can be achieved by this objective and quantitative approach. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

  6. Spectral domain optical coherence tomography as an effective screening test for hydroxychloroquine retinopathy (the "flying saucer" sign).

    Science.gov (United States)

    Chen, Eric; Brown, David M; Benz, Matthew S; Fish, Richard H; Wong, Tien P; Kim, Rosa Y; Major, James C

    2010-10-21

    While the long-term incidence of hydroxychloroquine (HCQ) retinopathy is low, there remains no definitive clinical screening test to recognize HCQ toxicity before ophthalmoscopic fundus changes or visual symptoms. Patients receiving HCQ were evaluated with spectral domain optical coherence tomography (SD OCT) to assess the feasibility of identifying HCQ retinopathy at an early stage. Twenty-five patients referred for the evaluation of hydroxychloroquine toxicity underwent a comprehensive ocular examination, Humphrey visual field (HVF) perimetry, time domain OCT, and SD OCT. Some patients with screening abnormalities also underwent further diagnostic testing at the discretion of the treating providers. Five patients were found to have SD OCT findings corresponding to HCQ toxicity and retinal damage as seen by clinical exam and/or HVF perimetry. Two patients with advanced toxicity were found to have significant outer retina disruption in the macula on SD OCT. Three patients with early HCQ toxicity and HVF 10-2 perifoveal defects were found to have loss of the perifoveal photoreceptor inner segment/outer segment (IS/OS) junction with intact outer retina directly under the fovea, creating the "flying saucer" sign. While two of these three patients had early ophthalmoscopic fundus changes, one had none. Outer retinal abnormalities including perifoveal photoreceptor IS/OS junction disruption can be identified by SD OCT in early HCQ toxicity, sometimes even before ophthalmoscopic fundus changes are apparent. SD OCT may have a potential complementary role in screening for HCQ retinopathy due to its quick acquisition and because it is more objective than automated perimetry.

  7. Intrasurgical Human Retinal Imaging With Manual Instrument Tracking Using a Microscope-Integrated Spectral-Domain Optical Coherence Tomography Device.

    Science.gov (United States)

    Hahn, Paul; Carrasco-Zevallos, Oscar; Cunefare, David; Migacz, Justin; Farsiu, Sina; Izatt, Joseph A; Toth, Cynthia A

    2015-07-01

    To characterize the first in-human intraoperative imaging using a custom prototype spectral-domain microscope-integrated optical coherence tomography (MIOCT) device during vitreoretinal surgery with instruments in the eye. Under institutional review board approval for a prospective intraoperative study, MIOCT images were obtained at surgical pauses with instruments held static in the vitreous cavity and then concurrently with surgical maneuvers. Postoperatively, MIOCT images obtained at surgical pauses were compared with images obtained with a high-resolution handheld spectral-domain OCT (HHOCT) system with objective endpoints, including acquisition of images acceptable for analysis and identification of predefined macular morphologic or pathologic features. Human MIOCT images were successfully obtained before incision and during pauses in surgical maneuvers. MIOCT imaging confirmed preoperative diagnoses, such as epiretinal membrane, full-thickness macular hole, and vitreomacular traction and demonstrated successful achievement of surgical goals. MIOCT and HHOCT images obtained at surgical pauses in two cohorts of five patients were comparable with greater than or equal to 80% correlation in 80% of patients. Real-time video-imaging concurrent with surgical manipulations enabled, for the first time using this device, visualization of dynamic instrument-retina interaction with targeted OCT tracking. MIOCT is successful for imaging at surgical pauses and for real-time image guidance with implementation of targeted OCT tracking. Even faster acquisition speeds are currently being developed with incorporation of a swept-source MIOCT engine. Further refinements and investigations will be directed toward continued integration for real-time volumetric imaging of surgical maneuvers. Ongoing development of seamless MIOCT systems will likely transform surgical visualization, approaches, and decision-making.

  8. Peripapillary Retinal Nerve Fiber Measurement with Spectral-Domain Optical Coherence Tomography in Age-Related Macular Degeneration

    Directory of Open Access Journals (Sweden)

    Simon K. Law

    2017-12-01

    Full Text Available Purpose: To evaluate the relationship between the peripapillary retinal nerve fiber layer (RNFL measurements with Spectral-domain Optical Coherence Tomography (OCT and Age-related macular degeneration (AMD. Methods: Patients >60 years of age without glaucoma or record of intraocular pressure >21 mmHg and no systemic or intraocular diseases or treatment or surgical intervention that affected the RNFL underwent OCT measurement of the RNFL. The severity of AMD was staged with the Clinical Age-Related Maculopathy Staging System. The relationship between RNFL measurements and AMD stages of one eye per patient was analyzed. Results: Eighty-six eyes (46 patients with AMD and no glaucoma or other exclusion criteria received OCT RNFL measurements. Nine eyes (10.5% were excluded because of distorted peripapillary anatomy from exudative AMD (7 eyes or failure of the RNFL segmentation algorithm (2 eyes. Mean age ± S.D. of the 43 patients analyzed was 81.2 ± 7.3 years. The mean stage ± S.D. of AMD of the 77 eyes was 3.77 ± 1.05. Higher stages of AMD were statistically significantly associated with lower average RNFL and inferior sector RNFL (p = 0.049, 0 0015, respectively. The association of inferior sector RNFL and AMD stage remained statistically significant after adjusting for age. Conclusions: Spectral domain OCT is generally useful in measuring the peripapillary RNFL in eyes with different stages of AMD. Higher stage of AMD is associated with thinner peripapillary RNFL, which may masquerade as early glaucomatous damage.

  9. Age, Sex, and Ethnic Variations in Inner and Outer Retinal and Choroidal Thickness on Spectral-Domain Optical Coherence Tomography.

    Science.gov (United States)

    Bafiq, Rinoza; Mathew, Raeba; Pearce, Elizabeth; Abdel-Hey, Ahmed; Richardson, Matthew; Bailey, Thomas; Sivaprasad, Sobha

    2015-11-01

    To evaluate age, sex, and ethnic variations in inner and outer retinal and choroidal thickness and foveal pit, using spectral-domain optical coherence tomography (SD OCT). Single-center observational cross-sectional study. Ninety randomly selected, healthy individuals of white, black, and South Asian origin underwent SD OCT raster and enhanced depth imaging scan. Manual measurements of inner and outer retinal thickness and choroidal thickness up to 3 mm nasal and temporal to the fovea were performed. The age, sex, and ethnic differences in these parameters were analyzed. The mean inner retinal thickness was lower by approximately 12 μm in black subjects across the central retina compared to white subjects (P ethnic groups but the temporal choroid was significantly thinner in black subjects (P < .05). The choroid showed an age-related decline in thickness of 2 μm per year of age of the subjects. Interethnic differences include wider fovea, lower central foveal thickness, and thinner inner retina in eyes of black subjects compared to their white and South Asian counterparts. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Automated circumferential construction of first-order aqueous humor outflow pathways using spectral-domain optical coherence tomography.

    Science.gov (United States)

    Huang, Alex S; Belghith, Akram; Dastiridou, Anna; Chopra, Vikas; Zangwill, Linda M; Weinreb, Robert N

    2017-06-01

    The purpose was to create a three-dimensional (3-D) model of circumferential aqueous humor outflow (AHO) in a living human eye with an automated detection algorithm for Schlemm’s canal (SC) and first-order collector channels (CC) applied to spectral-domain optical coherence tomography (SD-OCT). Anterior segment SD-OCT scans from a subject were acquired circumferentially around the limbus. A Bayesian Ridge method was used to approximate the location of the SC on infrared confocal laser scanning ophthalmoscopic images with a cross multiplication tool developed to initiate SC/CC detection automated through a fuzzy hidden Markov Chain approach. Automatic segmentation of SC and initial CC’s was manually confirmed by two masked graders. Outflow pathways detected by the segmentation algorithm were reconstructed into a 3-D representation of AHO. Overall, only time and time with 1.4% false positive detection. 3-D representation of AHO pathways demonstrated variably thicker and thinner SC with some clear CC roots. Circumferential (360 deg), automated, and validated AHO detection of angle structures in the living human eye with reconstruction was possible.

  11. Grading of Age-Related Macular Degeneration: Comparison between Color Fundus Photography, Fluorescein Angiography, and Spectral Domain Optical Coherence Tomography

    Directory of Open Access Journals (Sweden)

    Nils F. Mokwa

    2013-01-01

    Full Text Available Purpose. To compare color fundus photography (FP, fluorescein angiography (FA, and spectral domain optical coherence tomography (SDOCT for the detection of age-related macular degeneration (AMD, choroidal neovascularisation (CNV, and CNV activity. Methods. FPs, FAs, and SDOCT volume scans from 120 eyes of 66 AMD and control patients were randomly collected. Control eyes were required to show no AMD, but other retinal pathology was allowed. The presence of drusen, pigmentary changes, CNV, and signs for CNV activity was independently analyzed for all imaging modalities. Results. AMD was diagnosed based on FP in 75 eyes. SDOCT and FA showed sensitivity (specificity of 89% (76% and 92% (82%, respectively. CNV was present on FA in 68 eyes. Sensitivity (specificity was 78% (100% for FP and 94% (98% for SDOCT. CNV activity was detected by SDOCT or FA in 60 eyes with an agreement in 46 eyes. Sensitivity was 88% for SDOCT and 88% for FA. FP showed sensitivity of 38% and specificity of 98%. Conclusions. CNV lesions and activity may be missed by FP alone, but FP may help identifying drusen and pigmentary changes. SDOCT is highly sensitive for the detection of AMD, CNV, and CNV activity; however, it cannot fully replace FA.

  12. Fourier-Domain Optical Coherence Tomography for Monitoring the Lower Tear Meniscus in Dry Eye after Acupuncture Treatment

    Directory of Open Access Journals (Sweden)

    Tong Lin

    2015-01-01

    Full Text Available Dry eye is highly prevalent and has a significant impact on quality of life. Acupuncture was found to be effective to treat dry eye. However, little was known about the effect of acupuncture on different subtypes of dry eye. The objective of this study was to investigate the applicability of tear meniscus assessment by Fourier-domain optical coherence tomography in the evaluation of acupuncture treatment response in dry eye patients and to explore the effect of acupuncture on different subtypes of dry eye compared with artificial tear treatment. A total of 108 dry eye patients were randomized into acupuncture or artificial tear group. Each group was divided into three subgroups including lipid tear deficiency (LTD, Sjögren syndrome dry eye (SSDE, and non-Sjögren syndrome dry eye (Non-SSDE for data analysis. After 4-week treatment, the low tear meniscus parameters including tear meniscus height (TMH, tear meniscus depth (TMD, and tear meniscus area (TMA in the acupuncture group increased significantly for the LTD and Non-SSDE subgroups compared with both the baseline and the control groups (all P values < 0.05, but not for the SSDE. Acupuncture provided a measurable improvement of the tear meniscus dimensions for the Non-SSDE and LTD patients, but not for the SSDE patients.

  13. Effect of Hydroxychloroquine on the Retinal Layers: A Quantitative Evaluation with Spectral-Domain Optical Coherence Tomography

    Directory of Open Access Journals (Sweden)

    Hasim Uslu

    2016-01-01

    Full Text Available Purpose. To evaluate the effect of hydroxychloroquine on retinal pigment epithelium- (RPE- Bruch’s membrane complex, photoreceptor outer segment, and macular ganglion cell-inner plexiform layer (GCIPL thicknesses using spectral-domain optical coherence tomography (SD-OCT. Methods. In this prospective case-control study, 51 eyes of 51 hydroxychloroquine patients and 30 eyes of 30 healthy subjects were included. High-quality images were obtained using a Cirrus HD-OCT with 5-line raster mode; the photoreceptor inner segment (IS and outer segment (OS, sum of the segments (IS + OS, and RPE-Bruch’s membrane complex were analyzed. Results. The thicknesses of the IS + OS and OS layers were significantly lower in the hydroxychloroquine subjects compared to the control subjects (P<0.05. RPE-Bruch’s membrane complex thicknesses were significantly higher in the hydroxychloroquine subjects than for those of the control subjects (P<0.05. The minimum and temporal-inferior macular GCIPL thicknesses were significantly different between the patients with hydroxychloroquine use and the control subjects (P=0.04 and P=0.03, resp.. Conclusions. The foveal photoreceptor OS thinning, loss of GCIPL, and RPE-Bruch’s membrane thickening were detected in patients with hydroxychloroquine therapy. This quantitative approach using SD-OCT images may have important implications to use as an early indicator of retinal toxicity without any visible signs of hydroxychloroquine retinopathy.

  14. Automated 3-D method for the correction of axial artifacts in spectral-domain optical coherence tomography images

    Science.gov (United States)

    Antony, Bhavna; Abràmoff, Michael D.; Tang, Li; Ramdas, Wishal D.; Vingerling, Johannes R.; Jansonius, Nomdo M.; Lee, Kyungmoo; Kwon, Young H.; Sonka, Milan; Garvin, Mona K.

    2011-01-01

    The 3-D spectral-domain optical coherence tomography (SD-OCT) images of the retina often do not reflect the true shape of the retina and are distorted differently along the x and y axes. In this paper, we propose a novel technique that uses thin-plate splines in two stages to estimate and correct the distinct axial artifacts in SD-OCT images. The method was quantitatively validated using nine pairs of OCT scans obtained with orthogonal fast-scanning axes, where a segmented surface was compared after both datasets had been corrected. The mean unsigned difference computed between the locations of this artifact-corrected surface after the single-spline and dual-spline correction was 23.36 ± 4.04 μm and 5.94 ± 1.09 μm, respectively, and showed a significant difference (p < 0.001 from two-tailed paired t-test). The method was also validated using depth maps constructed from stereo fundus photographs of the optic nerve head, which were compared to the flattened top surface from the OCT datasets. Significant differences (p < 0.001) were noted between the artifact-corrected datasets and the original datasets, where the mean unsigned differences computed over 30 optic-nerve-head-centered scans (in normalized units) were 0.134 ± 0.035 and 0.302 ± 0.134, respectively. PMID:21833377

  15. Ability of spectral domain optical coherence tomography peripapillary retinal nerve fiber layer thickness measurements to identify early glaucoma

    Directory of Open Access Journals (Sweden)

    Tarannum Mansoori

    2011-01-01

    Full Text Available Purpose : To evaluate the ability of spectral domain optical coherence tomography (OCT peripapillary retinal nerve fiber layer thickness (RNFLT parameters to distinguish normal eyes from those with early glaucoma in Asian Indian eyes. Design : Observational cross-sectional study. Materials and Methods : One hundred and seventy eight eyes (83 glaucoma patients and 95 age matched healthy subjects of subjects more than 40 years of age were included in the study. All subjects underwent RNFLT measurement with spectral OCT/ scanning laser ophthalmoscope (SLO after dilatation. Sensitivity, specificity and area under the receiving operating characteristic curve (AROC were calculated for various OCT peripapillary RNFL parameters. Results: The mean RNFLT in healthy subjects and patients with early glaucoma were 105.7 ± 5.1 μm and 90.7 ± 7.5 μm, respectively. The largest AROC was found for 12 o′clock- hour (0.98, average (0.96 and superior quadrant RNFLT (0.9. When target specificity was set at ≥ 90% and ≥ 80%, the parameters with highest sensitivity were 12 o′clock -hour (91.6%, average RNFLT (85.3% and 12 o′ clock- hour (96.8 %, average RNFLT (94.7% respectively. Conclusion : Our study showed good ability of spectral OCT/ SLO to differentiate normal eyes from patients with early glaucoma and hence it may serve as an useful adjunct for early diagnosis of glaucoma.

  16. Simultaneous Confocal Scanning Laser Ophthalmoscopy Combined with High-Resolution Spectral-Domain Optical Coherence Tomography: A Review

    Directory of Open Access Journals (Sweden)

    Verônica Castro Lima

    2011-01-01

    Full Text Available We aimed to evaluate technical aspects and the clinical relevance of a simultaneous confocal scanning laser ophthalmoscope and a high-speed, high-resolution, spectral-domain optical coherence tomography (SDOCT device for retinal imaging. The principle of confocal scanning laser imaging provides a high resolution of retinal and choroidal vasculature with low light exposure. Enhanced contrast, details, and image sharpness are generated using confocality. The real-time SDOCT provides a new level of accuracy for assessment of the angiographic and morphological correlation. The combined system allows for simultaneous recordings of topographic and tomographic images with accurate correlation between them. Also it can provide simultaneous multimodal imaging of retinal pathologies, such as fluorescein and indocyanine green angiographies, infrared and blue reflectance (red-free images, fundus autofluorescence images, and OCT scans (Spectralis HRA + OCT; Heidelberg Engineering, Heidelberg, Germany. The combination of various macular diagnostic tools can lead to a better understanding and improved knowledge of macular diseases.

  17. “En-Face” Spectral-Domain Optical Coherence Tomography Findings in Multiple Evanescent White Dot Syndrome

    Directory of Open Access Journals (Sweden)

    Flore De bats

    2014-01-01

    Full Text Available Purpose. The recent use of “en-face” enhanced-depth imaging spectral-domain optical coherence tomography (EDI SD-OCT helps distinguish the retinal layers involved in the physiopathology of multiple evanescent white dot syndrome (MEWDS. Methods. Four patients presenting with MEWDS underwent a comprehensive ocular examination including C-scan (“en-face” EDI SD-OCT at the initial visit and during follow-up. Results. C-scans combined with the other multimodal imaging enabled the visualization of retinal damage. Acute lesions appeared as diffuse and focal disruptions occurring in the ellipsoid and interdigitation zones. The match between autofluorescence imaging, indocyanine green angiography, and “en-face” OCT helped identify the acute microstructural damages in the outer retina further than the choroid. Follow-up using “en-face” EDI-OCT revealed progressive and complete recovery of the central outer retinal layers. Conclusion. “En-face” EDI SD-OCT identified the site of initial damage in MEWDS as the photoreceptors and the interdigitation layers rather than the choroid. Moreover, “en-face” OCT is helpful in the follow-up of these lesions by being able to show the recovery of the outer retinal layers.

  18. Retinal pigment epithelial changes in chronic Vogt-Koyanagi-Harada disease: fundus autofluorescence and spectral domain optical coherence tomography findings

    Science.gov (United States)

    Vasconcelos-Santos, Daniel V.; Sohn, Elliott H.; Sadda, Srinivas; Rao, Narsing A.

    2009-01-01

    Purpose To determine whether fundus autofluorescence (FAF) and spectral-domain optical coherence tomography (SD-OCT) imaging allows better assessment of RPE and outer retina (OR) in subjects with chronic VKH compared to examination and angiography alone. Methods Cross-sectional analysis of a series of seven consecutive patients with chronic VKH undergoing FAF and SD-OCT. Chronic VKH was defined as during >3 months. Color fundus photographs were correlated to FAF and SD-OCT images. The images were later correlated to fluorescein angiography (FA) and indocyanine green angiography (ICG-A). Results All patients had sunset glow fundus, which resulted in no apparent corresponding abnormality on FAF or SD-OCT. Lesions with decreased autofluorescence signal were observed in 11 eyes (85%), being associated with loss of the RPE and involvement of OR on SD-OCT. In 5 eyes (38%) some of these lesions were very subtle on clinical examination but easily detected by FAF. Lesions with increased autofluorescence signal were seen in 8 eyes (61.5%), showing variable involvement of the OR on SD-OCT and corresponding clinically to areas of RPE proliferation and cystoid macular edema. Conclusion Combined use of FAF and SD-OCT imaging allowed noninvasive delineation of RPE/OR changes in patients with chronic VKH, which were consistent with previous histopathological reports. Some of these changes were not apparent on clinical examination. PMID:20010321

  19. Infrared autofluorescence, short-wave autofluorescence and spectral-domain optical coherence tomography of optic disk melanocytomas

    Directory of Open Access Journals (Sweden)

    Peng Zhang

    2016-05-01

    Full Text Available AIM: To investigate the findings of infrared fundus autofluorescence (IR-AF and spectral-domain optical coherence tomography (SD-OCT in eyes with optic disc melanocytoma (ODM. METHODS: IR-AF findings and those of other ophthalmologic imaging examinations, including short-wave autofluorescence (SW-AF, fluorescein angiography (FA, fundus color photography, and SD-OCT of 8 eyes of 8 consecutive cases with ODM were assessed. RESULTS: The ODMs in all cases (100% presented similar IR-AF, SW-AF, and FA findings. On IR-AF images, ODMs showed outstanding hyper-AF with well-defined outline. On SW-AF images, the area of ODMs presented as hypo-AF. FA images revealed the leaking retinal telangiectasia on the surface of the ODMs. On SD-OCT images in 8 cases (100%, the ODMs were sloped with highly reflective surface, which were disorganized retina and optic nerve layers. In 7 cases (87.5%, peripapillary choroids were involved. The melanocytomas of 8 cases (100% presented as optically empty spaces. Vitreous seeds were found in one case (12.5%. CONCLUSION: IR-AF imaging may provide a new modality to evaluate the pathologic features of ODMs, and together with SW-AF imaging, offers a new tool to study biological characteristics associated with ODMs. SD-OCT is a valuable tool in delimitating the tumor extension and providing morphological information about the adjacent retinal tissue.

  20. Morphometric analysis of fovea with spectral-domain optical coherence tomography and visual outcome postsurgery for retinal detachment

    Directory of Open Access Journals (Sweden)

    Manish Nagpal

    2014-01-01

    Full Text Available Purpose: The purpose of this study was to correlate the postoperative best-corrected visual acuity (BCVA with spectral-domain optical coherence tomography (SD-OCT findings in fovea involving rhegmatogenous retinal detachment (RRD surgery. Materials and Methods: Thirty eyes with preoperative fovea-involving RRD, who underwent scleral buckling (SB (6 eyes and pars plana vitrectomy (PPV (19 eyes and combined SB and PPV (5 eyes were recruited. Patients underwent clinical examination and SD-OCT scan of fovea preoperatively and at 30 days and 90 days postoperatively. The correlations between SD-OCT findings and BCVA were analyzed. Results: Inner segment/outer segment (IS/OS junction integrity was the indicator of better BCVA at 30 days and 90 days (P = 0.0002 and P = 0.0003, respectively whereas outer retinal corrugation (ORC was related to worse BCVA at 30 days and 90 days (P = 0.001. External limiting membrane did not have a co-relation with visual outcome, but cystoid macular edema showed co-relation at 90 days (P = 0.047. All eyes of SB and 3 eyes of PPV had a minimal subfoveal fluid at 30 days follow-up that had no effect on visual acuity. All retinas were attached at final follow-up. Conclusion: IS/OS junction integrity and ORC may be important predictors of postoperative visual outcome after anatomically successful RRD surgery.

  1. Comparison of peripapillary choroidal thickness measurements via spectral domain optical coherence tomography with and without enhanced depth imaging.

    Science.gov (United States)

    Ayyildiz, Onder; Kucukevcilioglu, Murat; Ozge, Gokhan; Koylu, Mehmet Talay; Ozgonul, Cem; Gokce, Gokcen; Mumcuoglu, Tarkan; Durukan, Ali Hakan; Mutlu, Fatih Mehmet

    2016-05-01

    To compare peripapillary choroidal thickness (PP-CT) measurements using a spectral domain optical coherence tomography (SD-OCT) device with and without enhanced depth imaging (EDI). Sixty healthy subjects aged from 18 to 40 years were included in this study. PP-CTs were measured in the right eyes by manual segmentation via SD-OCT both with and without EDI. The intraclass correlation coefficient (ICC) for each technique and comparison of PP-CT measurements between two techniques were evaluated. The correlation between retinal nerve fiber layer (RNFL) thickness and PP-CT was also explored on images of SD-OCT without EDI. The PP-CT measurements of 55 subjects were evaluated. The ICC was 0.999 (95% CI: 0.998-1.0, p  0.05). Additionally, there was no correlation between RNFL thickness and PP-CT (r = -0.109; p = 0.335). The PP-CT measurements via SD-OCT without EDI were consistent with the measurements via SD-OCT with EDI. Ophthalmologists who do not have access to EDI technology can use images of SD-OCT without EDI to measure the peripapillary choroid for research purposes. However, thicker peripapillary choroids cannot be measured using this technique and require further modifications or newer technologies, such as SD-OCT with EDI.

  2. 3D refraction correction and extraction of clinical parameters from spectral domain optical coherence tomography of the cornea.

    Science.gov (United States)

    Zhao, Mingtao; Kuo, Anthony N; Izatt, Joseph A

    2010-04-26

    Capable of three-dimensional imaging of the cornea with micrometer-scale resolution, spectral domain-optical coherence tomography (SDOCT) offers potential advantages over Placido ring and Scheimpflug photography based systems for accurate extraction of quantitative keratometric parameters. In this work, an SDOCT scanning protocol and motion correction algorithm were implemented to minimize the effects of patient motion during data acquisition. Procedures are described for correction of image data artifacts resulting from 3D refraction of SDOCT light in the cornea and from non-idealities of the scanning system geometry performed as a pre-requisite for accurate parameter extraction. Zernike polynomial 3D reconstruction and a recursive half searching algorithm (RHSA) were implemented to extract clinical keratometric parameters including anterior and posterior radii of curvature, central cornea optical power, central corneal thickness, and thickness maps of the cornea. Accuracy and repeatability of the extracted parameters obtained using a commercial 859nm SDOCT retinal imaging system with a corneal adapter were assessed using a rigid gas permeable (RGP) contact lens as a phantom target. Extraction of these parameters was performed in vivo in 3 patients and compared to commercial Placido topography and Scheimpflug photography systems. The repeatability of SDOCT central corneal power measured in vivo was 0.18 Diopters, and the difference observed between the systems averaged 0.1 Diopters between SDOCT and Scheimpflug photography, and 0.6 Diopters between SDOCT and Placido topography.

  3. Application of Novel Software Algorithms to Spectral-Domain Optical Coherence Tomography for Automated Detection of Diabetic Retinopathy.

    Science.gov (United States)

    Adhi, Mehreen; Semy, Salim K; Stein, David W; Potter, Daniel M; Kuklinski, Walter S; Sleeper, Harry A; Duker, Jay S; Waheed, Nadia K

    2016-05-01

    To present novel software algorithms applied to spectral-domain optical coherence tomography (SD-OCT) for automated detection of diabetic retinopathy (DR). Thirty-one diabetic patients (44 eyes) and 18 healthy, nondiabetic controls (20 eyes) who underwent volumetric SD-OCT imaging and fundus photography were retrospectively identified. A retina specialist independently graded DR stage. Trained automated software generated a retinal thickness score signifying macular edema and a cluster score signifying microaneurysms and/or hard exudates for each volumetric SD-OCT. Of 44 diabetic eyes, 38 had DR and six eyes did not have DR. Leave-one-out cross-validation using a linear discriminant at missed detection/false alarm ratio of 3.00 computed software sensitivity and specificity of 92% and 69%, respectively, for DR detection when compared to clinical assessment. Novel software algorithms applied to commercially available SD-OCT can successfully detect DR and may have potential as a viable screening tool for DR in future. [Ophthalmic Surg Lasers Imaging Retina. 2016;47:410-417.]. Copyright 2016, SLACK Incorporated.

  4. Assessment of Corneal Epithelial Thickness in Asymmetric Keratoconic Eyes and Normal Eyes Using Fourier Domain Optical Coherence Tomography

    Directory of Open Access Journals (Sweden)

    S. Catalan

    2016-01-01

    Full Text Available Purpose. To compare the characteristics of asymmetric keratoconic eyes and normal eyes by Fourier domain optical coherence tomography (OCT corneal mapping. Methods. Retrospective corneal and epithelial thickness OCT data for 74 patients were compared in three groups of eyes: keratoconic (n=22 and normal fellow eyes (n=22 in patients with asymmetric keratoconus and normal eyes (n=104 in healthy subjects. Areas under the curve (AUC of receiver operator characteristic (ROC curves for each variable were compared across groups to indicate their discrimination capacity. Results. Three variables were found to differ significantly between fellow eyes and normal eyes (all p<0.05: minimum corneal thickness, thinnest corneal point, and central corneal thickness. These variables combined showed a high discrimination power to differentiate fellow eyes from normal eyes indicated by an AUC of 0.840 (95% CI: 0.762–0.918. Conclusions. Our findings indicate that topographically normal fellow eyes in patients with very asymmetric keratoconus differ from the eyes of healthy individuals in terms of their corneal epithelial and pachymetry maps. This type of information could be useful for an early diagnosis of keratoconus in topographically normal eyes.

  5. Quantifying height of ultraprecisely machined steps on oxygen-free electronic copper disc using Fourier-domain short coherence interferometry

    CERN Document Server

    Montonen, Risto; Hæggström, Edward; Österberg, Kenneth

    2016-01-01

    The internal shape and alignment of accelerator discs is crucial for efficient collider operation at the future compact linear collider (CLIC). We applied a calibrated custom-made Fourier-domain short coherence interferometer to measure the height of 40 and 60μm60  μm ultraprecisely turned steps (surface roughness Ra≤25nmRa≤25  nm, flatness ≤2μm≤2  μm) on an oxygen-free electronic copper disc. The step heights were quantified to be (39.6±2.6)μm(39.6±2.6)  μm and (59.0±2.3)μm(59.0±2.3)  μm. The uncertainties are quoted at 95% confidence level and include contributions from calibration, refractive index of air, cosine error, surface roughness, and thermal expansion in comparison to standard temperature of 20°C. The results were verified by measuring the same steps using a commercial white light interferometer Veeco—NT3300. Our instrument can ensure that the accelerator discs of the CLIC are aligned within the tolerance required for efficient collider operation.

  6. Visualization of hair follicles using high-speed optical coherence tomography based on a Fourier domain mode locking laser

    Science.gov (United States)

    Tsai, M.-T.; Chang, F.-Y.

    2012-04-01

    In this study, a swept-source optical coherence tomography (SS-OCT) system with a Fourier domain mode locking (FDML) laser is proposed for a dermatology study. The homemade FDML laser is one kind of frequency-sweeping light source, which can provide output power of >20 mW and an output spectrum of 65 nm in bandwidth centered at 1300 nm, enabling imaging with an axial resolution of 12 μm in the OCT system. To eliminate the forward scans from the laser output and insert the delayed backward scans, a Mach-Zehnder configuration is implemented. Compared with conventional frequency-sweeping light sources, the FDML laser can achieve much higher scan rates, as high as ˜240 kHz, which can provide a three-dimensional imaging rate of 4 volumes/s. Furthermore, the proposed high-speed SS-OCT system can provide three-dimensional (3D) images with reduced motion artifacts. Finally, a high-speed SS-OCT system is used to visualize hair follicles, demonstrating the potential of this technology as a tool for noninvasive diagnosis of alopecia.

  7. Comparison of choroidal thickness using swept-source and spectral-domain optical coherence tomography in normal Indian eyes.

    Science.gov (United States)

    Narendran, Siddharth; Manayath, George; Venkatapathy, Narendran

    2018-01-01

    Choroidal thickness measurements are reported to differ between spectral-domain optical coherence tomography (SD-OCT) and swept-source OCT (SS-OCT). The aim of this study was to assess the comparability of choroidal thickness measurements using SS-OCT and SD-OCT devices among normal participants. This was a prospective study of 31 (62 eyes) normal participants. Choroidal imaging was performed sequentially with the Spectralis OCT (SD-OCT) and the deep range imaging OCT (DRI OCT-1) (SS-OCT) using standardized imaging protocols. The subfoveal choroidal thickness (SFChT) was measured manually by two masked retinal specialists. Paired t -tests and intraclass correlation coefficients (ICCs) were used to compare the measurements. The mean SFChT was 319.5 μm and 325.3 μm for DRI OCT-1 and Spectralis OCT, respectively ( P = 0.001), with a mean difference of 5.9 with ICC of 0.97. The mean difference in choroidal thickness between the OCT devices was larger among eyes with choroidal thickness > 350 μm compared with eyes with thinner choroids (8.0 μm vs. 4.7 μm). SFChT measurements are comparable between DRI OCT-1 and Spectralis OCT. The variability between the devices increases in thicker choroids.

  8. Automated circumferential construction of first-order aqueous humor outflow pathways using spectral-domain optical coherence tomography

    Science.gov (United States)

    Huang, Alex S.; Belghith, Akram; Dastiridou, Anna; Chopra, Vikas; Zangwill, Linda M.; Weinreb, Robert N.

    2017-06-01

    The purpose was to create a three-dimensional (3-D) model of circumferential aqueous humor outflow (AHO) in a living human eye with an automated detection algorithm for Schlemm's canal (SC) and first-order collector channels (CC) applied to spectral-domain optical coherence tomography (SD-OCT). Anterior segment SD-OCT scans from a subject were acquired circumferentially around the limbus. A Bayesian Ridge method was used to approximate the location of the SC on infrared confocal laser scanning ophthalmoscopic images with a cross multiplication tool developed to initiate SC/CC detection automated through a fuzzy hidden Markov Chain approach. Automatic segmentation of SC and initial CC's was manually confirmed by two masked graders. Outflow pathways detected by the segmentation algorithm were reconstructed into a 3-D representation of AHO. Overall, only <1% of images (5114 total B-scans) were ungradable. Automatic segmentation algorithm performed well with SC detection 98.3% of the time and <0.1% false positive detection compared to expert grader consensus. CC was detected 84.2% of the time with 1.4% false positive detection. 3-D representation of AHO pathways demonstrated variably thicker and thinner SC with some clear CC roots. Circumferential (360 deg), automated, and validated AHO detection of angle structures in the living human eye with reconstruction was possible.

  9. Relationship between macular ganglion cell complex thickness and macular outer retinal thickness: a spectral-domain optical coherence tomography study.

    Science.gov (United States)

    Kita, Yoshiyuki; Kita, Ritsuko; Takeyama, Asuka; Anraku, Ayako; Tomita, Goji; Goldberg, Ivan

    2013-01-01

    To assess the relationship between macular ganglion cell complex and macular outer retinal thicknesses. Case-control study. Forty-two normal eyes and 91 eyes with primary open-angle glaucoma were studied. Spectral-domain optical coherence tomography (RTVue-100) was used to measure the macular ganglion cell complex and macular outer retinal thickness. Ganglion cell complex to outer retinal thickness ratio was also calculated. The relationships between the ganglion cell complex and outer retinal thicknesses and between the ganglion cell complex to outer retinal thickness ratio and outer retinal thickness were evaluated. There was a positive correlation between ganglion cell complex and outer retinal thicknesses in the normal group and the glaucoma group (r = 0.53, P variation in the outer retinal thickness. Therefore, when determining the ganglion cell complex, it seems necessary to consider the outer retinal thickness as well. We propose the ratio as a suitable parameter to account for individual variations in outer retinal thickness. © 2013 The Authors. Clinical and Experimental Ophthalmology © 2013 Royal Australian and New Zealand College of Ophthalmologists.

  10. Impacts of age and sex on retinal layer thicknesses measured by spectral domain optical coherence tomography with Spectralis.

    Science.gov (United States)

    Nieves-Moreno, María; Martínez-de-la-Casa, José M; Morales-Fernández, Laura; Sánchez-Jean, Rubén; Sáenz-Francés, Federico; García-Feijoó, Julián

    2018-01-01

    To examine differences in individual retinal layer thicknesses measured by spectral domain optical coherence tomography (SD-OCT) (Spectralis®) produced with age and according to sex. Cross-sectional, observational study. The study was conducted in 297 eyes of 297 healthy subjects aged 18 to 87 years. In one randomly selected eye of each participant the volume and mean thicknesses of the different macular layers were measured by SD-OCT using the instrument's macular segmentation software. Volume and mean thickness of macular retinal nerve fiber layer (mRNFL), ganglion cell layer (GCL), inner plexiform layer (IPL), inner nuclear layer (INL), outer plexiform layer (OPL), outer nuclear layer (ONL), retinal pigmentary epithelium (RPE) and photoreceptor layer (PR). Retinal thickness was reduced by 0.24 μm for every one year of age. Age adjusted linear regression analysis revealed mean GCL, IPL, ONL and PR thickness reductions and a mean OPL thickness increase with age. Women had significantly lower mean GCL, IPL, INL, ONL and PR thicknesses and volumes and a significantly greater mRNFL volume than men. The thickness of most retinal layers varies both with age and according to sex. Longitudinal studies are needed to determine the rate of layer thinning produced with age.

  11. Spectral-domain low-coherence interferometry for phase-sensitive measurement of Faraday rotation at multiple depths.

    Science.gov (United States)

    Yeh, Yi-Jou; Black, Adam J; Akkin, Taner

    2013-10-10

    We describe a method for differential phase measurement of Faraday rotation from multiple depth locations simultaneously. A polarization-maintaining fiber-based spectral-domain interferometer that utilizes a low-coherent light source and a single camera is developed. Light decorrelated by the orthogonal channels of the fiber is launched on a sample as two oppositely polarized circular states. These states reflect from sample surfaces and interfere with the corresponding states of the reference arm. A custom spectrometer, which is designed to simplify camera alignment, separates the orthogonal channels and records the interference-related oscillations on both spectra. Inverse Fourier transform of the spectral oscillations in k-space yields complex depth profiles, whose amplitudes and phase difference are related to reflectivity and Faraday rotation within the sample, respectively. Information along a full depth profile is produced at the camera speed without performing an axial scan for a multisurface sample. System sensitivity for the Faraday rotation measurement is 0.86 min of arc. Verdet constants of clear liquids and turbid media are measured at 687 nm.

  12. Characterization of local fluid flow in 3D porous construct characterized by Fourier domain Doppler optical coherence tomography

    Science.gov (United States)

    Bagnaninchi, P. O.; Yang, Y.; El Haj, A.; Hinds, M. T.; Wang, R. K.

    2007-02-01

    In order to achieve functional tissue with the correct biomechanical properties it is critical to stimulate mechanically the cells. Perfusion bioreactor induces fluid shear stress that has been well characterized for two-dimensional culture where both simulation and experimental data are available. However these results can't be directly translated to tissue engineering that makes use of complex three-dimensional porous scaffold. Moreover, stimulated cells produce extensive extra-cellular matrix (ECM) that alter dramatically the micro-architecture of the constructs, changing the local flow dynamic. In this study a Fourier domain Doppler optical coherent tomography (FD-DOCT) system working at 1300nm with a bandwidth of 50nm has been used to determine the local flow rate inside different types of porous scaffolds used in tissue engineering. Local flow rates can then be linearly related, for Newtonian fluid, to the fluid shear stress occurring on the pores wall. Porous chitosan scaffolds (\\fgr 1.5mm x 3mm) with and without a central 250 μm microchannel have been produced by a freeze-drying technique. This techniques allow us to determine the actual shear stress applied to the cells and to optimise the input flow rate consequently, but also to relate the change of the flow distribution to the amount of ECM production allowing the monitoring of tissue formation.

  13. Retinal nerve fiber and optic disc morphology using spectral-domain optical coherence tomography in scleroderma patients.

    Science.gov (United States)

    Sahin-Atik, Sevinc; Koc, Feray; Akin-Sari, Sirin; Ozmen, Mustafa

    2017-05-11

    To evaluate the optic nerve head parameters and peripapillary retinal nerve fiber layer using spectral-domain optical coherence tomography (SD-OCT) in a systemic sclerosis (SSc) cohort and age-matched controls to determine whether SSc patients have an increased risk of normal-tension glaucoma (NTG). We examined 30 patients (3 male, 27 female) with SSc and 28 age- and sex-matched controls. Retinal nerve fiber and optic disc morphology were evaluated using Cirrus SD-OCT. Optic disc morphology measurements including disc area, rim area, average and vertical cup/disc (C/D) ratio, and cup volume were not significantly different between the study groups. The average and 4-quadrant retinal nerve fiber layer (RNFL) measurements of the C/D >0.3 subgroups were not significantly different in the patients and controls. These values were also similar for the C/D >0.5 subgroups except that the average inferior quadrant RNFL thickness of the right eyes in the patient subgroup was significantly thinner than in the control subgroup (p<0.05). Our SSc cohort had relatively shorter disease duration but increased prevalence of early glaucomatous damage signs. Our findings indicate that SSc is a risk factor for developing normal-tension glaucoma. Further studies combined with visual field evaluation are necessary to identify the long-term glaucomatous effects of SSc.

  14. A hierarchical cluster analysis of normal-tension glaucoma using spectral-domain optical coherence tomography parameters.

    Science.gov (United States)

    Bae, Hyoung Won; Ji, Yongwoo; Lee, Hye Sun; Lee, Naeun; Hong, Samin; Seong, Gong Je; Sung, Kyung Rim; Kim, Chan Yun

    2015-01-01

    Normal-tension glaucoma (NTG) is a heterogenous disease, and there is still controversy about subclassifications of this disorder. On the basis of spectral-domain optical coherence tomography (SD-OCT), we subdivided NTG with hierarchical cluster analysis using optic nerve head (ONH) parameters and retinal nerve fiber layer (RNFL) thicknesses. A total of 200 eyes of 200 NTG patients between March 2011 and June 2012 underwent SD-OCT scans to measure ONH parameters and RNFL thicknesses. We classified NTG into homogenous subgroups based on these variables using a hierarchical cluster analysis, and compared clusters to evaluate diverse NTG characteristics. Three clusters were found after hierarchical cluster analysis. Cluster 1 (62 eyes) had the thickest RNFL and widest rim area, and showed early glaucoma features. Cluster 2 (60 eyes) was characterized by the largest cup/disc ratio and cup volume, and showed advanced glaucomatous damage. Cluster 3 (78 eyes) had small disc areas in SD-OCT and were comprised of patients with significantly younger age, longer axial length, and greater myopia than the other 2 groups. A hierarchical cluster analysis of SD-OCT scans divided NTG patients into 3 groups based upon ONH parameters and RNFL thicknesses. It is anticipated that the small disc area group comprised of younger and more myopic patients may show unique features unlike the other 2 groups.

  15. Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior

    Science.gov (United States)

    Golji, Javad; Collins, Robert; Mofrad, Mohammad R. K.

    2009-01-01

    α-Actinin is an actin crosslinking molecule that can serve as a scaffold and maintain dynamic actin filament networks. As a crosslinker in the stressed cytoskeleton, α-actinin can retain conformation, function, and strength. α-Actinin has an actin binding domain and a calmodulin homology domain separated by a long rod domain. Using molecular dynamics and normal mode analysis, we suggest that the α-actinin rod domain has flexible terminal regions which can twist and extend under mechanical stress, yet has a highly rigid interior region stabilized by aromatic packing within each spectrin repeat, by electrostatic interactions between the spectrin repeats, and by strong salt bridges between its two anti-parallel monomers. By exploring the natural vibrations of the α-actinin rod domain and by conducting bending molecular dynamics simulations we also predict that bending of the rod domain is possible with minimal force. We introduce computational methods for analyzing the torsional strain of molecules using rotating constraints. Molecular dynamics extension of the α-actinin rod is also performed, demonstrating transduction of the unfolding forces across salt bridges to the associated monomer of the α-actinin rod domain. PMID:19436721

  16. Characterization of molecular outflows in the substellar domain

    International Nuclear Information System (INIS)

    Phan-Bao, Ngoc; Dang-Duc, Cuong; Lee, Chin-Fei; Ho, Paul T. P.; Li, Di

    2014-01-01

    We report here our latest search for molecular outflows from young brown dwarfs and very low-mass stars in nearby star-forming regions. We have observed three sources in Taurus with the Submillimeter Array and the Combined Array for Research in Millimeter-wave Astronomy at 230 GHz frequency to search for CO J = 2 → 1 outflows. We obtain a tentative detection of a redshifted and extended gas lobe at about 10 arcsec from the source GM Tau, a young brown dwarf in Taurus with an estimated mass of 73 M J , which is right below the hydrogen-burning limit. No blueshifted emission around the brown dwarf position is detected. The redshifted gas lobe that is elongated in the northeast direction suggests a possible bipolar outflow from the source with a position angle of about 36°. Assuming that the redshifted emission is outflow emission from GM Tau, we then estimate a molecular outflow mass in the range from 1.9 × 10 –6 M ☉ to 2.9 × 10 –5 M ☉ and an outflow mass-loss rate from 2.7 × 10 –9 M ☉ yr –1 to 4.1 × 10 –8 M ☉ yr –1 . These values are comparable to those we have observed in the young brown dwarf ISO-Oph 102 of 60 M J in ρ Ophiuchi and the very low-mass star MHO 5 of 90 M J in Taurus. Our results suggest that the outflow process in very low-mass objects is episodic with a duration of a few thousand years and the outflow rate of active episodes does not significantly change for different stages of the formation process of very low-mass objects. This may provide us with important implications that clarify the formation process of brown dwarfs.

  17. Characterization of molecular outflows in the substellar domain

    Energy Technology Data Exchange (ETDEWEB)

    Phan-Bao, Ngoc; Dang-Duc, Cuong [Department of Physics, International University-Vietnam National University HCM, Block 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City (Viet Nam); Lee, Chin-Fei; Ho, Paul T. P. [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 106, Taiwan (China); Li, Di, E-mail: pbngoc@hcmiu.edu.vn, E-mail: pbngoc@asiaa.sinica.edu.tw [National Astronomical Observatories, Chinese Academy of Science, Chaoyang District Datun Rd A20, Beijing (China)

    2014-11-01

    We report here our latest search for molecular outflows from young brown dwarfs and very low-mass stars in nearby star-forming regions. We have observed three sources in Taurus with the Submillimeter Array and the Combined Array for Research in Millimeter-wave Astronomy at 230 GHz frequency to search for CO J = 2 → 1 outflows. We obtain a tentative detection of a redshifted and extended gas lobe at about 10 arcsec from the source GM Tau, a young brown dwarf in Taurus with an estimated mass of 73 M {sub J}, which is right below the hydrogen-burning limit. No blueshifted emission around the brown dwarf position is detected. The redshifted gas lobe that is elongated in the northeast direction suggests a possible bipolar outflow from the source with a position angle of about 36°. Assuming that the redshifted emission is outflow emission from GM Tau, we then estimate a molecular outflow mass in the range from 1.9 × 10{sup –6} M {sub ☉} to 2.9 × 10{sup –5} M {sub ☉} and an outflow mass-loss rate from 2.7 × 10{sup –9} M {sub ☉} yr{sup –1} to 4.1 × 10{sup –8} M {sub ☉} yr{sup –1}. These values are comparable to those we have observed in the young brown dwarf ISO-Oph 102 of 60 M {sub J} in ρ Ophiuchi and the very low-mass star MHO 5 of 90 M {sub J} in Taurus. Our results suggest that the outflow process in very low-mass objects is episodic with a duration of a few thousand years and the outflow rate of active episodes does not significantly change for different stages of the formation process of very low-mass objects. This may provide us with important implications that clarify the formation process of brown dwarfs.

  18. Design of potentially active ligands for SH2 domains by molecular modeling methods

    Directory of Open Access Journals (Sweden)

    Hurmach V. V.

    2014-07-01

    Full Text Available Search for new chemical structures possessing specific biological activity is a complex problem that needs the use of the latest achievements of molecular modeling technologies. It is well known that SH2 domains play a major role in ontogenesis as intermediaries of specific protein-protein interactions. Aim. Developing an algorithm to investigate the properties of SH2 domain binding, search for new potential active compounds for the whole SH2 domains class. Methods. In this paper, we utilize a complex of computer modeling methods to create a generic set of potentially active compounds targeting universally at the whole class of SH2 domains. A cluster analysis of all available three-dimensional structures of SH2 domains was performed and general pharmacophore models were formulated. The models were used for virtual screening of collection of drug-like compounds provided by Enamine Ltd. Results. The design technique for library of potentially active compounds for SH2 domains class was proposed. Conclusions. The original algorithm of SH2 domains research with molecular docking method was developed. Using our algorithm, the active compounds for SH2 domains were found.

  19. Ultra-Widefield Steering-Based Spectral-Domain Optical Coherence Tomography Imaging of the Retinal Periphery.

    Science.gov (United States)

    Choudhry, Netan; Golding, John; Manry, Matthew W; Rao, Rajesh C

    2016-06-01

    To describe the spectral-domain optical coherence tomography (SD OCT) features of peripheral retinal findings using an ultra-widefield (UWF) steering technique to image the retinal periphery. Observational study. A total of 68 patients (68 eyes) with 19 peripheral retinal features. Spectral-domain OCT-based structural features. Nineteen peripheral retinal features, including vortex vein, congenital hypertrophy of the retinal pigment epithelium, pars plana, ora serrata pearl, typical cystoid degeneration (TCD), cystic retinal tuft, meridional fold, lattice and cobblestone degeneration, retinal hole, retinal tear, rhegmatogenous retinal detachment, typical degenerative senile retinoschisis, peripheral laser coagulation scars, ora tooth, cryopexy scars (retinal tear and treated retinoblastoma scar), bone spicules, white without pressure, and peripheral drusen, were identified by peripheral clinical examination. Near-infrared scanning laser ophthalmoscopy images and SD OCT of these entities were registered to UWF color photographs. Spectral-domain OCT resolved structural features of all peripheral findings. Dilated hyporeflective tubular structures within the choroid were observed in the vortex vein. Loss of retinal lamination, neural retinal attenuation, retinal pigment epithelium loss, or hypertrophy was seen in several entities, including congenital hypertrophy of the retinal pigment epithelium, ora serrata pearl, TCD, cystic retinal tuft, meridional fold, lattice, and cobblestone degenerations. Hyporeflective intraretinal spaces, indicating cystoid or schitic fluid, were seen in ora serrata pearl, ora tooth, TCD, cystic retinal tuft, meridional fold, retinal hole, and typical degenerative senile retinoschisis. The vitreoretinal interface, which often consisted of lamellae-like structures of the condensed cortical vitreous near or adherent to the neural retina, appeared clearly in most peripheral findings, confirming its association with many low-risk and vision

  20. Molecular assemblies and membrane domains in multivesicular endosome dynamics

    International Nuclear Information System (INIS)

    Falguieres, Thomas; Luyet, Pierre-Philippe; Gruenberg, Jean

    2009-01-01

    Along the degradation pathway, endosomes exhibit a characteristic multivesicular organization, resulting from the budding of vesicles into the endosomal lumen. After endocytosis and transport to early endosomes, activated signaling receptors are incorporated into these intralumenal vesicles through the action of the ESCRT machinery, a process that contributes to terminate signaling. Then, the vesicles and their protein cargo are further transported towards lysosomes for degradation. Evidence also shows that intralumenal vesicles can undergo 'back-fusion' with the late endosome limiting membrane, a route exploited by some pathogens and presumably followed by proteins and lipids that need to be recycled from within the endosomal lumen. This process depends on the late endosomal lipid lysobisphosphatidic acid and its putative effector Alix/AIP1, and is presumably coupled to the invagination of the endosomal limiting membrane at the molecular level via ESCRT proteins. In this review, we discuss the intra-endosomal transport routes in mammalian cells, and in particular the different mechanisms involved in membrane invagination, vesicle formation and fusion in a space inaccessible to proteins known to control intracellular membrane traffic.

  1. Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

    Energy Technology Data Exchange (ETDEWEB)

    Fattebert, J.-L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Richards, D.F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Glosli, J.N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2012-12-01

    We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·106 particles on 65,536 MPI tasks.

  2. The coherence lifetime-borrowing effect in vibronically coupled molecular aggregates under non-perturbative system-environment interactions.

    Science.gov (United States)

    Yeh, Shu-Hao; Engel, Gregory S.; Kais, Sabre

    Recently it has been suggested that the long-lived coherences in some photosynthetic pigment-protein systems, such as the Fenna-Matthews-Olson complex, could be attributed to the mixing of the pigments' electronic and vibrational degrees of freedom. In order to verify whether this is the case and to understand its underlying mechanism, a theoretical model capable of including both the electronic excitations and intramolecular vibrational modes of the pigments is necessary. Our model simultaneously considers the electronic and vibrational degrees of freedom, treating the system-environment interactions non-perturbatively by implementing the hierarchical equations of motion approach. Here we report the simulated two-dimensional electronic spectra of vibronically coupled molecular dimers to demonstrate how the electronic coherence lifetimes can be extended by borrowing the lifetime from the vibrational coherences. Funded by Qatar National Research Fund and Qatar Environment and Energy Research Institute.

  3. Acquiring molecular interference functions of X-ray coherent scattering for breast tissues by combination of simulation and experimental methods

    International Nuclear Information System (INIS)

    Chaparian, A.; Oghabian, M. A.; Changizi, V.

    2009-01-01

    Recently, it has been indicated that X-ray coherent scatter from biological tissues can be used to access signature of tissue. Some scientists are interested in studying this effect to get early detection of breast cancer. Since experimental methods for optimization are time consuming and expensive, some scientists suggest using simulation. Monte Carlo codes are the best option for radiation simulation: however, one permanent defect with Monte Carlo codes has been the lack of a sufficient physical model for coherent (Rayleigh) scattering, including molecular interference effects. Materials and Methods: It was decided to obtain molecular interference functions of coherent X-ray scattering for normal breast tissues by combination of modeling and experimental methods. A Monte Carlo simulation program was written to simulate the angular distribution of scattered photons for the normal breast tissue samples. Moreover, experimental diffraction patterns of these tissues were measured by means of energy dispersive X-ray diffraction method. The simulation and experimental data were used to obtain a tabulation of molecular interference functions for breast tissues. Results: With this study a tabulation of molecular interference functions for normal breast tissues Was prepared to facilitate the simulation diffraction patterns of the tissues without any experimental. Conclusion: The method may lead to design new systems for early detection of breast cancer.

  4. Macular laser photocoagulation guided by spectral-domain optical coherence tomography versus fluorescein angiography for diabetic macular edema

    Directory of Open Access Journals (Sweden)

    Gallego-Pinazo R

    2011-05-01

    Full Text Available Roberto Gallego-Pinazo1,2, Ana Marina Suelves-Cogollos1, Rosa Dolz-Marco1, J Fernando Arevalo3, Salvador García-Delpech1, J Luis Mullor4, Manuel Díaz-Llopis1,2,51Department of Ophthalmology, Hospital Universitario La Fe, Valencia, Spain; 2Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; 3Retina and Vitreous Service, Clinical Ophthalmology Center, Caracas, Venezuela; 4Unit of Experimental Ophthalmology, Hospital Universitario La Fe, Valencia, Spain; 5University of Valencia, Faculty of Medicine, Valencia, SpainBackground: The aim of this study was to compare the efficacy of spectral-domain optical coherence tomography (SD-OCT and fluorescein angiography (FA in the guidance of macular laser photocoagulation for diabetic macular edema.Methods: This was a prospective interventional clinical comparative pilot study. Forty eyes from 24 consecutive patients with diabetic macular edema were allocated to receive laser photocoagulation guided by SD-OCT or FA. Best-corrected visual acuity (BCVA, central macular thickness, and retinal volume were assessed at baseline and two months after treatment.Results: Subjects treated using FA-guided laser improved BCVA from the logarithm of the minimum angle of resolution (logMAR 0.52 ± 0.2 to 0.37 ± 0.2 (P < 0.001, and decreased mean central macular thickness from 397.25 ± 139.1 to 333.50 ± 105.7 µm (P < 0.001 and retinal volume from 12.61 ± 1.6 to 10.94 ± 1.4 mm3 (P < 0.001. Subjects treated using SD-OCT guided laser had improved BCVA from 0.48 ± 0.2 to 0.33 ± 0.2 logMAR (P < 0.001, and decreased mean central macular thickness from 425.90 ± 149.6 to 353.4 ± 140 µm (P < 0.001 and retinal volume from 12.38 ± 2.1 to 11.53 ± 1.1 mm3 (P < 0.001. No significant differences between the groups were found in two-month BCVA (P = 0.505, two-month central macular thickness (P = 0.660, or two-month retinal volume (P = 0.582.Conclusion: The short-term results of this pilot study

  5. Investigation of retinal morphology alterations using spectral domain optical coherence tomography in a mouse model of retinal branch and central retinal vein occlusion.

    Directory of Open Access Journals (Sweden)

    Andreas Ebneter

    Full Text Available Retinal vein occlusion is a leading cause of visual impairment. Experimental models of this condition based on laser photocoagulation of retinal veins have been described and extensively exploited in mammals and larger rodents such as the rat. However, few reports exist on the use of this paradigm in the mouse. The objective of this study was to investigate a model of branch and central retinal vein occlusion in the mouse and characterize in vivo longitudinal retinal morphology alterations using spectral domain optical coherence tomography. Retinal veins were experimentally occluded using laser photocoagulation after intravenous application of Rose Bengal, a photo-activator dye enhancing thrombus formation. Depending on the number of veins occluded, variable amounts of capillary dropout were seen on fluorescein angiography. Vascular endothelial growth factor levels were markedly elevated early and peaked at day one. Retinal thickness measurements with spectral domain optical coherence tomography showed significant swelling (p<0.001 compared to baseline, followed by gradual thinning plateauing two weeks after the experimental intervention (p<0.001. Histological findings at day seven correlated with spectral domain optical coherence tomography imaging. The inner layers were predominantly affected by degeneration with the outer nuclear layer and the photoreceptor outer segments largely preserved. The application of this retinal vein occlusion model in the mouse carries several advantages over its use in other larger species, such as access to a vast range of genetically modified animals. Retinal changes after experimental retinal vein occlusion in this mouse model can be non-invasively quantified by spectral domain optical coherence tomography, and may be used to monitor effects of potential therapeutic interventions.

  6. Prevalence of Split Nerve Fiber Layer Bundles in Healthy People Imaged with Spectral Domain Optical Coherence Tomography

    Directory of Open Access Journals (Sweden)

    Sirel Gür Güngör

    2016-12-01

    Full Text Available Objectives: The presence of retinal nerve fiber layer (RNFL split bundles was recently described in normal eyes scanned using scanning laser polarimetry and by histologic studies. Split bundles may resemble RNFL loss in healthy eyes. The aim of our study was to determine the prevalence of nerve fiber layer split bundles in healthy people. Materials and Methods: We imaged 718 eyes of 359 healthy persons with the spectral domain optical coherence tomography in this cross-sectional study. All eyes had intraocular pressure of 21 mmHg or less, normal appearance of the optic nerve head, and normal visual fields (Humphrey Field Analyzer 24-2 full threshold program. In our study, a bundle was defined as ‘split’ when there is localized defect not resembling a wedge defect in the RNFL deviation map with a symmetrically divided RNFL appearance on the RNFL thickness map. The classification was performed by two independent observers who used an identical set of reference examples to standardize the classification. Results: Inter-observer consensus was reached in all cases. Bilateral superior split bundles were seen in 19 cases (5.29% and unilateral superior split was observed in 15 cases (4.16%. In 325 cases (90.52% there was no split bundle. Conclusion: Split nerve fiber layer bundles, in contrast to single nerve fiber layer bundles, are not common findings in healthy eyes. In eyes with normal optic disc appearance, especially when a superior RNFL defect is observed in RNFL deviation map, the RNLF thickness map and graphs should also be examined for split nerve fiber layer bundles.

  7. Scanning laser polarimetry and spectral domain optical coherence tomography for the detection of retinal changes in Parkinson's disease.

    Science.gov (United States)

    Stemplewitz, Birthe; Keserü, Matthias; Bittersohl, Diana; Buhmann, Carsten; Skevas, Christos; Richard, Gisbert; Hassenstein, Andrea

    2015-12-01

    Whether retinal degeneration is part of the degenerative processes in patients with Parkinson's disease (PD) is still unclear. This cross-sectional study was undertaken to compare the retinal morphology of patients with PD and healthy controls using spectral domain optical coherence tomography (SD-OCT) and scanning laser polarimetry (SLP). Both eyes of patients with PD (n = 108) and healthy controls (n = 165) were examined using SD-OCT and SLP on the same day. Data on the thickness of the retinal nerve fibre layer (RNFL) of all quadrants and the macular area were acquired by OCT (Cirrus, Zeiss). The SLP device (Glaucoma diagnostics (GDx), Zeiss) measured the RNFL and calculated the nerve fibre index (NFI). All patients and probands were checked for concomitant ocular disorders by an ophthalmologist. Visual acuity, intraocular pressure (IOP), objective refraction and the anterior and posterior segment were assessed. Patients with PD showed a reduced macular volume and a reduced central subfield thickness in OCT examinations. The RNFL in the different quadrants did not differ significantly from that of controls. SLP data showed a reduced average RNFL thickness, a decreased thickness of the inferior quadrant and an increase of the NFI in patients with PD. PD may be associated with reduced thickness and volume of the macula and a reduced thickness of the RNFL in the inferior quadrant of the retina. Investigations using SD-OCT and SLP revealed distinct but significant differences between patients with PD and healthy controls. © 2015 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  8. Gabor-domain optical coherence microscopy with integrated dual-axis MEMS scanner for fast 3D imaging and metrology

    Science.gov (United States)

    Canavesi, Cristina; Cogliati, Andrea; Hayes, Adam; Santhanam, Anand P.; Tankam, Patrice; Rolland, Jannick P.

    2015-10-01

    Fast, robust, nondestructive 3D imaging is needed for characterization of microscopic structures in industrial and clinical applications. A custom micro-electromechanical system (MEMS)-based 2D scanner system was developed to achieve 55 kHz A-scan acquisition in a Gabor-domain optical coherence microscopy (GD-OCM) instrument with a novel multilevel GPU architecture for high-speed imaging. GD-OCM yields high-definition volumetric imaging with dynamic depth of focusing through a bio-inspired liquid lens-based microscope design, which has no moving parts and is suitable for use in a manufacturing setting or in a medical environment. A dual-axis MEMS mirror was chosen to replace two single-axis galvanometer mirrors; as a result, the astigmatism caused by the mismatch between the optical pupil and the scanning location was eliminated and a 12x reduction in volume of the scanning system was achieved. Imaging at an invariant resolution of 2 μm was demonstrated throughout a volume of 1 × 1 × 0.6 mm3, acquired in less than 2 minutes. The MEMS-based scanner resulted in improved image quality, increased robustness and lighter weight of the system - all factors that are critical for on-field deployment. A custom integrated feedback system consisting of a laser diode and a position-sensing detector was developed to investigate the impact of the resonant frequency of the MEMS and the driving signal of the scanner on the movement of the mirror. Results on the metrology of manufactured materials and characterization of tissue samples with GD-OCM are presented.

  9. Structure-function relationships with spectral-domain optical coherence tomography retinal nerve fiber layer and optic nerve head measurements.

    Science.gov (United States)

    Pollet-Villard, Frédéric; Chiquet, Christophe; Romanet, Jean-Paul; Noel, Christian; Aptel, Florent

    2014-05-02

    To evaluate the regional structure-function relationship between visual field sensitivity and retinal nerve fiber layer (RNFL) thickness and optic nerve head (ONH) measurements using spectral-domain optical coherence tomography (SD-OCT). Prospective cross-sectional study conducted on patients with glaucoma, suspected glaucoma, and healthy subjects. Eyes were tested on Cirrus OCT and standard achromatic perimetry. RNFL thickness of 12 peripapillary 30° sectors, neuroretinal rim thickness extracted from 36 neuroretinal rim scans, and Bruch membrane opening minimum rim width (BMO-MRW)-a recently defined parameter-extracted from 36 neuroretinal rim scans were obtained. Correlations between peripapillary RNFL thickness, neuroretinal rim thickness, all six sectors of BMO-MRW, and visual field sensitivity in the six corresponding areas were evaluated using logarithmic regression analysis. Receiver operating curve areas were calculated for each RNFL, ONH, and macular ganglion cell analysis parameter. We included 142 eyes of 142 subjects. The correlations (r(2)) between RNFL thickness, Cirrus-based neuroretinal rim thickness, BMO-MRW and visual field sensitivity ranged from 0.07 to 0.60, 0.15 to 0.49, and 0.24 to 0.66, respectively. The structure-function correlations were stronger with BMO-MRW than with Cirrus-based neuroretinal rim thickness. The largest areas under the receiver operating curve were seen for rim area (0.926 [95% confidence interval 0.875, 0.977]; P function relationship was significantly stronger with BMO-MRW than other ONH SD-OCT parameters. The best diagnostic capabilities were seen with rim area and average RNFL.

  10. High-resolution Fourier-Domain Optical Coherence Tomography and Microperimetric Findings After Macula-off Retinal Detachment Repair

    Science.gov (United States)

    Smith, Allison J.; Telander, David G.; Zawadzki, Robert J.; Choi, Stacey S.; Morse, Lawrence S.; Werner, John S.; Park, Susanna S.

    2009-01-01

    Objective To evaluate the morphologic changes in the macula of subjects with repaired macula-off retinal detachment (RD) using high-resolution Fourier-domain optical coherence tomography (FD OCT) and to perform functional correlation in a subset of patients using microperimetry (MP-1). Design Prospective observational case series. Participants Seventeen eyes from 17 subjects who had undergone anatomically successful repair for macula-off, rhegmatogenous RD at least 3 months earlier and without visually significant maculopathy on funduscopy. Methods FD OCT with axial and transverse resolution of 4.5 μm and 10 to 15 μm, respectively, was used to obtain rapid serial B-scans of the macula, which were compared with that from Stratus OCT. The FD OCT B-scans were used to create a 3-dimensional volume, from which en face C-scans were created. Among 11 patients, MP-1 was performed to correlate morphologic changes with visual function. Main Outcome Measures Stratus OCT scans, FD OCT scans, and MP-1 data. Results Stratus OCT and FD OCT images of the macula were obtained 3 to 30 months (mean 7 months) postoperatively in all eyes. Although Stratus OCT revealed photoreceptor disruption in 2 eyes (12%), FD OCT showed photoreceptor disruption in 13 eyes (76%). This difference was statistically significant (Pmacula-off RD repair is a common abnormality in the macula that is detected better with FD OCT than Stratus OCT. A good correlation between MP-1 abnormality and presence of photoreceptor disruption or subretinal fluid on FD OCT demonstrates that these anatomic abnormalities contribute to decreased visual function after successful repair. PMID:18672289

  11. UTILIZATION OF FUNDUS AUTOFLUORESCENCE, SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY, AND ENHANCED DEPTH IMAGING IN THE CHARACTERIZATION OF BIETTI CRYSTALLINE DYSTROPHY IN DIFFERENT STAGES.

    Science.gov (United States)

    Li, Qian; Li, Yang; Zhang, Xiaohui; Xu, Zhangxing; Zhu, Xiaoqing; Ma, Kai; She, Haicheng; Peng, Xiaoyan

    2015-10-01

    To characterize Bietti crystalline dystrophy (BCD) in different stages using multiple imaging modalities. Sixteen participants clinically diagnosed as BCD were included in the retrospective study and were categorized into 3 stages according to fundus photography. Eleven patients were genetically confirmed. Fundus autofluorescence, spectral domain optical coherence tomography, and enhanced depth imaging features of BCD were analyzed. On fundus autofluorescence, the abnormal autofluorescence was shown to enlarge in area and decrease in intensity with stages. Using spectral domain optical coherence tomography, the abnormalities in Stage 1 were observed to localize in outer retinal layers, whereas in Stage 2 and Stage 3, more extensive retinal atrophy was seen. In enhanced depth imaging, the subfoveal choroidal layers were delineated clearly in Stage 1; in Stage 2, destructions were primarily found in the choriocapillaris with associated alterations in the outer vessels; Stage 3 BCD displayed severe choroidal thinning. Choroidal neovascularization and macular edema were exhibited with high incidence. IVS6-8del17bp/inGC of the CYP4V2 gene was the most common mutant allele. Noninvasive fundus autofluorescence, spectral domain optical coherence tomography, and enhanced depth imaging may help to characterize the chorioretinal pathology of BCD at different degrees, and therefore, we propose staging of BCD depending on those methods. Physicians should be cautious of the vision-threatening complications of the disease.

  12. Rotational Coherence Encoded in an “Air-Laser” Spectrum of Nitrogen Molecular Ions in an Intense Laser Field

    Directory of Open Access Journals (Sweden)

    Haisu Zhang

    2013-10-01

    Full Text Available We investigate lasing action in aligned nitrogen molecular ions (N_{2}^{+} produced in an intense laser field. We find that, besides the population inversion between the B^{2}Σ_{u}^{+}-X^{2}Σ_{g}^{+} states, which is responsible for the observed simulated amplification of a seed pulse, a rotational wave packet in the ground vibrational state (v=0 of the excited electronic B^{2}Σ_{u}^{+} state has been created in N_{2}^{+}. The rotational coherence can faithfully encode its characteristics into the amplified seed pulses, enabling reconstruction of rotational wave packets of molecules in a single-shot detection manner from the frequency-resolved laser spectrum. Our results suggest that the air laser can potentially provide a promising tool for remote characterization of coherent molecular rotational wave packets.

  13. A primate specific extra domain in the molecular chaperone Hsp90.

    Directory of Open Access Journals (Sweden)

    Vishwadeepak Tripathi

    Full Text Available Hsp90 (heat shock protein 90 is an essential molecular chaperone that mediates folding and quality control of client proteins. Many of them such as protein kinases, steroid receptors and transcription factors are involved in cellular signaling processes. Hsp90 undergoes an ATP hydrolysis dependent conformational cycle to assist folding of the client protein. The canonical Hsp90 shows a typical composition of three distinct domains and interacts with individual cochaperone partners such as Hop, Cdc37 and Aha1 (activator of Hsp90 ATPase that regulate the reaction cycle of the molecular chaperone. A bioinformatic survey identified an additional domain of 122 amino acids in front of the canonical Hsp90 sequence. This extra domain (E domain is specific to the Catarrhini or drooping nose monkeys, a subdivision of the higher primates that includes man, the great apes and the old world monkeys but is absent from all other species. Our biochemical analysis reveals that Hsp103 associates with cochaperone proteins such as Hop, Cdc37 and Aha1 similar to Hsp90. However, the extra domain reduces the ATP hydrolysis rate to about half when compared to Hsp90 thereby acting as a negative regulator of the molecular chaperonés intrinsic ATPase activity.

  14. MADS interactomics : towards understanding the molecular mechanisms of plant MADS-domain transcription factor function

    NARCIS (Netherlands)

    Smaczniak, C.D.

    2013-01-01

    Protein-protein and protein-DNA interactions are essential for the molecular action of transcription factors. By combinatorial binding to target gene promoters, transcription factors are able to up- or down-regulate the expression of these genes. MADS-domain proteins comprise a large family of

  15. First-Principles Quantum Dynamics of Singlet Fission: Coherent versus Thermally Activated Mechanisms Governed by Molecular π Stacking

    Science.gov (United States)

    Tamura, Hiroyuki; Huix-Rotllant, Miquel; Burghardt, Irene; Olivier, Yoann; Beljonne, David

    2015-09-01

    Singlet excitons in π -stacked molecular crystals can split into two triplet excitons in a process called singlet fission that opens a route to carrier multiplication in photovoltaics. To resolve controversies about the mechanism of singlet fission, we have developed a first principles nonadiabatic quantum dynamical model that reveals the critical role of molecular stacking symmetry and provides a unified picture of coherent versus thermally activated singlet fission mechanisms in different acenes. The slip-stacked equilibrium packing structure of pentacene derivatives is found to enhance ultrafast singlet fission mediated by a coherent superexchange mechanism via higher-lying charge transfer states. By contrast, the electronic couplings for singlet fission strictly vanish at the C2 h symmetric equilibrium π stacking of rubrene. In this case, singlet fission is driven by excitations of symmetry-breaking intermolecular vibrations, rationalizing the experimentally observed temperature dependence. Design rules for optimal singlet fission materials therefore need to account for the interplay of molecular π -stacking symmetry and phonon-induced coherent or thermally activated mechanisms.

  16. Time Domains of the Hypoxic Ventilatory Response and Their Molecular Basis

    Science.gov (United States)

    Pamenter, Matthew E.; Powell, Frank L.

    2016-01-01

    Ventilatory responses to hypoxia vary widely depending on the pattern and length of hypoxic exposure. Acute, prolonged, or intermittent hypoxic episodes can increase or decrease breathing for seconds to years, both during the hypoxic stimulus, and also after its removal. These myriad effects are the result of a complicated web of molecular interactions that underlie plasticity in the respiratory control reflex circuits and ultimately control the physiology of breathing in hypoxia. Since the time domains of the physiological hypoxic ventilatory response (HVR) were identified, considerable research effort has gone toward elucidating the underlying molecular mechanisms that mediate these varied responses. This research has begun to describe complicated and plastic interactions in the relay circuits between the peripheral chemoreceptors and the ventilatory control circuits within the central nervous system. Intriguingly, many of these molecular pathways seem to share key components between the different time domains, suggesting that varied physiological HVRs are the result of specific modifications to overlapping pathways. This review highlights what has been discovered regarding the cell and molecular level control of the time domains of the HVR, and highlights key areas where further research is required. Understanding the molecular control of ventilation in hypoxia has important implications for basic physiology and is emerging as an important component of several clinical fields. PMID:27347896

  17. Low molecular weight dextran provides similar optical coherence tomography coronary imaging compared to radiographic contrast media.

    Science.gov (United States)

    Frick, Kyle; Michael, Tesfaldet T; Alomar, Mohammed; Mohammed, Atif; Rangan, Bavana V; Abdullah, Shuaib; Grodin, Jerrold; Hastings, Jeffrey L; Banerjee, Subhash; Brilakis, Emmanouil S

    2014-11-01

    Optical coherence tomography (OCT) coronary imaging requires displacement of red blood cells from the vessel lumen. This is usually accomplished using radiographic contrast. Low molecular weight dextran has low cost and is safe in low volumes. In the present study, we compared dextran with contrast for coronary OCT imaging. Fifty-one vessels in 26 patients were sequentially imaged using manual injection of radiographic contrast (iodixanol) and dextran. OCT images were analyzed at 1 mm intervals to determine the image clarity (defined as a visible lumen border > 270°) and to measure the lumen area and lumen diameter. To correct for the refractive index of dextran, the dextran area measurements were multiplied by 1.117 and the dextran length measurements were multiplied by 1.057. A total of 3,418 cross-sections (1,709 with contrast and 1,709 with dextran) were analyzed. There were no complications related to OCT imaging or to contrast or dextran administration. Clear image segments were observed in 97.0% vs. 96.7% of the cross-sections obtained with contrast and dextran, respectively (P = 0.45). The mean lumen areas were also similar: 6.69 ± 1.95 mm(2) with iodixanol vs. 7.06 ± 2.06 mm(2) with dextran (correlation coefficient 0.984). The image quality and measurements during OCT image acquisition are similar for dextran and contrast. Dextran could be used instead of contrast for OCT imaging, especially in patients in whom contrast load minimization is desired. © 2013 Wiley Periodicals, Inc.

  18. Molecular imaging needles: dual-modality optical coherence tomography and fluorescence imaging of labeled antibodies deep in tissue

    Science.gov (United States)

    Scolaro, Loretta; Lorenser, Dirk; Madore, Wendy-Julie; Kirk, Rodney W.; Kramer, Anne S.; Yeoh, George C.; Godbout, Nicolas; Sampson, David D.; Boudoux, Caroline; McLaughlin, Robert A.

    2015-01-01

    Molecular imaging using optical techniques provides insight into disease at the cellular level. In this paper, we report on a novel dual-modality probe capable of performing molecular imaging by combining simultaneous three-dimensional optical coherence tomography (OCT) and two-dimensional fluorescence imaging in a hypodermic needle. The probe, referred to as a molecular imaging (MI) needle, may be inserted tens of millimeters into tissue. The MI needle utilizes double-clad fiber to carry both imaging modalities, and is interfaced to a 1310-nm OCT system and a fluorescence imaging subsystem using an asymmetrical double-clad fiber coupler customized to achieve high fluorescence collection efficiency. We present, to the best of our knowledge, the first dual-modality OCT and fluorescence needle probe with sufficient sensitivity to image fluorescently labeled antibodies. Such probes enable high-resolution molecular imaging deep within tissue. PMID:26137379

  19. Human Hsp70 molecular chaperone binds two calcium ions within the ATPase domain.

    Science.gov (United States)

    Sriram, M; Osipiuk, J; Freeman, B; Morimoto, R; Joachimiak, A

    1997-03-15

    The 70 kDa heat shock proteins (Hsp70) are a family of molecular chaperones, which promote protein folding and participate in many cellular functions. The Hsp70 chaperones are composed of two major domains. The N-terminal ATPase domain binds to and hydrolyzes ATP, whereas the C-terminal domain is required for polypeptide binding. Cooperation of both domains is needed for protein folding. The crystal structure of bovine Hsc70 ATPase domain (bATPase) has been determined and, more recently, the crystal structure of the peptide-binding domain of a related chaperone, DnaK, in complex with peptide substrate has been obtained. The molecular chaperone activity and conformational switch are functionally linked with ATP hydrolysis. A high-resolution structure of the ATPase domain is required to provide an understanding of the mechanism of ATP hydrolysis and how it affects communication between C- and N-terminal domains. The crystal structure of the human Hsp70 ATPase domain (hATPase) has been determined and refined at 1. 84 A, using synchrotron radiation at 120K. Two calcium sites were identified: the first calcium binds within the catalytic pocket, bridging ADP and inorganic phosphate, and the second calcium is tightly coordinated on the protein surface by Glu231, Asp232 and the carbonyl of His227. Overall, the structure of hATPase is similar to bATPase. Differences between them are found in the loops, the sites of amino acid substitution and the calcium-binding sites. Human Hsp70 chaperone is phosphorylated in vitro in the presence of divalent ions, calcium being the most effective. The structural similarity of hATPase and bATPase and the sequence similarity within the Hsp70 chaperone family suggest a universal mechanism of ATP hydrolysis among all Hsp70 molecular chaperones. Two calcium ions have been found in the hATPase structure. One corresponds to the magnesium site in bATPase and appears to be important for ATP hydrolysis and in vitro phosphorylation. Local changes

  20. Spectral domain optical coherence tomography cross-sectional image of optic nerve head during intraocular pressure elevation

    Directory of Open Access Journals (Sweden)

    Ji Young Lee

    2014-12-01

    Full Text Available AIM: To analyze changes of the optic nerve head (ONH and peripapillary region during intraocular pressure (IOP elevation in patients using spectral domain optical coherence tomography (SD-OCT.METHODS: Both an optic disc 200×200 cube scan and a high-definition 5-line raster scan were obtained from open angle glaucoma patients presented with monocular elevation of IOP (≥30 mm Hg using SD-OCT. Additional baseline characteristics included age, gender, diagnosis, best-corrected visual acuity, refractive error, findings of slit lamp biomicroscopy, findings of dilated stereoscopic examination of the ONH and fundus, IOP, pachymetry findings, and the results of visual field.RESULTS: The 24 patients were selected and divided into two groups:group 1 patients had no history of IOP elevation or glaucoma (n=14, and group 2 patients did have history of IOP elevation or glaucoma (n=10. In each patient, the study eye with elevated IOP was classified into group H (high, and the fellow eye was classified into group L (low. The mean deviation (MD differed significantly between groups H and L when all eyes were considered (P=0.047 and in group 2 (P=0.042, not in group 1 (P=0.893. Retinal nerve fiber layer (RNFL average thickness (P=0.050, rim area (P=0.015, vertical cup/disc ratio (P=0.011, cup volume (P=0.028, inferior quadrant RNFL thickness (P=0.017, and clock-hour (1, 5, and 6 RNFL thicknesses (P=0.050, 0.012, and 0.018, respectively, cup depth (P=0.008, central prelaminar layer thickness (P=0.023, mid-inferior prelaminar layer thickness (P=0.023, and nasal retinal slope (P=0.034 were significantly different between the eyes with groups H and L.CONCLUSION:RNFL average thickness, rim area, vertical cup/disc ratio, cup volume, inferior quadrant RNFL thickness, and clock-hour (1, 5, and 6 RNFL thicknesses significantly changed during acute IOP elevation.

  1. Comparison of Scheimpflug imaging and spectral domain anterior segment optical coherence tomography for detection of narrow anterior chamber angles.

    Science.gov (United States)

    Grewal, D S; Brar, G S; Jain, R; Grewal, S P S

    2011-05-01

    To compare the performance of anterior chamber volume (ACV) and anterior chamber depth (ACD) obtained using Scheimpflug imaging with angle opening distance (AOD500) and trabecular-iris space area (TISA500) obtained using spectral domain anterior segment optical coherence tomography (SD-ASOCT) in detecting narrow angles classified using gonioscopy. In this prospective, cross-sectional observational study, 265 eyes of 265 consecutive patients underwent sequential Scheimpflug imaging, SD-ASOCT imaging, and gonioscopy. Correlations between gonioscopy grading, ACV, ACD, AOD500, and TISA500 were evaluated. Area under receiver operating characteristic curve (AUC), sensitivity, specificity, and likelihood ratios (LRs) were calculated to assess the performance of ACV, ACD, AOD500, and TISA500 in detecting narrow angles (defined as Shaffer grade ≤1 in all quadrants). SD-ASOCT images were obtained at the nasal and temporal quadrants only. Twenty-eight eyes (10.6%) were classified as narrow angles on gonioscopy. ACV correlated with gonioscopy grading (P<0.001) for temporal (r=0.204), superior (r=0.251), nasal (r=0.213), and inferior (r=0.236) quadrants. ACV correlated with TISA500 for nasal (r=0.135, P=0.029) and temporal (P=0.160, P=0.009) quadrants and also with AOD500 for nasal (r=0.498, P<0.001) and temporal (r=0.517, P<0.001) quadrants. For detection of narrow angles, ACV (AUC=0.935; 95% confidence interval (CI) =0.898-0.961) performed similar to ACD (AUC=0.88, P=0.06) and significantly better than AOD500 nasal (AUC=0.761, P=0.001), AOD500 temporal (AUC=0.808, P<0.001), TISA500 nasal (AUC=0.756, P<0.001), and TISA500 temporal (AUC=0.738, P<0.001). Using a cutoff of 113 mm(3), ACV had 90% sensitivity and 88% specificity for detecting narrow angles. Positive and negative LRs for ACV were 8.63 (95% CI=7.4-10.0) and 0.11 (95% CI=0.03-0.4), respectively. ACV measurements using Scheimpflug imaging outperformed AOD500 and TISA500 using SD-ASOCT for detecting narrow angles.

  2. Spectral domain optical coherence tomography changes following intravitreal dexamethasone implant, Ozurdex ® in patients with uveitic cystoid macular edema

    Directory of Open Access Journals (Sweden)

    Pooja Bansal

    2015-01-01

    Full Text Available Purpose: To correlate the structural and functional changes following intravitreal injection of dexamethasone 0.7 mg (Ozurdex ® implant in patients with recalcitrant uveitic cystoid macular edema (CME. Materials and Methods: In a prospective, interventional, nonrandomized study, 30 eyes (27 patients with uveitic CME received Ozurdex ® implant and were followed-up for 24 weeks at periodic intervals to monitor structural alterations seen on spectral domain optical coherence tomography (SD-OCT. The outcome measures included change in central macular thickness (CMT and best-corrected visual acuity (BCVA as well as structural alterations seen on OCT such as change in the height of cystoid spaces (CSs and sub-foveal serous retinal detachment (SSRD. The integrity of external limiting membrane and inner-outer segment junction was assessed at baseline and follow-up visits. Results: Mean age of the patients was 46.09 ± 15.66 years. The mean CMT decreased by 96 μm at 1-day, 231.64 μm at 1-week, 254.21 μm at 4 weeks and 249.14 μm at 12 weeks (P < 0.001 compared with baseline. BCVA improved from a baseline mean of 0.62 LogMAR units to 0.49 on day 1 to 0.31 at 24 weeks (P < 0.001. A decrease in the mean height of CS, that is, 133.28 μm from a baseline of 317.71 μm was noted on the 1 st day (P < 0.001. 4 eyes demonstrated the presence of CS at 4 weeks, 1 eye at 6 weeks and 3 eyes at 12 weeks. At baseline, 16 eyes (53.33% demonstrated the presence of SSRD. Among these, 11 eyes showed resolution of SSRD on day 1. SSRD resolved in all patients at 4 weeks and was maintained up to 24 weeks. Conclusions: Ozurdex ® implant improves the visual outcome of patients with recalcitrant uveitic CME. Reversibility of retinal changes may be possible following treatment with dexamethasone implant. Thus final visual outcome may be independent of pretreatment CMT, the height of CS or SSRD.

  3. Autofluorescence Imaging and Spectral-Domain Optical Coherence Tomography in Incomplete Congenital Stationary Night Blindness and Comparison with Retinitis Pigmentosa

    Science.gov (United States)

    CHEN, ROYCE W. S.; GREENBERG, JONATHAN P.; LAZOW, MARGOT A.; RAMACHANDRAN, RITHU; LIMA, LUIZ H.; HWANG, JOHN C.; SCHUBERT, CARL; BRAUNSTEIN, ALEXANDRA; ALLIKMETS, RANDO; TSANG, STEPHEN H.

    2015-01-01

    PURPOSE To test the hypothesis that the evaluation of retinal structure can have diagnostic value in differentiating between incomplete congenital stationary night blindness (CSNB2) and retinitis pigmentosa (RP). To compare retinal thickness differences between patients with CSNB2 and myopic controls. DESIGN Prospective cross-sectional study. METHODS Ten eyes of 5 patients diagnosed with CSNB2 (4 X-linked recessive, 1 autosomal recessive) and 6 eyes of 3 patients with RP (2 autosomal dominant, 1 autosomal recessive) were evaluated with spectral-domain optical coherence tomography (SD OCT) and fundus autofluorescence (FAF). Diagnoses of CSNB2 and RP were confirmed by full-field electroretinography (ERG). Manual segmentation of retinal layers, aided by a computer program, was performed by 2 professional segmenters on SD OCT images of all CSNB2 patients and 4 age-similar, normal myopic controls. Seven patients were screened for mutations with congenital stationary night blindness and RP genotyping arrays. RESULTS Patients with CSNB2 had specific findings on SD OCT and FAF that were distinct from those found in RP. CSNB2 patients showed qualitatively normal SD OCT results with preserved photoreceptor inner segment/outer segment junction, whereas this junction was lost in RP patients. In addition, CSNB2 patients had normal FAF images, whereas patients with RP demonstrated a ring of increased autofluorescence around the macula. On SD OCT segmentation, the inner and outer retinal layers of both X-linked recessive and autosomal recessive CSNB2 patients were thinner compared with those of normal myopic controls, with means generally outside of normal 95% confidence intervals. The only layers that demonstrated similar thickness between CSNB2 patients and the controls were the retinal nerve fiber layer and, temporal to the fovea, the combined outer segment layer and retinal pigment epithelium. A proband and his 2 affected brothers from a family segregating X-linked recessive

  4. Automated detection of exudative age-related macular degeneration in spectral domain optical coherence tomography using deep learning.

    Science.gov (United States)

    Treder, Maximilian; Lauermann, Jost Lennart; Eter, Nicole

    2018-02-01

    Our purpose was to use deep learning for the automated detection of age-related macular degeneration (AMD) in spectral domain optical coherence tomography (SD-OCT). A total of 1112 cross-section SD-OCT images of patients with exudative AMD and a healthy control group were used for this study. In the first step, an open-source multi-layer deep convolutional neural network (DCNN), which was pretrained with 1.2 million images from ImageNet, was trained and validated with 1012 cross-section SD-OCT scans (AMD: 701; healthy: 311). During this procedure training accuracy, validation accuracy and cross-entropy were computed. The open-source deep learning framework TensorFlow™ (Google Inc., Mountain View, CA, USA) was used to accelerate the deep learning process. In the last step, a created DCNN classifier, using the information of the above mentioned deep learning process, was tested in detecting 100 untrained cross-section SD-OCT images (AMD: 50; healthy: 50). Therefore, an AMD testing score was computed: 0.98 or higher was presumed for AMD. After an iteration of 500 training steps, the training accuracy and validation accuracies were 100%, and the cross-entropy was 0.005. The average AMD scores were 0.997 ± 0.003 in the AMD testing group and 0.9203 ± 0.085 in the healthy comparison group. The difference between the two groups was highly significant (p deep learning-based approach using TensorFlow™, it is possible to detect AMD in SD-OCT with high sensitivity and specificity. With more image data, an expansion of this classifier for other macular diseases or further details in AMD is possible, suggesting an application for this model as a support in clinical decisions. Another possible future application would involve the individual prediction of the progress and success of therapy for different diseases by automatically detecting hidden image information.

  5. Consistency and stability of narrative coherence: An examination of personal narrative as a domain of adult personality.

    Science.gov (United States)

    Waters, Theodore E A; Köber, Christin; Raby, K Lee; Habermas, Tilmann; Fivush, Robyn

    2018-03-02

    Narrative theories of personality assume that individual differences in coherence reflect consistent and stable differences in narrative style rather than situational and event-specific differences (e.g., McAdams & McLean, 2013). However, this assumption has received only modest empirical attention. Therefore, we present two studies testing the theoretical assumption of a consistent and stable coherent narrative style. Study 1 focused on the two most traumatic and most positive life events of 224 undergraduates. These event-specific narratives were coded for three coherence dimensions: theme, context, and chronology (NaCCs; Reese et al., 2011). Study 2 focused on two life narratives told 4 years apart by 98 adults, which were coded for thematic, causal, and temporal coherence (Köber, Schmiedek, & Habermas, 2015). Confirmatory factor analysis in both studies revealed that individual differences in the coherence ratings were best explained by a model including both narrative style and event-/narration-specific latent variables. The ways in which we tell autobiographical narratives reflect a stable feature of individual differences. Further, they suggest that this stable element of personality is necessary, but not sufficient, in accounting for specific event and life narrative coherence. © 2018 Wiley Periodicals, Inc.

  6. Optical coherence tomography-based decision making in exudative age-related macular degeneration: comparison of time- vs spectral-domain devices.

    Science.gov (United States)

    Cukras, C; Wang, Y D; Meyerle, C B; Forooghian, F; Chew, E Y; Wong, W T

    2010-05-01

    To determine whether optical coherence tomography (OCT) device-type influences clinical grading of OCT imaging in the context of exudative age-related macular degeneration (AMD). Ninety-six paired OCT scans from 49 patients with active exudative AMD were obtained on both the time-domain Stratus OCT system and the spectral-domain Cirrus OCT system at the same visit. Three independent graders judged each scan for the presence of intraretinal fluid (IRF) or subretinal fluid (SRF). The degree of grader consensus was evaluated and the ability of the systems to detect the presence of disease activity was analysed. Cirrus OCT generated a higher degree of inter-grader consensus than Stratus OCT with higher intraclass correlation coefficients for all parameters analysed. A pair-wise comparison of Cirrus OCT with Stratus OCT systems revealed that Cirrus-based gradings more frequently reported the presence of SRF and IRF and detected overall neovascular activity at a higher rate (P<0.05) compared with Stratus-based gradings. The choice of time-domain (Stratus) vs spectra-domain (Cirrus) OCT systems has a measurable impact on clinical decision making in exudative AMD. Spectral-domain OCT systems may be able to generate more consensus in clinical interpretation and, in particular cases, detect disease activity not detected by time-domain systems. Clinical trials using OCT-based clinical evaluations of exudative AMD may need to account for these inter-system differences in planning and analysis.

  7. Propagator formalism and computer simulation of restricted diffusion behaviors of inter-molecular multiple-quantum coherences

    International Nuclear Information System (INIS)

    Cai Congbo; Chen Zhong; Cai Shuhui; Zhong Jianhui

    2005-01-01

    In this paper, behaviors of single-quantum coherences and inter-molecular multiple-quantum coherences under restricted diffusion in nuclear magnetic resonance experiments were investigated. The propagator formalism based on the loss of spin phase memory during random motion was applied to describe the diffusion-induced signal attenuation. The exact expression of the signal attenuation under the short gradient pulse approximation for restricted diffusion between two parallel plates was obtained using this propagator method. For long gradient pulses, a modified formalism was proposed. The simulated signal attenuation under the effects of gradient pulses of different width based on the Monte Carlo method agrees with the theoretical predictions. The propagator formalism and computer simulation can provide convenient, intuitive and precise methods for the study of the diffusion behaviors

  8. Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations

    Science.gov (United States)

    Yu, Hang; Schulten, Klaus

    2013-01-01

    Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called scaffolding mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domains 3-helix bundle structure. A CG simulation covering more than 350 µs provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified the optimal lattice type for membrane sculpting, which matches closely the lattices seen through cryo-electron microscopy. PMID:23382665

  9. Rift Valley fever phlebovirus NSs protein core domain structure suggests molecular basis for nuclear filaments.

    Science.gov (United States)

    Barski, Michal; Brennan, Benjamin; Miller, Ona K; Potter, Jane A; Vijayakrishnan, Swetha; Bhella, David; Naismith, James H; Elliott, Richard M; Schwarz-Linek, Ulrich

    2017-09-15

    Rift Valley fever phlebovirus (RVFV) is a clinically and economically important pathogen increasingly likely to cause widespread epidemics. RVFV virulence depends on the interferon antagonist non-structural protein (NSs), which remains poorly characterized. We identified a stable core domain of RVFV NSs (residues 83-248), and solved its crystal structure, a novel all-helical fold organized into highly ordered fibrils. A hallmark of RVFV pathology is NSs filament formation in infected cell nuclei. Recombinant virus encoding the NSs core domain induced intranuclear filaments, suggesting it contains all essential determinants for nuclear translocation and filament formation. Mutations of key crystal fibril interface residues in viruses encoding full-length NSs completely abrogated intranuclear filament formation in infected cells. We propose the fibrillar arrangement of the NSs core domain in crystals reveals the molecular basis of assembly of this key virulence factor in cell nuclei. Our findings have important implications for fundamental understanding of RVFV virulence.

  10. Molecular representation of molar domain (volume), evolution equations, and linear constitutive relations for volume transport.

    Science.gov (United States)

    Eu, Byung Chan

    2008-09-07

    In the traditional theories of irreversible thermodynamics and fluid mechanics, the specific volume and molar volume have been interchangeably used for pure fluids, but in this work we show that they should be distinguished from each other and given distinctive statistical mechanical representations. In this paper, we present a general formula for the statistical mechanical representation of molecular domain (volume or space) by using the Voronoi volume and its mean value that may be regarded as molar domain (volume) and also the statistical mechanical representation of volume flux. By using their statistical mechanical formulas, the evolution equations of volume transport are derived from the generalized Boltzmann equation of fluids. Approximate solutions of the evolution equations of volume transport provides kinetic theory formulas for the molecular domain, the constitutive equations for molar domain (volume) and volume flux, and the dissipation of energy associated with volume transport. Together with the constitutive equation for the mean velocity of the fluid obtained in a previous paper, the evolution equations for volume transport not only shed a fresh light on, and insight into, irreversible phenomena in fluids but also can be applied to study fluid flow problems in a manner hitherto unavailable in fluid dynamics and irreversible thermodynamics. Their roles in the generalized hydrodynamics will be considered in the sequel.

  11. New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Yesylevskyy S. O.

    2010-04-01

    Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed

  12. Development of a phase-sensitive Fourier domain optical coherence tomography system to measure mouse organ of Corti vibrations in two cochlear turns

    Energy Technology Data Exchange (ETDEWEB)

    Ramamoorthy, Sripriya [Oregon Hearing Research Center, Oregon Health & Science University, Portland, Oregon (United States); Zhang, Yuan; Jacques, Steven [Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon (United States); Petrie, Tracy; Wang, Ruikang [Department of Bioengineering, University of Washington, Seattle, Washington (United States); Nuttall, Alfred L. [Oregon Hearing Research Center, Oregon Health & Science University, Portland, Oregon (United States); Kresge Hearing Research Institute, The University of Michigan, Ann Arbor, Michigan (United States)

    2015-12-31

    In this study, we have developed a phase-sensitive Fourier-domain optical coherence tomography system to simultaneously measure the in vivo inner ear vibrations in the hook area and second turn of the mouse cochlea. This technical development will enable measurement of intra-cochlear distortion products at ideal locations such as the distortion product generation site and reflection site. This information is necessary to un-mix the complex mixture of intra-cochlear waves comprising the DPOAE and thus leads to the non-invasive identification of the local region of cochlear damage.

  13. A parallel adaptive finite element simplified spherical harmonics approximation solver for frequency domain fluorescence molecular imaging

    International Nuclear Information System (INIS)

    Lu Yujie; Zhu Banghe; Rasmussen, John C; Sevick-Muraca, Eva M; Shen Haiou; Wang Ge

    2010-01-01

    Fluorescence molecular imaging/tomography may play an important future role in preclinical research and clinical diagnostics. Time- and frequency-domain fluorescence imaging can acquire more measurement information than the continuous wave (CW) counterpart, improving the image quality of fluorescence molecular tomography. Although diffusion approximation (DA) theory has been extensively applied in optical molecular imaging, high-order photon migration models need to be further investigated to match quantitation provided by nuclear imaging. In this paper, a frequency-domain parallel adaptive finite element solver is developed with simplified spherical harmonics (SP N ) approximations. To fully evaluate the performance of the SP N approximations, a fast time-resolved tetrahedron-based Monte Carlo fluorescence simulator suitable for complex heterogeneous geometries is developed using a convolution strategy to realize the simulation of the fluorescence excitation and emission. The validation results show that high-order SP N can effectively correct the modeling errors of the diffusion equation, especially when the tissues have high absorption characteristics or when high modulation frequency measurements are used. Furthermore, the parallel adaptive mesh evolution strategy improves the modeling precision and the simulation speed significantly on a realistic digital mouse phantom. This solver is a promising platform for fluorescence molecular tomography using high-order approximations to the radiative transfer equation.

  14. Long-lived coherences: Improved dispersion in the frequency domain using continuous-wave and reduced-power windowed sustaining irradiation

    Science.gov (United States)

    Sadet, A.; Fernandes, L.; Kateb, F.; Balzan, R.; Vasos, P. R.

    2014-08-01

    Long-lived coherences (LLC's) are detectable magnetisation modes with favourable relaxation times that translate as sharp resonances upon Fourier transform. The frequency domain of LLC's was previously limited to the range of J-couplings within pairs of homonuclear spins. LLC evolution at high magnetic fields needs to be sustained by radio-frequency irradiation. We show that LLC-based spectral dispersion can be extended beyond the J-couplings domain using adapted carrier offsets and introduce a new reduced-power sustaining method to preserve LLC's within the required range of offsets. Spectral resolution is enhanced as the natively narrow lines of LLC's are further dispersed, making them potential probes for the study of biomolecules featuring strong resonance overlap and for media where NMR spectroscopy is commonly hindered by line broadening.

  15. Long-lived coherences: Improved dispersion in the frequency domain using continuous-wave and reduced-power windowed sustaining irradiation

    International Nuclear Information System (INIS)

    Sadet, A.; Fernandes, L.; Kateb, F.; Balzan, R.; Vasos, P. R.

    2014-01-01

    Long-lived coherences (LLC’s) are detectable magnetisation modes with favourable relaxation times that translate as sharp resonances upon Fourier transform. The frequency domain of LLC's was previously limited to the range of J-couplings within pairs of homonuclear spins. LLC evolution at high magnetic fields needs to be sustained by radio-frequency irradiation. We show that LLC-based spectral dispersion can be extended beyond the J-couplings domain using adapted carrier offsets and introduce a new reduced-power sustaining method to preserve LLC's within the required range of offsets. Spectral resolution is enhanced as the natively narrow lines of LLC's are further dispersed, making them potential probes for the study of biomolecules featuring strong resonance overlap and for media where NMR spectroscopy is commonly hindered by line broadening

  16. Long-lived coherences: Improved dispersion in the frequency domain using continuous-wave and reduced-power windowed sustaining irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Sadet, A.; Fernandes, L.; Kateb, F., E-mail: fatiha.kateb@parisdescartes.fr, E-mail: balzan.riccardo@parisdescartes.fr; Balzan, R., E-mail: fatiha.kateb@parisdescartes.fr, E-mail: balzan.riccardo@parisdescartes.fr; Vasos, P. R. [Laboratoire de Chimie et Biochimie Toxicologiques et Pharmacologiques UMR-8601, Université Paris Descartes - CNRS, PRES Paris Sorbonne Cité, 75006 Paris (France)

    2014-08-07

    Long-lived coherences (LLC’s) are detectable magnetisation modes with favourable relaxation times that translate as sharp resonances upon Fourier transform. The frequency domain of LLC's was previously limited to the range of J-couplings within pairs of homonuclear spins. LLC evolution at high magnetic fields needs to be sustained by radio-frequency irradiation. We show that LLC-based spectral dispersion can be extended beyond the J-couplings domain using adapted carrier offsets and introduce a new reduced-power sustaining method to preserve LLC's within the required range of offsets. Spectral resolution is enhanced as the natively narrow lines of LLC's are further dispersed, making them potential probes for the study of biomolecules featuring strong resonance overlap and for media where NMR spectroscopy is commonly hindered by line broadening.

  17. Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily.

    Science.gov (United States)

    Civera, Concepcion; Simon, Bernd; Stier, Gunter; Sattler, Michael; Macias, Maria J

    2005-02-01

    Pleckstrin1 is a major substrate for protein kinase C in platelets and leukocytes, and comprises a central DEP (disheveled, Egl-10, pleckstrin) domain, which is flanked by two PH (pleckstrin homology) domains. DEP domains display a unique alpha/beta fold and have been implicated in membrane binding utilizing different mechanisms. Using multiple sequence alignments and phylogenetic tree reconstructions, we find that 6 subfamilies of the DEP domain exist, of which pleckstrin represents a novel and distinct subfamily. To clarify structural determinants of the DEP fold and to gain further insight into the role of the DEP domain, we determined the three-dimensional structure of the pleckstrin DEP domain using heteronuclear NMR spectroscopy. Pleckstrin DEP shares main structural features with the DEP domains of disheveled and Epac, which belong to different DEP subfamilies. However, the pleckstrin DEP fold is distinct from these structures and contains an additional, short helix alpha4 inserted in the beta4-beta5 loop that exhibits increased backbone mobility as judged by NMR relaxation measurements. Based on sequence conservation, the helix alpha4 may also be present in the DEP domains of regulator of G-protein signaling (RGS) proteins, which are members of the same DEP subfamily. In pleckstrin, the DEP domain is surrounded by two PH domains. Structural analysis and charge complementarity suggest that the DEP domain may interact with the N-terminal PH domain in pleckstrin. Phosphorylation of the PH-DEP linker, which is required for pleckstrin function, could regulate such an intramolecular interaction. This suggests a role of the pleckstrin DEP domain in intramolecular domain interactions, which is distinct from the functions of other DEP domain subfamilies found so far.

  18. Optimal identification of semi-rigid domains in macromolecules from molecular dynamics simulation.

    Directory of Open Access Journals (Sweden)

    Stefan Bernhard

    Full Text Available Biological function relies on the fact that biomolecules can switch between different conformations and aggregation states. Such transitions involve a rearrangement of parts of the biomolecules involved that act as dynamic domains. The reliable identification of such domains is thus a key problem in biophysics. In this work we present a method to identify semi-rigid domains based on dynamical data that can be obtained from molecular dynamics simulations or experiments. To this end the average inter-atomic distance-deviations are computed. The resulting matrix is then clustered by a constrained quadratic optimization problem. The reliability and performance of the method are demonstrated for two artificial peptides. Furthermore we correlate the mechanical properties with biological malfunction in three variants of amyloidogenic transthyretin protein, where the method reveals that a pathological mutation destabilizes the natural dimer structure of the protein. Finally the method is used to identify functional domains of the GroEL-GroES chaperone, thus illustrating the efficiency of the method for large biomolecular machines.

  19. Optical Coherence Tomography-Based Decision Making in Exudative Age-related Macular Degeneration: Comparison of Time- versus Spectral-Domain Devices

    Science.gov (United States)

    Cukras, Catherine; Wang, Yunqing D.; Meyerle, Catherine B.; Forooghian, Farzin; Chew, Emily Y.; Wong, Wai T.

    2010-01-01

    Purpose To determine if optical coherence tomography (OCT) device-type influences clinical grading of OCT imaging in the context of exudative age-related macular degeneration (AMD). Methods Ninety-six paired OCT scans from 49 patients with active exudative AMD were obtained on both the time-domain Stratus™ OCT system and the spectral-domain Cirrus™ OCT system at the same visit. Three independent graders judged each scan for the presence of intraretinal fluid (IRF) or subretinal fluid (SRF). The degree of grader consensus was evaluated and the ability of the systems to detect the presence of disease activity was analyzed. Results Cirrus™ OCT generated a higher degree of inter-grader consensus than Stratus OCT with higher intraclass correlation coefficients (ICC) for all parameters analyzed. A pair-wise comparison of Cirrus™ OCT to Stratus™ OCT systems revealed that Cirrus™-based gradings more frequently reported the presence of SRF and IRF and detected overall neovascular activity at a higher rate (p<0.05) compared to Stratus™-based gradings Conclusions The choice of time-domain (Stratus™) versus spectra-domain (Cirrus™) OCT systems has a measurable impact on clinical decision making in exudative AMD. Spectral-domain OCT systems may be able to generate more consensus in clinical interpretation and, in particular cases, detect disease activity not detected by time-domain systems. Clinical trials employing OCT-based clinical evaluations of exudative AMD may need to account for these inter-system differences in planning and analysis. PMID:19696804

  20. Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

    Science.gov (United States)

    Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

    2018-02-12

    The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

  1. Multiscale Modeling using Molecular Dynamics and Dual Domain Material Point Method

    Energy Technology Data Exchange (ETDEWEB)

    Dhakal, Tilak Raj [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division. Fluid Dynamics and Solid Mechanics Group, T-3; Rice Univ., Houston, TX (United States)

    2016-07-07

    For problems involving large material deformation rate, the material deformation time scale can be shorter than the material takes to reach a thermodynamical equilibrium. For such problems, it is difficult to obtain a constitutive relation. History dependency become important because of thermodynamic non-equilibrium. Our goal is to build a multi-scale numerical method which can bypass the need for a constitutive relation. In conclusion, multi-scale simulation method is developed based on the dual domain material point (DDMP). Molecular dynamics (MD) simulation is performed to calculate stress. Since the communication among material points is not necessary, the computation can be done embarrassingly parallel in CPU-GPU platform.

  2. Exploring coherent transport through π-stacked systems for molecular electronic devices

    DEFF Research Database (Denmark)

    Li, Qian; Solomon, Gemma

    2014-01-01

    Understanding electron transport across π-stacked systems can help to elucidate the role of intermolecular tunneling in molecular junctions and potentially with the design of high-efficiency molecular devices. Here we show how conjugation length and substituent groups influence the electron trans...

  3. Rapid spectro-polarimetry to probe molecular symmetry in multiplex coherent anti-Stokes Raman scattering.

    Science.gov (United States)

    Würthwein, Thomas; Brinkmann, Maximilian; Hellwig, Tim; Fallnich, Carsten

    2017-11-21

    We present the simultaneous detection of the spectrum and the complete polarization state of a multiplex coherent anti-Stokes Raman scattering signal with a fast division-of-amplitude spectro-polarimeter. The spectro-polarimeter is based on a commercial imaging spectrograph, a birefringent wedge prism, and a segmented polarizer. Compared to the standard rotating-retarder fixed-analyzer spectro-polarimeter, only a single measurement is required and an up to 21-fold reduced acquisition time is shown. The measured Stokes parameters allow us to differentiate between vibrational symmetries and to determine the depolarization ratio ρ by data post-processing.

  4. Metrological-grade tunable coherent source in the mid-infrared for molecular precision spectroscopy

    Science.gov (United States)

    Insero, G.; Clivati, C.; D'Ambrosio, D.; Cancio Pastor, P.; Verde, M.; Schunemann, P. G.; Zondy, J.-J.; Inguscio, M.; Calonico, D.; Levi, F.; De Natale, P.; Santambrogio, G.; Borri, S.

    2018-02-01

    We report on a metrological-grade mid-IR source with a 10-14 short-term instability for high-precision spectroscopy. Our source is based on the combination of a quantum cascade laser and a coherent radiation obtained by difference-frequency generation in an orientation-patterned gallium phosphide (OP-GaP) crystal. The pump and signal lasers are locked to an optical frequency comb referenced to the primary frequency standard via an optical fiber link. We demonstrate the robustness of the apparatus by measuring a vibrational transition around 6 μm on a metastable state of CO molecuels with 11 digits of precision.

  5. On the coherent behavior of pancreatic beta cell clusters

    Energy Technology Data Exchange (ETDEWEB)

    Loppini, Alessandro, E-mail: a.loppini@unicampus.it [Nonlinear Physics and Mathematical Modeling Lab, University Campus Bio-Medico, Via A. del Portillo 21, I-00128 Rome (Italy); Capolupo, Antonio, E-mail: capolupo@sa.infn.it [Physics Department, University of Salerno, Fisciano, 84084 (Italy); Cherubini, Christian, E-mail: c.cherubini@unicampus.it [Nonlinear Physics and Mathematical Modeling Lab, University Campus Bio-Medico, Via A. del Portillo 21, I-00128 Rome (Italy); International Center for Relativistic Astrophysics, University Campus Bio-Medico, Via A. del Portillo 21, I-00128, Rome (Italy); Gizzi, Alessio, E-mail: a.gizzi@unicampus.it [Nonlinear Physics and Mathematical Modeling Lab, University Campus Bio-Medico, Via A. del Portillo 21, I-00128 Rome (Italy); Bertolaso, Marta, E-mail: m.bertolaso@unicampus.it [Faculty of Engineering and Institute of Philosophy of Scientific and Technological Practice, University Campus Bio-Medico, Via A. del Portillo 21, I-00128 Rome (Italy); Filippi, Simonetta, E-mail: s.filippi@unicampus.it [Nonlinear Physics and Mathematical Modeling Lab, University Campus Bio-Medico, Via A. del Portillo 21, I-00128 Rome (Italy); International Center for Relativistic Astrophysics, University Campus Bio-Medico, Via A. del Portillo 21, I-00128, Rome (Italy); Vitiello, Giuseppe, E-mail: vitiello@sa.infn.it [Physics Department, University of Salerno, Fisciano, 84084 (Italy)

    2014-09-12

    Beta cells in pancreas represent an example of coupled biological oscillators which via communication pathways, are able to synchronize their electrical activity, giving rise to pulsatile insulin release. In this work we numerically analyze scale free self-similarity features of membrane voltage signal power density spectrum, through a stochastic dynamical model for beta cells in the islets of Langerhans fine tuned on mouse experimental data. Adopting the algebraic approach of coherent state formalism, we show how coherent molecular domains can arise from proper functional conditions leading to a parallelism with “phase transition” phenomena of field theory. - Highlights: • Beta cells in pancreas are coupled oscillators able to synchronize their activity. • We analyze scale free self-similarity features for beta cells. • We adopt the algebraic approach of coherent state formalism. • We show that coherent molecular domains arise from functional conditions.

  6. Breaching Biological Barriers: Protein Translocation Domains as Tools for Molecular Imaging and Therapy

    Directory of Open Access Journals (Sweden)

    Benjamin L. Franc

    2003-10-01

    Full Text Available The lipid bilayer of a cell presents a significant barrier for the delivery of many molecular imaging reagents into cells at target sites in the body. Protein translocation domains (PTDs are peptides that breach this barrier. Conjugation of PTDs to imaging agents can be utilized to facilitate the delivery of these agents through the cell wall, and in some cases, into the cell nucleus, and have potential for in vitro and in vivo applications. PTD imaging conjugates have included small molecules, peptides, proteins, DNA, metal chelates, and magnetic nanoparticles. The full potential of the use of PTDs in novel in vivo molecular probes is currently under investigation. Cells have been labeled in culture using magnetic nanoparticles derivatized with a PTD and monitored in vivo to assess trafficking patterns relative to cells expressing a target antigen. In vivo imaging of PTD-mediated gene transfer to cells of the skin has been demonstrated in living animals. Here we review several natural and synthetic PTDs that have evolved in the quest for easier translocation across biological barriers and the application of these peptide domains to in vivo delivery of imaging agents.

  7. Molecular determinants of tetramerization in the KcsA cytoplasmic domain.

    Science.gov (United States)

    Kamnesky, Guy; Hirschhorn, Orel; Shaked, Hadassa; Chen, Jingfei; Yao, Lishan; Chill, Jordan H

    2014-10-01

    The cytoplasmic C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is an amphiphilic domain that forms a helical bundle with four-fold symmetry mediated by hydrophobic and electrostatic interactions. Previously we have established that a CTD-derived 34-residue peptide associates into a tetramer in a pH-dependent manner (Kamnesky et al., JMB 2012;418:237-247). Here we further investigate the molecular determinants of tetramer formation in the CTD by characterizing the kinetics of monomer-tetramer equilibrium for 10 alanine mutants using NMR, sedimentation equilibrium (SE) and molecular dynamics simulation. NMR and SE concur in finding single-residue contributions to tetramer stability to be in the 0.5 to 3.5 kcal/mol range. Hydrophobic interactions between residues lining the tetramer core generally contributed more to formation of tetramer than electrostatic interactions between residues R147, D149 and E152. In particular, alanine replacement of residue R147, a key contributor to inter-subunit salt bridges, resulted in only a minor effect on tetramer dissociation. Mutations outside of the inter-subunit interface also influenced tetramer stability by affecting the tetramerization on-rate, possibly by changing the inherent helical propensity of the peptide. These findings are interpreted in the context of established paradigms of protein-protein interactions and protein folding, and lay the groundwork for further studies of the CTD in full-length KcsA channels. © 2014 The Protein Society.

  8. Discovery of new molecular entities able to strongly interfere with Hsp90 C-terminal domain.

    Science.gov (United States)

    Terracciano, Stefania; Russo, Alessandra; Chini, Maria G; Vaccaro, Maria C; Potenza, Marianna; Vassallo, Antonio; Riccio, Raffaele; Bifulco, Giuseppe; Bruno, Ines

    2018-01-26

    Heat shock protein 90 (Hsp90) is an ATP dependent molecular chaperone deeply involved in the complex network of cellular signaling governing some key functions, such as cell proliferation and survival, invasion and angiogenesis. Over the past years the N-terminal protein domain has been fully investigated as attractive strategy against cancer, but despite the many efforts lavished in the field, none of the N-terminal binders (termed "classical inhibitors"), currently in clinical trials, have yet successfully reached the market, because of the detrimental heat shock response (HSR) that showed to induce; thus, recently, the selective inhibition of Hsp90 C-terminal domain has powerfully emerged as a more promising alternative strategy for anti-cancer therapy, not eliciting this cell rescue cascade. However, the structural complexity of the target protein and, mostly, the lack of a co-crystal structure of C-terminal domain-ligand, essential to drive the identification of new hits, represent the largest hurdles in the development of new selective C-terminal inhibitors. Continuing our investigations on the identification of new anticancer drug candidates, by using an orthogonal screening approach, here we describe two new potent C-terminal inhibitors able to induce cancer cell death and a considerable down-regulation of Hsp90 client oncoproteins, without triggering the undesired heat shock response.

  9. Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain

    Directory of Open Access Journals (Sweden)

    Hussain Abrar

    2011-11-01

    Full Text Available Abstract Background The Elk-1 transcription factor is a member of a group of proteins called ternary complex factors, which serve as a paradigm for gene regulation in response to extracellular signals. Its deregulation has been linked to multiple human diseases including the development of tumours. The work herein aims to inform the design of potential peptidomimetic compounds that can inhibit the formation of the Elk-1 dimer, which is key to Elk-1 stability. We have conducted molecular dynamics simulations of the Elk-1 ETS domain followed by virtual screening. Results We show the ETS dimerisation site undergoes conformational reorganisation at the α1β1 loop. Through exhaustive screening of di- and tri-peptide libraries against a collection of ETS domain conformations representing the dynamics of the loop, we identified a series of potential binders for the Elk-1 dimer interface. The di-peptides showed no particular preference toward the binding site; however, the tri-peptides made specific interactions with residues: Glu17, Gln18 and Arg49 that are pivotal to the dimer interface. Conclusions We have shown molecular dynamics simulations can be combined with virtual peptide screening to obtain an exhaustive docking protocol that incorporates dynamic fluctuations in a receptor. Based on our findings, we suggest experimental binding studies to be performed on the 12 SILE ranked tri-peptides as possible compounds for the design of inhibitors of Elk-1 dimerisation. It would also be reasonable to consider the score-ranked tri-peptides as a comparative test to establish whether peptide size is a determinant factor of binding to the ETS domain.

  10. 3D wide field-of-view Gabor-domain optical coherence microscopy advancing real-time in-vivo imaging and metrology

    Science.gov (United States)

    Canavesi, Cristina; Cogliati, Andrea; Hayes, Adam; Tankam, Patrice; Santhanam, Anand; Rolland, Jannick P.

    2017-02-01

    Real-time volumetric high-definition wide-field-of-view in-vivo cellular imaging requires micron-scale resolution in 3D. Compactness of the handheld device and distortion-free images with cellular resolution are also critically required for onsite use in clinical applications. By integrating a custom liquid lens-based microscope and a dual-axis MEMS scanner in a compact handheld probe, Gabor-domain optical coherence microscopy (GD-OCM) breaks the lateral resolution limit of optical coherence tomography through depth, overcoming the tradeoff between numerical aperture and depth of focus, enabling advances in biotechnology. Furthermore, distortion-free imaging with no post-processing is achieved with a compact, lightweight handheld MEMS scanner that obtained a 12-fold reduction in volume and 17-fold reduction in weight over a previous dual-mirror galvanometer-based scanner. Approaching the holy grail of medical imaging - noninvasive real-time imaging with histologic resolution - GD-OCM demonstrates invariant resolution of 2 μm throughout a volume of 1 x 1 x 0.6 mm3, acquired and visualized in less than 2 minutes with parallel processing on graphics processing units. Results on the metrology of manufactured materials and imaging of human tissue with GD-OCM are presented.

  11. Can Excited State Electronic Coherence Be Tuned via Molecular Structural Modification? A First-Principles Quantum Electronic Dynamics Study of Pyrazolate-Bridged Pt(II) Dimers

    Energy Technology Data Exchange (ETDEWEB)

    Lingerfelt, David B.; Lestrange, Patrick J.; Radler, Joseph J.; Brown-Xu, Samantha E.; Kim, Pyosang; Castellano, Felix N.; Chen, Lin X.; Li, Xiaosong

    2017-02-24

    Materials and molecular systems exhibiting long-lived electronic coherence can facilitate coherent transport, opening the door to efficient charge and energy transport beyond traditional methods. Recently, signatures of a possible coherent, recurrent electronic motion were identified in femtosecond pump-probe spectroscopy experiments on a binuclear platinum complex, where a persistent periodic beating in the transient absorption signal’s anisotropy was observed. In this study, we investigate the excitonic dynamics that underlie the suspected electronic coherence for a series of binuclear platinum complexes exhibiting a range of interplatinum distances. Results suggest that the long-lived coherence can only result when competitive electronic couplings are in balance. At longer Pt-Pt distances, the electronic couplings between the two halves of the binuclear system weaken, and exciton localization and recombination is favored on short time scales. For short Pt-Pt distances, electronic couplings between the states in the coherent superposition are stronger than the coupling with other excitonic states, leading to long-lived coherence.

  12. Mechanism of Retinal Pigment Epithelium Tear Formation Following Intravitreal Anti–Vascular Endothelial Growth Factor Therapy Revealed by Spectral-Domain Optical Coherence Tomography

    DEFF Research Database (Denmark)

    Nagiel, Aaron; Freund, K Bailey; Spaide, Richard F

    2013-01-01

    to the retracted RPE. In all eyes, the RPE ruptured along a segment of bare RPE not in contact with the CNV or Bruch membrane. CONCLUSIONS: Eyes with vascularized PEDs secondary to AMD may show specific OCT findings that increase the risk for RPE tear following intravitreal anti-VEGF injection. Rapid involution......PURPOSE: To demonstrate the mechanism by which retinal pigment epithelium (RPE) tears occur in eyes with neovascular age-related macular degeneration (AMD) treated with intravitreal anti-vascular endothelial growth factor (VEGF) agents using spectral-domain optical coherence tomography (OCT......). DESIGN: Retrospective observational case series. METHODS: OCT images of 8 eyes that developed RPE tears following the administration of intravitreal anti-VEGF agents for neovascular AMD were evaluated. Pretear and posttear images were compared in order to elucidate the mechanism by which RPE tears occur...

  13. Imaging vibration of the cochlear partition of an excised guinea pig cochlea using phase-sensitive Fourier domain optical coherence tomography

    Science.gov (United States)

    Choudhury, Niloy; Zeng, Yaguang; Fridberger, Anders; Chen, Fangyi; Zha, Dingjun; Nuttall, Alfred L.; Wang, Ruikang K.

    2011-03-01

    Studying the sound stimulated vibrations of various membranes that form the complex structure of the organ of Corti in the cochlea of the inner ear is essential for understanding how the travelling sound wave of the basilar membrane couples its energy to the organ structures. In this paper we report the feasibility of using phase-sensitive Fourier domain optical coherence tomography (FD-OCT) to image the vibration of various micro-structures of the cochlea at the same time. An excised cochlea of a guinea pig was stimulated using sounds at various frequencies and vibration image was obtained. When measuring the apex area, vibration signal from different turns, which have different best response frequencies are obtained in the same image. The method has the potential to measure the response from a much wider region of the cochlea than any other currently used method. The noise floor for vibration image for the system at 200 Hz was ~0.3nm.

  14. Absolute measurement of subnanometer scale vibration of cochlear partition of an excised guinea pig cochlea using spectral-domain phase-sensitive optical coherence tomography

    Science.gov (United States)

    Subhash, Hrebesh M.; Choudhury, Niloy; Jacques, Steven L.; Wang, Ruikang K.; Chen, Fangyi; Zha, Dingjun; Nuttall, Alfred L.

    2012-01-01

    Direct measurement of absolute vibration parameters from different locations within the mammalian organ of Corti is crucial for understanding the hearing mechanics such as how sound propagates through the cochlea and how sound stimulates the vibration of various structures of the cochlea, namely, basilar membrane (BM), recticular lamina, outer hair cells and tectorial membrane (TM). In this study we demonstrate the feasibility a modified phase-sensitive spectral domain optical coherence tomography system to provide subnanometer scale vibration information from multiple angles within the imaging beam. The system has the potential to provide depth resolved absolute vibration measurement of tissue microstructures from each of the delay-encoded vibration images with a noise floor of ~0.3nm at 200Hz.

  15. Two dimensional vibrations of the guinea pig apex organ of Corti measured in vivo using phase sensitive Fourier domain optical coherence tomography

    Science.gov (United States)

    Ramamoorthy, Sripriya; Zhang, Yuan; Petrie, Tracy; Fridberger, Anders; Ren, Tianying; Wang, Ruikang; Jacques, Steven L.; Nuttall, Alfred L.

    2015-02-01

    In this study, we measure the in vivo apical-turn vibrations of the guinea pig organ of Corti in both axial and radial directions using phase-sensitive Fourier domain optical coherence tomography. The apical turn in guinea pig cochlea has best frequencies around 100 - 500 Hz which are relevant for human speech. Prior measurements of vibrations in the guinea pig apex involved opening the otic capsule, which has been questioned on the basis of the resulting changes to cochlear hydrodynamics. Here this limitation is overcome by measuring the vibrations through bone without opening the otic capsule. Furthermore, we have significantly reduced the surgery needed to access the guinea pig apex in the axial direction by introducing a miniature mirror inside the bulla. The method and preliminary data are discussed in this article.

  16. Evaluation of Macular Ganglion Cell-inner Plexiform Layer and Choroid in Psoriasis Patients Using Enhanced Depth Imaging Spectral Domain Optical Coherence Tomography.

    Science.gov (United States)

    Ersan, Ismail; Kilic, Sevilay; Arikan, Sedat; Kara, Selcuk; Işik, Selda; Gencer, Baran; Ogretmen, Zerrin

    2017-08-01

    To evaluate changes in the thickness of the central macula, macular ganglion cell-inner plexiform layer (mGCIPL), and subfoveal choroid in patients with psoriasis using spectral domain optical coherence tomography (SD-OCT). The measurements of macular, mGCIPL thicknesses and subfoveal choroidal thickness (SFCT) obtained by SD-OCT of psoriasis patients (n = 46). These measurements were compared with those of 50 healthy controls. The macular, mGCIPL, and choroidal thicknesses did not differ between the controls and psoriatic subjects (p>0.05). When the patients were divided into two distinct groups, only the SFCT was significantly thicker in the severe psoriasis group compared with the mild psoriasis group (p = 0.003). These findings suggest that choroidal alterations are seen without macular changes in patients with psoriasis. Severe psoriasis appears to be related to increases in SFCT as a consequence of possible inflammatory cascades that are part of the disease's pathogenesis.

  17. Changes in Tear Volume after 3% Diquafosol Treatment in Patients with Dry Eye Syndrome: An Anterior Segment Spectral-domain Optical Coherence Tomography Study.

    Science.gov (United States)

    Lee, Kwan Bok; Koh, Kyung Min; Kwon, Young A; Song, Sang Wroul; Kim, Byoung Yeop; Chung, Jae Lim

    2017-08-01

    To evaluate changes in the tear meniscus area and tear meniscus height over time in patients with dry eye syndrome, using anterior segment spectral-domain optical coherence tomography after the instillation of 3% diquafosol ophthalmic solution. Sixty eyes from 30 patients with mild to moderate dry eye syndrome were included. Tear meniscus images acquired by anterior segment spectral-domain optical coherence tomography were analyzed using National Institutes of Health's image-analysis software (ImageJ 1.44p). Tear meniscus area and tear meniscus height were measured at baseline, 5 minutes, 10 minutes, and 30 minutes after instillation of a drop of diquafosol in one eye and normal saline in the other eye. Changes in ocular surface disease index score, tear film break-up time, corneal staining score by Oxford schema, and meibomian expressibility were also evaluated at baseline, and after 1 week and 1 month of a diquafosol daily regimen. Sixty eyes from 30 subjects (mean age, 29.3 years; 8 men and 22 women) were included. In eyes receiving diquafosol, tear volume was increased at 5 and 10 minutes compared with baseline. It was also higher than saline instilled eyes at 5, 10, and 30 minutes. Changes in tear volume with respect to baseline were not statistically different after the use of diquafosol for 1 month. Ocular surface disease index score, tear film break-up time, and Oxford cornea stain score were significantly improved after 1 week and 1 month of daily diquafosol instillation, but meibomian expressibility did not change. Topical diquafosol ophthalmic solution effectively increased tear volume for up to 30 minutes, compared to normal saline in patients with dry eye syndrome. © 2017 The Korean Ophthalmological Society

  18. Impact of retinal pigment epithelium pathology on spectral-domain optical coherence tomography-derived macular thickness and volume metrics and their intersession repeatability.

    Science.gov (United States)

    Hanumunthadu, Daren; Wang, Jin Ping; Chen, Wei; Wong, Evan N; Chen, Yi; Morgan, William H; Patel, Praveen J; Chen, Fred K

    2017-04-01

    To determine the impact of retinal pigment epithelium (RPE) pathology on intersession repeatability of retinal thickness and volume metrics derived from Spectralis spectral-domain optical coherence tomography (Heidelberg Engineering, Heidelberg, Germany). Prospective cross-sectional single centre study. A total of 56 eyes of 56 subjects were divided into three groups: (i) normal RPE band (25 eyes); (ii) RPE elevation: macular soft drusen (13 eyes); and (iii) RPE attenuation: geographic atrophy or inherited retinal diseases (18 eyes). Each subject underwent three consecutive follow-up macular raster scans (61 B-scans at 119 μm separation) at 1-month intervals. Retinal thicknesses and volumes for each zone of the macular subfields before and after manual correction of segmentation error. Coefficients of repeatability (CR) were calculated. Mean (range) age was 57 (21-88) years. Mean central subfield thickness (CST) and total macular volume were 264 and 258 μm (P = 0.62), and 8.0 and 7.8 mm 3 (P = 0.31), before and after manual correction. Intersession CR (95% confidence interval) for CST and total macular volume were reduced from 40 (38-41) to 8.3 (8.1-8.5) and 0.62 to 0.16 mm 3 after manual correction of segmentation lines. CR for CST were 7.4, 23.5 and 66.7 μm before and 7.0, 10.9 and 7.6 μm after manual correction in groups i, ii and iii. Segmentation error in eyes with RPE disease has a significant impact on intersession repeatability of Spectralis spectral-domain optical coherence tomography macular thickness and volume metrics. Careful examination of each B-scan and manual adjustment can enhance the utility of quantitative measurement. Improved automated segmentation algorithms are needed. © 2016 Royal Australian and New Zealand College of Ophthalmologists.

  19. Is Spectral-Domain Optical Coherence Tomography Essential for Flexible Treatment Regimens with Ranibizumab for Neovascular Age-Related Macular Degeneration?

    Directory of Open Access Journals (Sweden)

    Abdullah Ozkaya

    2013-01-01

    Full Text Available Purpose. To evaluate the ability of spectral-domain optical coherence tomography to detect subtle amounts of retinal fluid when the choroidal neovascularization is detected as inactive via time-domain optical coherence tomography and clinical examination in neovascular age-related macular degeneration (nAMD patients. Methods. Forty-nine eyes of 49 patients with nAMD after ranibizumab treatment were included in this cross-sectional, prospective study. All patients were imaged with TD-OCT and SD-OCT at the same visit one month after a ranibizumab injection. The presence of subretinal, intraretinal, and subretinal pigment epithelium fluid (subRPE in SD-OCT was evaluated; also mean central retinal thickness (CRT and the rate of vitreoretinal surface disorders detected via the two devices were evaluated. Results. The mean CRT via TD-OCT and SD-OCT was 218.1±51.3 and 325.7±78.8 microns. Sixteen patients (32.6% showed any kind of retinal fluid via SD-OCT. In detail, 8 patients (16.3% showed subretinal fluid, 10 patients (20.4% showed intraretinal fluid, and 3 patients (6.1% showed SubRPE fluid. The ability of detecting vitreoretinal surface disorders was comparable between the two devices, except vitreomacular traction. Conclusion. SD-OCT is essential for the nAMD patients who are on an as-needed treatment regimen with ranibizumab. Only TD-OCT and clinical examination may cause insufficient treatment in this group of patients.

  20. Preclinical evaluation and intraoperative human retinal imaging with a high-resolution microscope-integrated spectral domain optical coherence tomography device.

    Science.gov (United States)

    Hahn, Paul; Migacz, Justin; O'Donnell, Rachelle; Day, Shelley; Lee, Annie; Lin, Phoebe; Vann, Robin; Kuo, Anthony; Fekrat, Sharon; Mruthyunjaya, Prithvi; Postel, Eric A; Izatt, Joseph A; Toth, Cynthia A

    2013-01-01

    The authors have recently developed a high-resolution microscope-integrated spectral domain optical coherence tomography (MIOCT) device designed to enable OCT acquisition simultaneous with surgical maneuvers. The purpose of this report is to describe translation of this device from preclinical testing into human intraoperative imaging. Before human imaging, surgical conditions were fully simulated for extensive preclinical MIOCT evaluation in a custom model eye system. Microscope-integrated spectral domain OCT images were then acquired in normal human volunteers and during vitreoretinal surgery in patients who consented to participate in a prospective institutional review board-approved study. Microscope-integrated spectral domain OCT images were obtained before and at pauses in surgical maneuvers and were compared based on predetermined diagnostic criteria to images obtained with a high-resolution spectral domain research handheld OCT system (HHOCT; Bioptigen, Inc) at the same time point. Cohorts of five consecutive patients were imaged. Successful end points were predefined, including ≥80% correlation in identification of pathology between MIOCT and HHOCT in ≥80% of the patients. Microscope-integrated spectral domain OCT was favorably evaluated by study surgeons and scrub nurses, all of whom responded that they would consider participating in human intraoperative imaging trials. The preclinical evaluation identified significant improvements that were made before MIOCT use during human surgery. The MIOCT transition into clinical human research was smooth. Microscope-integrated spectral domain OCT imaging in normal human volunteers demonstrated high resolution comparable to tabletop scanners. In the operating room, after an initial learning curve, surgeons successfully acquired human macular MIOCT images before and after surgical maneuvers. Microscope-integrated spectral domain OCT imaging confirmed preoperative diagnoses, such as full-thickness macular hole

  1. A Micropulse eye-safe all-fiber molecular backscatter coherent temperature lidar

    Directory of Open Access Journals (Sweden)

    Abari Cyrus F.

    2016-01-01

    Full Text Available In this paper, we analyze the performance of an all-fiber, micropulse, 1.5 μm coherent lidar for remote sensing of atmospheric temperature. The proposed system benefits from the recent advances in optics/electronics technology, especially an all-fiber image-reject homodyne receiver, where a high resolution spectrum in the baseband can be acquired. Due to the presence of a structured spectra resulting from the spontaneous Rayleigh-Brillouine scattering, associated with the relevant operating regimes, an accurate estimation of the temperature can be carried out. One of the main advantages of this system is the removal of the contaminating Mie backscatter signal by electronic filters at the baseband (before signal conditioning and amplification. The paper presents the basic concepts as well as a Monte-Carlo system simulation as the proof of concept.

  2. In vivo visualization of photoreceptor layer and lipofuscin accumulation in Stargardt’s disease and fundus flavimaculatus by high resolution spectral-domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Giuseppe Querques

    2009-12-01

    Full Text Available Giuseppe Querques, Rosy Prato, Gabriel Coscas, Gisèle Soubrane, Eric H SouiedDepartment of Ophthalmology, Hopital Intercommunal de Creteil, University Paris XII, FranceIntroduction: To assess photoreceptor (PR layer morphology in patients with Stargardt’s disease (STGD and fundus flavimaculatus (FFM using high resolution spectral domain optical coherence tomography (HD-OCT; OCT 4000 Cirrus, Humphrey-Zeiss, San Leandro, CA.Methods: This was a prospective observational case series. Sixteen consecutive patients with STGD and FFM underwent a complete ophthalmologic examination. Optical coherence tomography examination was performed with HD-OCT, a high-speed (27,000 axial scans per second OCT system using spectral/Fourier domain detection, with an axial image resolution of 5 µm.Results: A total of 31 eyes were included in the study. Transverse loss of the PR layer in the foveal region was shown by HD-OCT. Twenty eyes with clinically evident central atrophy had a disruption of either the Verhoeff‘s membrane (VM or the layer corresponding to the interface of inner segment (IS and outer segment (OS of PR in the foveal region. Among these eyes, 12/20 eyes had a loss of the PR layer (loss of both VM and IS-OS interface in the foveal region. Eleven eyes (11/31 without clinically evident central atrophy had an intact interface of IS and OS of PR centrally. Moreover, we observed hyperreflective deposits: type 1 lesions located within the retinal pigment epithelium (RPE layer and at the level of the outer segments of PR, and type 2 lesions located at the level of the outer nuclear layer and clearly separated from the RPE layer. Type 1 lesions alone were associated with absence of loss of the PR layer in the foveal region in all eyes; type 2 lesions were always associated with presence of type 1 lesions, and often (8/12 eyes associated with loss of the PR layer within the foveal region. Mean best-corrected visual acuity (BCVA was significantly

  3. Computational domain length and Reynolds number effects on large-scale coherent motions in turbulent pipe flow

    Science.gov (United States)

    Feldmann, Daniel; Bauer, Christian; Wagner, Claus

    2018-03-01

    We present results from direct numerical simulations (DNS) of turbulent pipe flow at shear Reynolds numbers up to Reτ = 1500 using different computational domains with lengths up to ?. The objectives are to analyse the effect of the finite size of the periodic pipe domain on large flow structures in dependency of Reτ and to assess a minimum ? required for relevant turbulent scales to be captured and a minimum Reτ for very large-scale motions (VLSM) to be analysed. Analysing one-point statistics revealed that the mean velocity profile is invariant for ?. The wall-normal location at which deviations occur in shorter domains changes strongly with increasing Reτ from the near-wall region to the outer layer, where VLSM are believed to live. The root mean square velocity profiles exhibit domain length dependencies for pipes shorter than 14R and 7R depending on Reτ. For all Reτ, the higher-order statistical moments show only weak dependencies and only for the shortest domain considered here. However, the analysis of one- and two-dimensional pre-multiplied energy spectra revealed that even for larger ?, not all physically relevant scales are fully captured, even though the aforementioned statistics are in good agreement with the literature. We found ? to be sufficiently large to capture VLSM-relevant turbulent scales in the considered range of Reτ based on our definition of an integral energy threshold of 10%. The requirement to capture at least 1/10 of the global maximum energy level is justified by a 14% increase of the streamwise turbulence intensity in the outer region between Reτ = 720 and 1500, which can be related to VLSM-relevant length scales. Based on this scaling anomaly, we found Reτ⪆1500 to be a necessary minimum requirement to investigate VLSM-related effects in pipe flow, even though the streamwise energy spectra does not yet indicate sufficient scale separation between the most energetic and the very long motions.

  4. Snapshot polarization-sensitive plug-in optical module for a Fourier-domain optical coherence tomography system

    Science.gov (United States)

    Marques, Manuel J.; Rivet, Sylvain; Bradu, Adrian; Podoleanu, Adrian

    2018-02-01

    In this communication, we present a proof-of-concept polarization-sensitive Optical Coherence Tomography (PS-OCT) which can be used to characterize the retardance and the axis orientation of a linear birefringent sample. This module configuration is an improvement from our previous work1, 2 since it encodes the two polarization channels on the optical path difference, effectively carrying out the polarization measurements simultaneously (snapshot measurement), whilst retaining all the advantages (namely the insensitivity to environmental parameters when using SM fibers) of these two previous configurations. Further progress consists in employing Master Slave OCT technology,3 which is used to automatically compensate for the dispersion mismatch introduced by the elements in the module. This is essential given the encoding of the polarization states on two different optical path lengths, each of them having dissimilar dispersive properties. By utilizing this method instead of the commonly used re-linearization and numerical dispersion compensation methods an improvement in terms of the calculation time required can be achieved.

  5. Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain

    OpenAIRE

    Rabbani, Hossein; Sonka, Milan; Abramoff, Michael D.

    2013-01-01

    In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture th...

  6. Real-time processing for full-range Fourier-domain optical-coherence tomography with zero-filling interpolation using multiple graphic processing units.

    Science.gov (United States)

    Watanabe, Yuuki; Maeno, Seiya; Aoshima, Kenji; Hasegawa, Haruyuki; Koseki, Hitoshi

    2010-09-01

    The real-time display of full-range, 2048?axial pixelx1024?lateral pixel, Fourier-domain optical-coherence tomography (FD-OCT) images is demonstrated. The required speed was achieved by using dual graphic processing units (GPUs) with many stream processors to realize highly parallel processing. We used a zero-filling technique, including a forward Fourier transform, a zero padding to increase the axial data-array size to 8192, an inverse-Fourier transform back to the spectral domain, a linear interpolation from wavelength to wavenumber, a lateral Hilbert transform to obtain the complex spectrum, a Fourier transform to obtain the axial profiles, and a log scaling. The data-transfer time of the frame grabber was 15.73?ms, and the processing time, which includes the data transfer between the GPU memory and the host computer, was 14.75?ms, for a total time shorter than the 36.70?ms frame-interval time using a line-scan CCD camera operated at 27.9?kHz. That is, our OCT system achieved a processed-image display rate of 27.23 frames/s.

  7. Topography of somatostatin gene expression relative to molecular progenitor domains during ontogeny of the mouse hypothalamus

    Directory of Open Access Journals (Sweden)

    Nicanor eMorales-Delgado

    2011-02-01

    Full Text Available The hypothalamus comprises alar, basal and floor plate developmental compartments. Recent molecular data support a rostro-caudal subdivision into rostral (terminal and caudal (peduncular halves. In this context, the distribution of neuronal populations expressing somatostatin (Sst mRNA was analyzed in the developing mouse hypothalamus, comparing with the expression pattern of the genes Orthopedia (Otp, Distal-less 5 (Dlx5, Sonic Hedgehog (Shh and Nk2 homeobox 1 (Nkx2.1. At embryonic day 10.5 (E10.5, Sst mRNA was first detectable in the anterobasal nucleus, a Nkx2.1-, Shh- and Otp- positive basal domain. By E13.5, nascent Sst expression was also related to two additional Otp-positive domains within the alar plate and one in the basal plate. In the alar plate, Sst-positive cells were observed in rostral and caudal ventral subdomains of the Otp-positive paraventricular complex. An additional basal Sst-expressing cell group was found within a longitudinal Otp-positive periretromamillary band that separates the retromamillary area from tuberal areas. Apart of subsequent growth of these initial populations, at E13.5 and E15.5 some Sst-positive derivatives migrate tangentially into neighboring regions. A subset of cells produced at the anterobasal nucleus disperses ventralwards into the shell of the ventromedial hypothalamic nucleus and the arcuate nucleus. Cells from the rostroventral paraventricular subdomain reach the suboptic nucleus, whereas a caudal contingent migrates radially into lateral paraventricular, perifornical and entopeduncular nuclei. Our data provide a topologic map of molecularly-defined progenitor areas originating a specific neuron type during early hypothalamic development. Identification of four main separate sources helps to understand causally its complex adult organization.

  8. The ER stress sensor PERK luminal domain functions as a molecular chaperone to interact with misfolded proteins

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Peng; Li, Jingzhi; Sha, Bingdong

    2016-11-29

    PERK is one of the major sensor proteins which can detect the protein-folding imbalance generated by endoplasmic reticulum (ER) stress. It remains unclear how the sensor protein PERK is activated by ER stress. It has been demonstrated that the PERK luminal domain can recognize and selectively interact with misfolded proteins but not native proteins. Moreover, the PERK luminal domain may function as a molecular chaperone to directly bind to and suppress the aggregation of a number of misfolded model proteins. The data strongly support the hypothesis that the PERK luminal domain can interact directly with misfolded proteins to induce ER stress signaling. To illustrate the mechanism by which the PERK luminal domain interacts with misfolded proteins, the crystal structure of the human PERK luminal domain was determined to 3.2 Å resolution. Two dimers of the PERK luminal domain constitute a tetramer in the asymmetric unit. Superimposition of the PERK luminal domain molecules indicated that the β-sandwich domain could adopt multiple conformations. It is hypothesized that the PERK luminal domain may utilize its flexible β-sandwich domain to recognize and interact with a broad range of misfolded proteins.

  9. Short-term dynamics of North Sea bacterioplankton-dissolved organic matter coherence on molecular level

    Directory of Open Access Journals (Sweden)

    Judith eLucas

    2016-03-01

    Full Text Available Remineralisation and transformation of dissolved organic matter (DOM by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition at Helgoland Roads (North Sea in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of twenty days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS, respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom towards the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen concentration, temperature and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of bacterial community composition variation.

  10. Exploiting Molecular Weight Distribution Shape to Tune Domain Spacing in Block Copolymer Thin Films.

    Science.gov (United States)

    Gentekos, Dillon T; Jia, Junteng; Tirado, Erika S; Barteau, Katherine P; Smilgies, Detlef-M; DiStasio, Robert A; Fors, Brett P

    2018-04-04

    We report a method for tuning the domain spacing ( D sp ) of self-assembled block copolymer thin films of poly(styrene- block-methyl methacrylate) (PS- b-PMMA) over a large range of lamellar periods. By modifying the molecular weight distribution (MWD) shape (including both the breadth and skew) of the PS block via temporal control of polymer chain initiation in anionic polymerization, we observe increases of up to 41% in D sp for polymers with the same overall molecular weight ( M n ≈ 125 kg mol -1 ) without significantly changing the overall morphology or chemical composition of the final material. In conjunction with our experimental efforts, we have utilized concepts from population statistics and least-squares analysis to develop a model for predicting D sp based on the first three moments of the MWDs. This statistical model reproduces experimental D sp values with high fidelity (with mean absolute errors of 1.2 nm or 1.8%) and provides novel physical insight into the individual and collective roles played by the MWD moments in determining this property of interest. This work demonstrates that both MWD breadth and skew have a profound influence over D sp , thereby providing an experimental and conceptual platform for exploiting MWD shape as a simple and modular handle for fine-tuning D sp in block copolymer thin films.

  11. Second-order Monte Carlo wave-function approach to the relaxation effects on ringing revivals in a molecular system interacting with a strongly squeezed coherent field

    International Nuclear Information System (INIS)

    Nakano, Masayoshi; Kishi, Ryohei; Nitta, Tomoshige; Yamaguchi, Kizashi

    2004-01-01

    We investigate the relaxation effects on the quantum dynamics in a two-state molecular system interacting with a single-mode strongly amplitude-squeezed coherent field using the second-order Monte Carlo wave-function method. The molecular population inversion (collapse-revival behavior of Rabi oscillations) is known to show the echoes after each revival, which are referred to as ringing revivals, in the case of strongly squeezed coherent fields with oscillatory photon-number distributions due to the phase-space interference effect. Two types of relaxation effects, i.e., cavity relaxation (the dissipation of an internal single mode to outer mode) and molecular coherent (phase) relaxation caused by nuclear vibrations on ringing revivals are investigated from the viewpoint of the quantum-phase dynamics using the quasiprobability (Q function) distribution of a single-mode field and the off-diagonal molecular density matrix ρ elec1,2 (t). It turns out that the molecular phase relaxation attenuates both the entire revival-collapse behavior and the increase in ρ elec1,2 (t) during the quiescent region, whereas a very slight cavity relaxation particularly suppresses the echoes in ringing revivals more significantly than the first revival but hardly changes a primary variation in envelope of ρ elec1,2 (t) in the nonrelaxation case

  12. Ganglion cell-inner plexiform layer and retinal nerve fibre layer changes within the macula in retinitis pigmentosa: a spectral domain optical coherence tomography study.

    Science.gov (United States)

    Yoon, Chang Ki; Yu, Hyeong Gon

    2018-03-01

    To investigate how macular ganglion cell-inner plexiform layer (GCIPL) and retinal nerve fibre layer (RNFL) thicknesses within the macula change with retinitis pigmentosa (RP) severity. Spectral domain optical coherence tomography (SD-OCT) was used to examine 177 patients with RP and 177 normal controls. An optical coherence tomography (OCT) line scan was used to grade RP severity. Retinitis pigmentosa (RP) was categorized as more advanced if there was no identifiable inner segment ellipsoid (ISe) band (NISE) and as less advanced if an ISe band could be identified and peripheral loss of ISe was apparent (IISE). Ganglion cell-inner plexiform layer (GCIPL) and RNFL thicknesses were manually measured on OCT images and analysed. Pearson's correlation analyses were used to examine correlations between GCIPL thickness, RNFL thickness, visual acuity (VA) and visual field extent in patients and controls. Ganglion cell-inner plexiform layer (GCIPL) was significantly thicker in IISE than in control eyes (p layer (RNFL) was significantly thicker in eyes with IISE and NISE than in control eyes in both horizontal and vertical meridians (all p layer (GCIPL) thickness showed a weak positive correlation with vision, and RNFL thickness showed a weak negative correlation with vision and visual field extent. Based on these results, the inner retina, including the GCIPL and RNFL, maintains its gross integrity longer than the photoreceptor layer in RP. Additionally, thickening of the inner retina may have some functional implications in patients with RP. © 2017 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  13. Coherent molecular transistor: control through variation of the gate wave function.

    Science.gov (United States)

    Ernzerhof, Matthias

    2014-03-21

    In quantum interference transistors (QUITs), the current through the device is controlled by variation of the gate component of the wave function that interferes with the wave function component joining the source and the sink. Initially, mesoscopic QUITs have been studied and more recently, QUITs at the molecular scale have been proposed and implemented. Typically, in these devices the gate lead is subjected to externally adjustable physical parameters that permit interference control through modifications of the gate wave function. Here, we present an alternative model of a molecular QUIT in which the gate wave function is directly considered as a variable and the transistor operation is discussed in terms of this variable. This implies that we specify the gate current as well as the phase of the gate wave function component and calculate the resulting current through the source-sink channel. Thus, we extend on prior works that focus on the phase of the gate wave function component as a control parameter while having zero or certain discrete values of the current. We address a large class of systems, including finite graphene flakes, and obtain analytic solutions for how the gate wave function controls the transistor.

  14. Coherent molecular transistor: Control through variation of the gate wave function

    International Nuclear Information System (INIS)

    Ernzerhof, Matthias

    2014-01-01

    In quantum interference transistors (QUITs), the current through the device is controlled by variation of the gate component of the wave function that interferes with the wave function component joining the source and the sink. Initially, mesoscopic QUITs have been studied and more recently, QUITs at the molecular scale have been proposed and implemented. Typically, in these devices the gate lead is subjected to externally adjustable physical parameters that permit interference control through modifications of the gate wave function. Here, we present an alternative model of a molecular QUIT in which the gate wave function is directly considered as a variable and the transistor operation is discussed in terms of this variable. This implies that we specify the gate current as well as the phase of the gate wave function component and calculate the resulting current through the source-sink channel. Thus, we extend on prior works that focus on the phase of the gate wave function component as a control parameter while having zero or certain discrete values of the current. We address a large class of systems, including finite graphene flakes, and obtain analytic solutions for how the gate wave function controls the transistor

  15. Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain.

    Science.gov (United States)

    Rabbani, Hossein; Sonka, Milan; Abramoff, Michael D

    2013-01-01

    In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR.

  16. Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain

    Directory of Open Access Journals (Sweden)

    Hossein Rabbani

    2013-01-01

    Full Text Available In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR.

  17. Normative spectral domain optical coherence tomography data on macular and retinal nerve fiber layer thickness in Indians

    Directory of Open Access Journals (Sweden)

    Bindu Appukuttan

    2014-01-01

    Full Text Available Aim: To provide the normative data of macular and retinal nerve fiber layer (RNFL thickness in Indians using spectral domain OCT (Spectralis OCT, Heidelberg Engineering, Germany and to evaluate the effects of age, gender, and refraction on these parameters. Design: Observational, cross-sectional study. Materials and Methods: The eyes of 105 healthy patients aged between 20-75 years, with no ocular disease and best corrected visual acuity of 20/20, were scanned using standard scanning protocols by a single examiner. Exclusion criteria included glaucoma, retinal diseases, diabetes, history of prior intraocular surgery or laser treatment. The mean macular and RNFL thickness were recorded, and the effects of age, gender, and refraction on these parameters were evaluated. This data was compared with published literature on Caucasians to assess the ethnic variations of these parameters. Results: The normal central foveal thickness in healthy Indian eyes measured using Spectralis OCT was 260.1 ± 18.19 ΅m. The nasal inner quadrant showed maximum retinal thickness (338.88 ± 18.17 ΅m.The mean RNFL thickness was 101.43 ± 8.63 ΅m with maximum thickness in the inferior quadrant. The central foveal thickness showed a gender-based difference (P = 0.005 but did not correlate significantly with age (P = 0.134, whereas the parafoveal, perifoveal thickness, macular volume, and RNFL thickness showed significant negative correlation with age. Conclusions: Our study provides the normative database for Indians on Spectralis OCT. It also suggests that age should be considered while interpreting the macular thickness and RNFL, whereas gender should also be given consideration in central foveal thickness.

  18. Visualizing Macular Structures During Membrane Peeling Surgery With an Intraoperative Spectral-Domain Optical Coherence Tomography Device.

    Science.gov (United States)

    Leisser, Christoph; Hackl, Christoph; Hirnschall, Nino; Luft, Nikolaus; Döller, Birgit; Draschl, Petra; Rigal, Karl; Findl, Oliver

    2016-04-01

    The aim of this study was to examine the quality of intraoperative visualization of the posterior hyaloid, epiretinal membrane (ERM), inner limiting membrane (ILM), and hyporeflective subfoveal zone with a commercially available, microscope-integrated spectral-domain OCT setup (mi-SD-OCT) (Rescan 700; Carl Zeiss Meditec AG, Germany). Twenty patients prospectively scheduled for pars plana vitrectomy with membrane peeling due to an idiopathic ERM were included. Standard 23-gauge, three-port pars plana vitrectomy with membrane peeling and staining of the ERM with a trypan blue-based chromovitrectomy dye was performed in all cases. Intraoperative SD-OCT was performed before and after peeling and visualization of the posterior hyaloid, ERM, ILM, and presence of subfoveal hyporeflective zones were examined. OCT follow-ups were performed 2 days and 3 months after surgery. The study was approved by the local ethics committee of the city of Vienna. Successful intraoperative visualization of ERM by mi-SD-OCT was possible in all cases. The posterior hyaloid and ILM could not be seen in the mi-SD-OCT scans, whereas an intraoperative subfoveal hyporeflective zone presented in 35% of cases. In 12.5% an independent subfoveal hyporeflective zone presented postoperatively. Visual acuity improved in 93.8% of patients after surgery. mi-SD-OCT appears to be a valuable tool for intraoperative visualization of the ERM and offers immediate visualization of retinal anatomy during peeling. Therefore, it adds to the understanding of intraoperative traumatic changes due to the peeling procedure. Copyright 2016, SLACK Incorporated.

  19. Molecular Features of the Copper Binding Sites in the Octarepeat Domain of the Prion Protein†

    Science.gov (United States)

    Burns, Colin S.; Aronoff-Spencer, Eliah; Dunham, Christine M.; Lario, Paula; Avdievich, Nikolai I.; Antholine, William E.; Olmstead, Marilyn M.; Vrielink, Alice; Gerfen, Gary J.; Peisach, Jack; Scott, William G.; Millhauser, Glenn L.

    2010-01-01

    Recent evidence suggests that the prion protein (PrP) is a copper binding protein. The N-terminal region of human PrP contains four sequential copies of the highly conserved octarepeat sequence PHGGGWGQ spanning residues 60–91. This region selectively binds Cu2+ in vivo. In a previous study using peptide design, EPR, and CD spectroscopy, we showed that the HGGGW segment within each octarepeat comprises the fundamental Cu2+ binding unit [Aronoff-Spencer et al. (2000) Biochemistry 40, 13760–13771]. Here we present the first atomic resolution view of the copper binding site within an octarepeat. The crystal structure of HGGGW in a complex with Cu2+ reveals equatorial coordination by the histidine imidazole, two deprotonated glycine amides, and a glycine carbonyl, along with an axial water bridging to the Trp indole. Companion S-band EPR, X-band ESEEM, and HYSCORE experiments performed on a library of 15N-labeled peptides indicate that the structure of the copper binding site in HGGGW and PHGGGWGQ in solution is consistent with that of the crystal structure. Moreover, EPR performed on PrP(23–28, 57–91) and an 15N-labeled analogue demonstrates that the identified structure is maintained in the full PrP octarepeat domain. It has been shown that copper stimulates PrP endocytosis. The identified Gly–Cu linkage is unstable below pH ≈6.5 and thus suggests a pH-dependent molecular mechanism by which PrP detects Cu2+ in the extracellular matrix or releases PrP-bound Cu2+ within the endosome. The structure also reveals an unusual complementary interaction between copper-structured HGGGW units that may facilitate molecular recognition between prion proteins, thereby suggesting a mechanism for transmembrane signaling and perhaps conversion to the pathogenic form. PMID:11900542

  20. Change of Retinal Nerve Layer Thickness in Non-Arteritic Anterior Ischemic Optic Neuropathy Revealed by Fourier Domain Optical Coherence Tomography.

    Science.gov (United States)

    Han, Mei; Zhao, Chen; Han, Quan-Hong; Xie, Shiyong; Li, Yan

    2016-08-01

    To examine the changes of non-arteritic anterior ischemic optic neuropathy (NAION) by serial morphometry using Fourier domain optical coherence tomography (FD-OCT). Retrospective study in patients with newly diagnosed NAION (n=33, all unilateral) and controls (n=75 unilateral NAION patients with full contralateral eye vision) who underwent FD-OCT of the optic disk, optic nerve head (ONH), and macula within 1 week of onset and again 1, 3, 6, and 12 months later. The patients showed no improvement in vision during follow-up. Within 1 week of onset, all NAION eyes exhibited severe ONH fiber crowding and peripapillary retinal nerve fiber layer (RNFL) edema. Four had subretinal fluid accumulation and 12 had posterior vitreous detachment (PVD) at the optic disc surface. Ganglion cell complex (GCC) and RNFL thicknesses were reduced at 1 and 3 months (p < 0.05), with no deterioration thereafter. Initial RNFL/GCC contraction magnitude in the superior hemisphere correlated with the severity of inferior visual field deficits. NAION progression is characterized by an initial phase of accelerated RNFL and GCC deterioration. These results reveal that the kinetic change of neural retina in NAION and may have implication on the time window for treatment of NAION. FD-OCT is useful in the evaluation of NAION.

  1. Multivendor Spectral-Domain Optical Coherence Tomography Dataset, Observer Annotation Performance Evaluation, and Standardized Evaluation Framework for Intraretinal Cystoid Fluid Segmentation

    Directory of Open Access Journals (Sweden)

    Jing Wu

    2016-01-01

    Full Text Available Development of image analysis and machine learning methods for segmentation of clinically significant pathology in retinal spectral-domain optical coherence tomography (SD-OCT, used in disease detection and prediction, is limited due to the availability of expertly annotated reference data. Retinal segmentation methods use datasets that either are not publicly available, come from only one device, or use different evaluation methodologies making them difficult to compare. Thus we present and evaluate a multiple expert annotated reference dataset for the problem of intraretinal cystoid fluid (IRF segmentation, a key indicator in exudative macular disease. In addition, a standardized framework for segmentation accuracy evaluation, applicable to other pathological structures, is presented. Integral to this work is the dataset used which must be fit for purpose for IRF segmentation algorithm training and testing. We describe here a multivendor dataset comprised of 30 scans. Each OCT scan for system training has been annotated by multiple graders using a proprietary system. Evaluation of the intergrader annotations shows a good correlation, thus making the reproducibly annotated scans suitable for the training and validation of image processing and machine learning based segmentation methods. The dataset will be made publicly available in the form of a segmentation Grand Challenge.

  2. Semiautomated segmentation and analysis of retinal layers in three-dimensional spectral-domain optical coherence tomography images of patients with atrophic age-related macular degeneration.

    Science.gov (United States)

    Hu, Zhihong; Shi, Yue; Nandanan, Kiran; Sadda, Srinivas R

    2017-01-01

    Historically, regular drusen and geographic atrophy (GA) have been recognized as the hallmarks of nonneovascular age-related macular degeneration (AMD). Recent imaging developments have revealed another distinct nonneovascular AMD phenotype, reticular pseudodrusen (RPD). We develop an approach to semiautomatically quantify retinal surfaces associated with various AMD lesions (i.e., regular drusen, RPD, and GA) in spectral domain (SD) optical coherence tomography (OCT) images. More specifically, a graph-based algorithm was used to segment multiple retinal layers in SD-OCT volumes. Varying surface feasibility constraints based on the presegmentation were applied on the double-surface graph search to refine the surface segmentation. The thicknesses of these layers and their correlation with retinal functional measurements, including microperimetry (MP) sensitivity and visual acuity (VA), were investigated. The photoreceptor outer segment layer demonstrated significant thinning with a reduction in MP sensitivity and VA score when atrophic AMD lesions were present. Regular drusen and RPD were separately segmented on SD-OCT images to allow their characteristics and distribution to be studied separately. The mean thickness of regular drusen was found to significantly correlate with the VA score. RPD appeared to be distributed evenly throughout the macula and regular drusen appeared to be more concentrated centrally.

  3. Long ranging swept-source optical coherence tomography-based angiography outperforms its spectral-domain counterpart in imaging human skin microcirculations

    Science.gov (United States)

    Xu, Jingjiang; Song, Shaozhen; Men, Shaojie; Wang, Ruikang K.

    2017-11-01

    There is an increasing demand for imaging tools in clinical dermatology that can perform in vivo wide-field morphological and functional examination from surface to deep tissue regions at various skin sites of the human body. The conventional spectral-domain optical coherence tomography-based angiography (SD-OCTA) system is difficult to meet these requirements due to its fundamental limitations of the sensitivity roll-off, imaging range as well as imaging speed. To mitigate these issues, we demonstrate a swept-source OCTA (SS-OCTA) system by employing a swept source based on a vertical cavity surface-emitting laser. A series of comparisons between SS-OCTA and SD-OCTA are conducted. Benefiting from the high system sensitivity, long imaging range, and superior roll-off performance, the SS-OCTA system is demonstrated with better performance in imaging human skin than the SD-OCTA system. We show that the SS-OCTA permits remarkable deep visualization of both structure and vasculature (up to ˜2 mm penetration) with wide field of view capability (up to 18×18 mm2), enabling a more comprehensive assessment of the morphological features as well as functional blood vessel networks from the superficial epidermal to deep dermal layers. It is expected that the advantages of the SS-OCTA system will provide a ground for clinical translation, benefiting the existing dermatological practice.

  4. Cross-Sectional Analysis of Neurocognitive Function, Retinopathy, and Retinal Thinning by Spectral-Domain Optical Coherence Tomography in Sickle Cell Patients.

    Science.gov (United States)

    Oltra, Erica Z; Chow, Clement C; Wubben, Thomas; Lim, Jennifer I; Chau, Felix Y; Moss, Heather E

    2016-01-01

    The purpose was to examine the relationship between neurocognitive function and two distinct forms of retinopathy in sickle cell disease. Patients with sickle cell disease (n = 44, age range: 19-56 years, 70% female) were prospectively recruited for this cross-sectional study. Retinopathy was characterized by: (1) Presence of focal retinal thinning on spectral domain optical coherence tomography and (2) determination of the sickle retinopathy stage on funduscopic exam based on Goldberg classification. Neurocognitive function was assessed using the Philadelphia Brief Assessment of Cognition (PBAC), a validated test of cognition. Univariate and multivariate analyses for PBAC score outcomes were performed. Retinal thinning and retinopathy stage were primary variables of interest and age, gender, genotype, education, and history of stroke were covariates. Univariate analysis revealed associations with total PBAC score and age (P = 0.049), history of stroke (P = 0.04), and genotype (P retinopathy stage were not associated with each other in this sample. Neither the presence of focal retinal thinning nor degree of retinopathy was associated with total PBAC score in univariate or multivariate analyses. We find an association between lower cognitive function and older age, history of stroke and sickle cell genotype SS in patients with sickle cell disease. Our data do not provide evidence to support an association between cognitive function and retinopathy in sickle cell patients.

  5. Dynamic changes of photorecrptor layer in eyes with acute central serous chorioretinopathy after laser treatment by fourier-domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Li-Qin Zhou

    2014-10-01

    Full Text Available AIM: To dynamically observe the feeling change of the photorecrptor layer in the eyes with acute central serous chorioretinopathy(CSCRkrypton laser treatment by fourier-domain optical coherence tomography(FD-OCT, and to study their correlation with the chang of vision.METHODS: This is a retrospective case series study. The clinical diagnosis of 52 patients with monocular initial onset of central serous chorioretinopathy, krypton laser photocoagulation before treatment, after 1, 2, 4, 6, 8wk, 6mo, FD-OCT were performed to observe the morphological changes characteristic of photoreceptor layer and changes in vision. RESULTS: After 1wk treatment, all cases were improved; 2wk, 6 cases were cured; 4wk, 38 cases were cured; 6wk, 41 cases were cured; 8wk, 45 cases were cured, the OCT showed macular retinal neuroepithelial layer(RNLfrom fully absorbed; 6mo with the same 8wk. Before and after treatment in patients with best corrected visual acuity and from the height difference between the macular region of RNL was statistically significant(PPPCONCLUSION: FD-OCT can dynamicaly observed acute central serous chorioretinopathy krypton laser treatment of photoreceptor ultrastruture changes. Photoreceptor layer of complete and incomplete best corrected visual acuity difference was statistically significant(P<0.01.

  6. Analysis of pulsatile retinal movements by spectral-domain low-coherence interferometry: influence of age and glaucoma on the pulse wave.

    Directory of Open Access Journals (Sweden)

    Carolyne Dion

    Full Text Available Recent studies have shown that ocular hemodynamics and eye tissue biomechanical properties play an important role in the pathophysiology of glaucoma. Nevertheless, better, non-invasive methods to assess these characteristics in vivo are essential for a thorough understanding of degenerative mechanisms. Here, we propose to measure ocular tissue movements induced by cardiac pulsations and study the ocular pulse waveform as an indicator of tissue compliance. Using a novel, low-cost and non-invasive device based on spectral-domain low coherence interferometry (SD-LCI, we demonstrate the potential of this technique to differentiate ocular hemodynamic and biomechanical properties. We measured the axial movement of the retina driven by the pulsatile ocular blood flow in 11 young healthy individuals, 12 older healthy individuals and 15 older treated glaucoma patients using our custom-made SD-OCT apparatus. The cardiac pulse was simultaneously measured through the use of an oximeter to allow comparison. Spectral components up to the second harmonic were obtained and analyzed. For the different cohorts, we computed a few parameters that characterize the three groups of individuals by analyzing the movement of the retinal tissue at two locations, using this simple, low-cost interferometric device. Our pilot study indicates that spectral analysis of the fundus pulsation has potential for the study of ocular biomechanical and vascular properties, as well as for the study of ocular disease.

  7. Spectral-domain optical coherence tomography analysis of persistent subretinal fluid after scleral buckling surgery for macula-off retinal detachment

    Science.gov (United States)

    Gharbiya, M; Malagola, R; Mariotti, C; Parisi, F; De Vico, U; Ganino, C; Grandinetti, F

    2015-01-01

    Purpose To determine the predictive value of markers for persistent subretinal fluid (SRF) absorption and the influence of subfoveal fluid on visual outcome after scleral buckle (SB) surgery for rhegmatogenous retinal detachment (RRD). Patients and methods This was a retrospective, observational study. We reviewed the medical records of 64 eyes of 64 patients who underwent SB surgery for macula-off RRD. Patients underwent clinical examination and spectral-domain optical coherence tomography before surgery, at 1 month and every 3 months postoperatively. The height and width of SRF bleb(s) were measured over time. Results Persistent SRF at 1 month was observed in 40 eyes (62.5%). SRF blebs were first detected 1.7±2.2 months postoperatively. In 29 cases that could be fully followed up, SRF blebs were completely absorbed 7.8±4.4 months postoperatively. Resolution of fluid was associated with an improvement of VA (P=0.003). Serial measurements of SRF bleb size showed that bleb width decreased significantly at all time points during the 12-month follow-up period (P0.05). The cut-off value of the bleb width-to-height ratio level for predicting bleb absorption at 6 months was 7, with 89% sensitivity and 83% specificity. Conclusions Visual improvement may occur with late resolution of residual subfoveal fluid. A bleb width-to-height ratio >7 indicates a higher risk of SRF to persist beyond 6 months after surgery. PMID:26139048

  8. Integration of spectral domain optical coherence tomography with microperimetry generates unique datasets for the simultaneous identification of visual function and retinal structure in ophthalmological applications

    Science.gov (United States)

    Koulen, Peter; Gallimore, Gary; Vincent, Ryan D.; Sabates, Nelson R.; Sabates, Felix N.

    2011-06-01

    Conventional perimeters are used routinely in various eye disease states to evaluate the central visual field and to quantitatively map sensitivity. However, standard automated perimetry proves difficult for retina and specifically macular disease due to the need for central and steady fixation. Advances in instrumentation have led to microperimetry, which incorporates eye tracking for placement of macular sensitivity values onto an image of the macular fundus thus enabling a precise functional and anatomical mapping of the central visual field. Functional sensitivity of the retina can be compared with the observed structural parameters that are acquired with high-resolution spectral domain optical coherence tomography and by integration of scanning laser ophthalmoscope-driven imaging. Findings of the present study generate a basis for age-matched comparison of sensitivity values in patients with macular pathology. Microperimetry registered with detailed structural data performed before and after intervention treatments provides valuable information about macular function, disease progression and treatment success. This approach also allows for the detection of disease or treatment related changes in retinal sensitivity when visual acuity is not affected and can drive the decision making process in choosing different treatment regimens and guiding visual rehabilitation. This has immediate relevance for applications in central retinal vein occlusion, central serous choroidopathy, age-related macular degeneration, familial macular dystrophy and several other forms of retina related visual disability.

  9. Development of ultraviolet- and visible-light one-shot spectral domain optical coherence tomography and in situ measurements of human skin

    Science.gov (United States)

    Hirayama, Heijiro; Nakamura, Sohichiro

    2015-07-01

    We have developed ultraviolet (UV)- and visible-light one-shot spectral domain (SD) optical coherence tomography (OCT) that enables in situ imaging of human skin with an arbitrary wavelength in the UV-visible-light region (370-800 nm). We alleviated the computational burden for each color OCT image by physically dispersing the irradiating light with a color filter. The system consists of SD-OCT with multicylindrical lenses; thus, mechanical scanning of the mirror or stage is unnecessary to obtain an OCT image. Therefore, only a few dozens of milliseconds are necessary to obtain single-image data. We acquired OCT images of one subject's skin in vivo and of a skin excision ex vivo for red (R, 650±20 nm), green (G, 550±20 nm), blue (B, 450±20 nm), and UV (397±5 nm) light. In the visible-light spectrum, R light penetrated the skin and was reflected at a lower depth than G or B light. On the skin excision, we demonstrated that UV light reached the dermal layer. We anticipated that basic knowledge about the spectral properties of human skin in the depth direction could be acquired with this system.

  10. Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein.

    Science.gov (United States)

    Sharma, Monika; Anirudh, C R

    2017-10-03

    STAR proteins are evolutionary conserved mRNA-binding proteins that post-transcriptionally regulate gene expression at all stages of RNA metabolism. These proteins possess conserved STAR domain that recognizes identical RNA regulatory elements as YUAAY. Recently reported crystal structures show that STAR domain is composed of N-terminal QUA1, K-homology domain (KH) and C-terminal QUA2, and mRNA binding is mediated by KH-QUA2 domain. Here, we present simulation studies done to investigate binding of mRNA to STAR protein, mammalian Quaking protein (QKI). We carried out conventional MD simulations of STAR domain in presence and absence of mRNA, and studied the impact of mRNA on the stability, dynamics and underlying allosteric mechanism of STAR domain. Our unbiased simulations results show that presence of mRNA stabilizes the overall STAR domain by reducing the structural deviations, correlating the 'within-domain' motions, and maintaining the native contacts information. Absence of mRNA not only influenced the essential modes of motion of STAR domain, but also affected the connectivity of networks within STAR domain. We further explored the dissociation of mRNA from STAR domain using umbrella sampling simulations, and the results suggest that mRNA binding to STAR domain occurs in multi-step: first conformational selection of mRNA backbone conformations, followed by induced fit mechanism as nucleobases interact with STAR domain.

  11. Molecular determinants for the complex binding specificity of the PDZ domain in PICK1

    DEFF Research Database (Denmark)

    Madsen, Kenneth L; Beuming, Thijs; Niv, Masha Y

    2005-01-01

    PICK1 (protein interacting with C kinase 1) contains a single PDZ domain known to mediate interaction with the C termini of several receptors, transporters, ion channels, and kinases. In contrast to most PDZ domains, the PICK1 PDZ domain interacts with binding sequences classifiable as type I (te...

  12. Common molecular determinants of tarantula huwentoxin-IV inhibition of Na+ channel voltage sensors in domains II and IV.

    Science.gov (United States)

    Xiao, Yucheng; Jackson, James O; Liang, Songping; Cummins, Theodore R

    2011-08-05

    The voltage sensors of domains II and IV of sodium channels are important determinants of activation and inactivation, respectively. Animal toxins that alter electrophysiological excitability of muscles and neurons often modify sodium channel activation by selectively interacting with domain II and inactivation by selectively interacting with domain IV. This suggests that there may be substantial differences between the toxin-binding sites in these two important domains. Here we explore the ability of the tarantula huwentoxin-IV (HWTX-IV) to inhibit the activity of the domain II and IV voltage sensors. HWTX-IV is specific for domain II, and we identify five residues in the S1-S2 (Glu-753) and S3-S4 (Glu-811, Leu-814, Asp-816, and Glu-818) regions of domain II that are crucial for inhibition of activation by HWTX-IV. These data indicate that a single residue in the S3-S4 linker (Glu-818 in hNav1.7) is crucial for allowing HWTX-IV to interact with the other key residues and trap the voltage sensor in the closed configuration. Mutagenesis analysis indicates that the five corresponding residues in domain IV are all critical for endowing HWTX-IV with the ability to inhibit fast inactivation. Our data suggest that the toxin-binding motif in domain II is conserved in domain IV. Increasing our understanding of the molecular determinants of toxin interactions with voltage-gated sodium channels may permit development of enhanced isoform-specific voltage-gating modifiers.

  13. Electromagnetic spatial coherence wavelets

    International Nuclear Information System (INIS)

    Castaneda, R.; Garcia-Sucerquia, J.

    2005-10-01

    The recently introduced concept of spatial coherence wavelets is generalized for describing the propagation of electromagnetic fields in the free space. For this aim, the spatial coherence wavelet tensor is introduced as an elementary amount, in terms of which the formerly known quantities for this domain can be expressed. It allows analyzing the relationship between the spatial coherence properties and the polarization state of the electromagnetic wave. This approach is completely consistent with the recently introduced unified theory of coherence and polarization for random electromagnetic beams, but it provides a further insight about the causal relationship between the polarization states at different planes along the propagation path. (author)

  14. Targeted Molecular Dynamics to determine Focal Adhesion Targeting Domain Folding Intermediates

    Directory of Open Access Journals (Sweden)

    Pallavi Mohanty

    2017-10-01

    Full Text Available The Focal adhesion kinase (FAT domain of Focal Adhesion Kinase is a four helical bundle known for conformational plasticity. FAT adopts two distinctly different conformations i.e., close (cFAT and arm-exchanged (aeFAT states under native conditions [1]. The slow transition from cFAT to aeFAT is likely to proceed through an open intermediate state that allows YENV motif to attain β-turn conformation and phosphorylation of Y925 by Src kinases [2]. The two end states of FAT are known to interact with Paxillin and are responsible for maintaining steady state in Heart while intermediate conformation interacts with Grb2-SH2 leading to Pathological Cardiac Hypertrophy (PAH [2]. 10ns Targeted Molecular Dynamics (TMD was done between c- and aeFAT in order to explore the conformational transition and to capture pathologically relevant oFAT. Cluster and dynamic cross correlation analysis (DCCA of TMD generated trajectory was done and the selected FAT intermediate was docked with Grb2-SH2 using HADDOCK v2.2 docking followed by molecular dynamics. Conservation analysis of FAT-Grb2 binding site was done using CONSURF [3]. A Pharmacophore FAT-Grb2 complex was generated using SPARKv1.2 and submitted for Virtual screening using BLAZE v4. Drug likeliness and ADMET properties were calculated using MOLINSPIRATION tool. TMD reveals six clusters and DCCA showed positively and negatively correlated region along the transition pathway. Intermediates with competence for Grb2 interaction were docked with Grb2 and best binding complex was further refined. MMPBSA binding energy calculations revealed the best binding pose where the phosphorylated YENV motif of Human FAT interacted with a charged and hydrophobic pocket of Grb2. The conservation analysis showed that the charged pocket was more conserved in comparison with the hydrophobic pocket, hence providing useful insights on binding and specificity determining residues in Grb2. Virtual screening using the pharmacophore

  15. Multi-scale calculation based on dual domain material point method combined with molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Dhakal, Tilak Raj [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-02-27

    This dissertation combines the dual domain material point method (DDMP) with molecular dynamics (MD) in an attempt to create a multi-scale numerical method to simulate materials undergoing large deformations with high strain rates. In these types of problems, the material is often in a thermodynamically non-equilibrium state, and conventional constitutive relations are often not available. In this method, the closure quantities, such as stress, at each material point are calculated from a MD simulation of a group of atoms surrounding the material point. Rather than restricting the multi-scale simulation in a small spatial region, such as phase interfaces, or crack tips, this multi-scale method can be used to consider non-equilibrium thermodynamic e ects in a macroscopic domain. This method takes advantage that the material points only communicate with mesh nodes, not among themselves; therefore MD simulations for material points can be performed independently in parallel. First, using a one-dimensional shock problem as an example, the numerical properties of the original material point method (MPM), the generalized interpolation material point (GIMP) method, the convected particle domain interpolation (CPDI) method, and the DDMP method are investigated. Among these methods, only the DDMP method converges as the number of particles increases, but the large number of particles needed for convergence makes the method very expensive especially in our multi-scale method where we calculate stress in each material point using MD simulation. To improve DDMP, the sub-point method is introduced in this dissertation, which provides high quality numerical solutions with a very small number of particles. The multi-scale method based on DDMP with sub-points is successfully implemented for a one dimensional problem of shock wave propagation in a cerium crystal. The MD simulation to calculate stress in each material point is performed in GPU using CUDA to accelerate the

  16. Biodiversity at the molecular level: the domains, kingdoms and phyla of life.

    Science.gov (United States)

    Embley, T M; Hirt, R P; Williams, D M

    1994-07-29

    The results of comparative sequence analysis, mainly of small subunit (SSU) ribosomal (r)RNA sequences, have suggested that all of cellular life can be placed in one of three domains: the Archaea, Bacteria or Eucarya. There is some evidence that the Archaea may not be a monophyletic assemblage, but as yet this issue has not been resolved. Most of the lineages, and all of the deepest ones, in the tree based upon SSU rRNA sequences, are microbial. Traditional ideas of classification such as Whittaker's five kingdom scheme do not adequately describe life's diversity as revealed by sequence comparisons. There are many microbial groups that demonstrate much greater amounts of SSU rRNA sequence divergence than do members of the classical kingdoms, Animalia, Plantae and Fungi. The old microbial kingdoms Monera and Protista are clearly paraphyletic but as yet there is no consensus as to how they should be reorganized in taxonomic terms. New data from environmental analysis suggests that much of the microbial world is unknown. Every environment which has been analysed by molecular methods has revealed many previously unrecorded lineages. Some of these show great divergence from the sequences of cultured microorganisms suggesting that fundamentally new microbial groups remain to be isolated. The relationships of some of these new lineages may be expected to affect how the tree of life is organized into higher taxa, and to also influence which features will be recognized as synapomorphies. There is currently no objective measure whereby microbial diversity can be quantified and compared to the figures which are widely quoted for arthropods and other Metazoa.

  17. Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains.

    Science.gov (United States)

    Keren, Ido; Klipcan, Liron; Bezawork-Geleta, Ayenachew; Kolton, Max; Shaya, Felix; Ostersetzer-Biran, Oren

    2008-08-22

    CRM (chloroplast RNA splicing and ribosome maturation) is a recently recognized RNA-binding domain of ancient origin that has been retained in eukaryotic genomes only within the plant lineage. Whereas in bacteria CRM domains exist as single domain proteins involved in ribosome maturation, in plants they are found in a family of proteins that contain between one and four repeats. Several members of this family with multiple CRM domains have been shown to be required for the splicing of specific plastidic group II introns. Detailed biochemical analysis of one of these factors in maize, CRS1, demonstrated its high affinity and specific binding to the single group II intron whose splicing it facilitates, the plastid-encoded atpF intron RNA. Through its association with two intronic regions, CRS1 guides the folding of atpF intron RNA into its predicted "catalytically active" form. To understand how multiple CRM domains cooperate to achieve high affinity sequence-specific binding to RNA, we analyzed the RNA binding affinity and specificity associated with each individual CRM domain in CRS1; whereas CRM3 bound tightly to the RNA, CRM1 associated specifically with a unique region found within atpF intron domain I. CRM2, which demonstrated only low binding affinity, also seems to form specific interactions with regions localized to domains I, III, and IV. We further show that CRM domains share structural similarities and RNA binding characteristics with the well known RNA recognition motif domain.

  18. Spectral Domain Optical Coherence Tomography in Glaucoma: Qualitative and Quantitative Analysis of the Optic Nerve Head and Retinal Nerve Fiber Layer (An AOS Thesis)

    Science.gov (United States)

    Chen, Teresa C.

    2009-01-01

    Purpose: To demonstrate that video-rate spectral domain optical coherence tomography (SDOCT) can qualitatively and quantitatively evaluate optic nerve head (ONH) and retinal nerve fiber layer (RNFL) glaucomatous structural changes. To correlate quantitative SDOCT parameters with disc photography and visual fields. Methods: SDOCT images from 4 glaucoma eyes (4 patients) with varying stages of open-angle glaucoma (ie, early, moderate, late) were qualitatively contrasted with 2 age-matched normal eyes (2 patients). Of 61 other consecutive patients recruited in an institutional setting, 53 eyes (33 patients) met inclusion/exclusion criteria for quantitative studies. Images were obtained using two experimental SDOCT systems, one utilizing a superluminescent diode and the other a titanium:sapphire laser source, with axial resolutions of about 6 μm and 3 μm, respectively. Results: Classic glaucomatous ONH and RNFL structural changes were seen in SDOCT images. An SDOCT reference plane 139 μm above the retinal pigment epithelium yielded cup-disc ratios that best correlated with masked physician disc photography cup-disc ratio assessments. The minimum distance band, a novel SDOCT neuroretinal rim parameter, showed good correlation with physician cup-disc ratio assessments, visual field mean deviation, and pattern standard deviation (P values range, .0003–.024). RNFL and retinal thickness maps correlated well with disc photography and visual field testing. Conclusions: To our knowledge, this thesis presents the first comprehensive qualitative and quantitative evaluation of SDOCT images of the ONH and RNFL in glaucoma. This pilot study provides basis for developing more automated quantitative SDOCT-specific glaucoma algorithms needed for future prospective multicenter national trials. PMID:20126502

  19. Evaluation of Macular Ganglion Cell Complex and Peripapillary Retinal Nerve Fiber Layer in Primary Craniopharyngioma by Fourier-Domain Optical Coherence Tomography.

    Science.gov (United States)

    Yang, Liu; Qu, Yuanzhen; Lu, Wen; Liu, Fengjun

    2016-07-03

    BACKGROUND The aim of this study was to compare the differences in macular ganglion cell complex (GCC) and peripapillary retinal nerve fiber layer (pRNFL) in child and adult patients with primary craniopharyngioma by Fourier-domain optical coherence tomography (FD-OCT) and to evaluate their significance in the diagnosis of primary craniopharyngioma. MATERIAL AND METHODS Ninety-six participants were divided into 3 groups: 32 in the child craniopharyngioma group (CCG) and 32 in the adult craniopharyngioma group (ACG) who were treated in Beijing Tiantan Hospital between November 2013 and October 2014, and 32 in the normal group (NG). All subjects were scanned by FD-OCT to map GCC and pRNFL thicknesses. Spearman correlation coefficient was used to assess the correlation between GCC and pRNFL thickness, and pRNFL thickness and optic nerve head (ONH) parameters, including horizontal cup-disc ratio (HCDR), vertical cup-disc ratio (VCDR), optic disc area (ODA), and cup area (CA), respectively. RESULTS The correlation between GCC and pRNFL thickness in the CCG was slightly stronger compared with the ACG. A significant difference in GCC thickness was observed among the CCG, ACG, and NG. Although the pRNFL thickness in both the CCG and ACG was significantly higher than that in NG, no significant difference in pRNFL thickness was detected between the 2 craniopharyngioma groups. The average, superior, and inferior pRNFL thicknesses were negatively correlated with VCDR in the CCG (in double eyes) and ACG (only in left eyes). CONCLUSIONS GCC was more sensitive than pRNFL in detecting optic nerve damage in the eyes of craniopharyngioma patients. A thinner pRNFL was especially correlated with VCDR in child craniopharyngioma patients.

  20. In vivo imaging of palisades of Vogt in dry eye versus normal subjects using en-face spectral-domain optical coherence tomography.

    Directory of Open Access Journals (Sweden)

    Wajdene Ghouali

    Full Text Available To evaluate a possible clinical application of spectral-domain optical coherence tomography (SD-OCT using en-face module for the imaging of the corneoscleral limbus in normal subjects and dry eye patients.Seventy-six subjects were included in this study. Seventy eyes of 35 consecutive patients with dry eye disease and 82 eyes of 41 healthy control subjects were investigated. All subjects were examined with the Avanti RTVue® anterior segment OCT. En-face OCT images of the corneoscleral limbus were acquired in four quadrants (inferior, superior, nasal and temporal and then were analyzed semi-quantitatively according to whether or not palisades of Vogt (POV were visible. En-face OCT images were then compared to in vivo confocal microscopy (IVCM in eleven eyes of 7 healthy and dry eye patients.En-face SD-OCT showed POV as a radially oriented network, located in superficial corneoscleral limbus, with a good correlation with IVCM features. It provided an easy and reproducible identification of POV without any special preparation or any direct contact, with a grading scale from 0 (no visualization to 3 (high visualization. The POV were found predominantly in superior (P<0.001 and inferior (P<0.001 quadrants when compared to the nasal and temporal quadrants for all subjects examined. The visibility score decreased with age (P<0.001 and was lower in dry eye patients (P<0.01. In addition, the score decreased in accordance with the severity of dry eye disease (P<0.001.En-face SD-OCT is a non-contact imaging technique that can be used to evaluate the POV, thus providing valuable information about differences in the limbal anatomy of dry eye patients as compared to healthy patients.

  1. Influence of corneal power on circumpapillary retinal nerve fiber layer and optic nerve head measurements by spectral-domain optical coherence tomography

    Directory of Open Access Journals (Sweden)

    Kazunori Hirasawa

    2017-09-01

    Full Text Available AIM: To evaluate the influence of corneal power on circumpapillary retinal nerve fiber layer (cpRNFL and optic nerve head (ONH measurements by spectral-domain optical coherence tomography (SD-OCT. METHODS: Twenty-five eyes of 25 healthy participants (mean age 23.6±3.6y were imaged by SD-OCT using horizontal raster scans. Disposable soft contact lenses of different powers (from −11 to +5 diopters including 0 diopter were worn to induce 2-diopter changes in corneal power. Differences in the cpRNFL and ONH measurements per diopter of change in corneal power were analyzed. RESULTS: As corneal power increased by 1 diopter, total and quadrant cpRNFL thicknesses, except for the nasal sector, decreased by −0.19 to −0.32 μm (P<0.01. Furthermore, the disc, cup, and rim areas decreased by −0.017, −0.007, and −0.015 mm2, respectively (P<0.001; the cup and rim volumes decreased by −0.0013 and −0.006 mm3, respectively (P<0.01; and the vertical and horizontal disc diameters decreased by −0.006 and −0.007 mm, respectively (P<0.001. CONCLUSION: For more precise OCT imaging, the ocular magnification should be corrected by considering both the axial length and corneal power. However, the effect of corneal power changes on cpRNFL thickness and ONH topography are small when compare with those of the axial length.

  2. The diagnostic use of choroidal thickness analysis and its correlation with visual field indices in glaucoma using spectral domain optical coherence tomography.

    Directory of Open Access Journals (Sweden)

    Zhongjing Lin

    Full Text Available To evaluate the quantitative characteristics of choroidal thickness in primary open-angle glaucoma (POAG, normal tension glaucoma (NTG and in normal eyes using spectral-domain optical coherence tomography (SD-OCT. To evaluate the diagnostic ability of choroidal thickness in glaucoma and to determine the correlation between choroidal thickness and visual field parameters in glaucoma.A total of 116 subjects including 40 POAG, 30 NTG and 46 healthy subjects were enrolled in this study. Choroidal thickness measurements were acquired in the macular and peripapillary regions using SD-OCT. All subjects underwent white-on-white (W/W and blue-on-yellow (B/Y visual field tests using Humphrey Field Analyzer. The receiver operating characteristic (ROC curve and the area under curve (AUC were generated to assess the discriminating power of choroidal thickness for glaucoma. Pearson's correlation coefficients were calculated to assess the structure function correlation for glaucoma patients.No significant differences were observed for macular choroidal thickness among the different groups (all P > 0.05. Regarding the peripapillary choroidal thickness (PPCT, significant differences were observed among the three groups (all P 0.05, but showed significant correlations with B/Y MD (all P < 0.05. In the early glaucomatous eyes, PPCT showed significant correlations with W/W MD and B/Y MD (all P < 0.05.In our study, peripapillary choroidal thickness measured on OCT showed a low to moderate but statistically significant diagnostic power and a significant correlation with blue-on-yellow visual field indices in glaucoma. This may indicate a potential adjunct for peripapillary choroidal thickness in glaucoma diagnosis.

  3. Reliability of Entire Corneal Thickness Mapping in Normal Post-Laser in situ Keratomileusis and Keratoconus Eyes Using Long Scan Depth Spectral Domain Optical Coherence Tomography.

    Science.gov (United States)

    Xu, Zhe; Chen, Sisi; Yang, Chun; Huang, Shenghai; Shen, Meixiao; Wang, Yuanyuan

    2018-01-01

    To investigate the repeatability and reproducibility of mapping the entire corneal thickness using spectral domain optical coherence tomography (SD-OCT). Thirty normal eyes, 30 post-laser in situ keratomileusis (LASIK) surgery eyes, and 30 keratoconus eyes were analyzed. A custom-built long scan depth SD-OCT device was used to obtain entire corneal images. Ten-millimeter-diameter corneal thickness maps were generated by an automated segmentation algorithm. Intraclass correlation coefficients of repeatability (ICC1) and reproducibility (ICC2), and coefficients of repeatability (CoR1) and reproducibility (CoR2), were calculated to quantify the precision and accuracy of corneal pachymetry measurements using the Bland-Altman method. For SD-OCT measurements in healthy subjects, CoR1 and CoR2 were less than 5.00 and 5.53 μm. ICC1 and ICC2 were more than 0.997 and 0.996. For SD-OCT measurements in LASIK patients, CoR1 and CoR2 were less than 5.09 and 5.34 μm. ICC1 and ICC2 were more than 0.997 and 0.996. For SD-OCT measurements in keratoconus patients, CoR1 and CoR2 were less than 11.57 and 10.92 μm. ICC1 and ICC2 were more than 0.995 and 0.996. The measurements of corneal pachymetric mapping by long scan depth SD-OCT can be assessed over the entire corneal area with good repeatability and reproducibility. © 2017 S. Karger AG, Basel.

  4. Retinal pigment epithelial changes in chronic Vogt-Koyanagi-Harada disease: fundus autofluorescence and spectral domain-optical coherence tomography findings.

    Science.gov (United States)

    Vasconcelos-Santos, Daniel V; Sohn, Elliott H; Sadda, Srinivas; Rao, Narsing A

    2010-01-01

    The purpose of this study was to determine whether fundus autofluorescence (FAF) and spectral domain-optical coherence tomography (SD-OCT) imaging allow better assessment of retinal pigment epithelium and the outer retina in subjects with chronic Vogt-Koyanagi-Harada disease compared with examination and angiography alone. A cross-sectional analysis of a series of seven consecutive patients with chronic Vogt-Koyanagi-Harada disease undergoing FAF and SD-OCT was conducted. Chronic disease was defined as duration of intraocular inflammation >3 months. Color fundus photographs were correlated to FAF and SD-OCT images. The images were later correlated to fluorescein angiography and indocyanine green angiography. All patients had sunset glow fundus, which resulted in no apparent corresponding abnormality on FAF or SD-OCT. Lesions with decreased autofluorescence signal were observed in 11 eyes (85%), being associated with loss of the retinal pigment epithelium and involvement of the outer retina on SD-OCT. In 5 eyes (38%), some of these lesions were very subtle on clinical examination but easily detected by FAF. Lesions with increased autofluorescence signal were seen in 8 eyes (61.5%), showing variable involvement of the outer retina on SD-OCT and corresponding clinically to areas of retinal pigment epithelium proliferation and cystoid macular edema. Combined use of FAF and SD-OCT imaging allowed noninvasive delineation of retinal pigment epithelium/outer retina changes in patients with chronic Vogt-Koyanagi-Harada disease, which were consistent with previous histopathologic reports. Some of these changes were not apparent on clinical examination.

  5. Segmentation error and macular thickness measurements obtained with spectral-domain optical coherence tomography devices in neovascular age-related macular degeneration

    Directory of Open Access Journals (Sweden)

    Moosang Kim

    2013-01-01

    Full Text Available Purpose: To evaluate frequency and severity of segmentation errors of two spectral-domain optical coherence tomography (SD-OCT devices and error effect on central macular thickness (CMT measurements. Materials and Methods: Twenty-seven eyes of 25 patients with neovascular age-related macular degeneration, examined using the Cirrus HD-OCT and Spectralis HRA + OCT, were retrospectively reviewed. Macular cube 512 × 128 and 5-line raster scans were performed with the Cirrus and 512 × 25 volume scans with the Spectralis. Frequency and severity of segmentation errors were compared between scans. Results: Segmentation error frequency was 47.4% (baseline, 40.7% (1 month, 40.7% (2 months, and 48.1% (6 months for the Cirrus, and 59.3%, 62.2%, 57.8%, and 63.7%, respectively, for the Spectralis, differing significantly between devices at all examinations (P < 0.05, except at baseline. Average error score was 1.21 ± 1.65 (baseline, 0.79 ± 1.18 (1 month, 0.74 ± 1.12 (2 months, and 0.96 ± 1.11 (6 months for the Cirrus, and 1.73 ± 1.50, 1.54 ± 1.35, 1.38 ± 1.40, and 1.49 ± 1.30, respectively, for the Spectralis, differing significantly at 1 month and 2 months (P < 0.02. Automated and manual CMT measurements by the Spectralis were larger than those by the Cirrus. Conclusions: The Cirrus HD-OCT had a lower frequency and severity of segmentation error than the Spectralis HRA + OCT. SD-OCT error should be considered when evaluating retinal thickness.

  6. Simultaneous Fluorescein Angiography and Spectral Domain Optical Coherence Tomography Correlate Retinal Thickness Changes to Vascular Abnormalities in an In Vivo Mouse Model of Retinopathy of Prematurity

    Directory of Open Access Journals (Sweden)

    Olachi J. Mezu-Ndubuisi

    2017-01-01

    Full Text Available Background. Retinopathy of prematurity (ROP is a condition of abnormal retinal vascular development (RVD in premature infants. Fluorescein angiography (FA has depicted phases (early, mid, late, and mature of RVD in oxygen-induced retinopathy (OIR mice. We sought to establish the relationship between retinal structural and vascular changes using simultaneous FA and spectral domain optical coherence tomography (SD-OCT. Method. 63 mice were exposed to 77% oxygen at postnatal day 7 (P7 for 5 days, while 63 mice remained in room air (RA. Total retinal thickness (TRT, inner retinal thickness (IRT, and outer retinal thickness (ORT were calculated at early (P19, mid (P24, late (P32, and mature (P47 phases of RVD. Results. TRT was reduced in OIR (162.66 ± 17.75 μm, n=13 compared to RA mice at P19 (197.57 ± 3.49 μm, n=14, P24, P32, and P49 (P0.05. IRT was reduced in OIR (71.60 ± 17.14 μm compared to RA (103.07 ± 3.47 μm mice at P19 and all ages (P<0.0001. Conclusion. We have shown the spatial and temporal relationship between retinal structure and vascular development in OIR. Significant inner retinal thinning in OIR mice persisted despite revascularization of the capillary network; further studies will elucidate its functional implications in ROP.

  7. A Simple Novel Technique of Infrared Meibography by Means of Spectral-Domain Optical Coherence Tomography: A Cross-Sectional Clinical Study.

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    Pietro Emanuele Napoli

    Full Text Available To compare a novel spectral-domain optical coherence tomography (SD-OCT technique with traditional lid transillumination for evaluation of meibomian glands (MGs and to assess the relation of MG morphologic changes to the glandular atrophy.Evaluation of diagnostic technology.Sixty-one patients with obstructive MGD (30 men, 31 women; age [mean ± standard deviation] 45.1 ± 12.1 years, and 75 control subjects (32 men, 43 women; 44.1 ± 12.5 years were recruited in order to have a balanced distribution of glandular features.Agreement between SD-OCT and lid transillumination examination for the detection of drop-out (partial or complete loss of MGs and microscopic changes (i.e. shortening, distortion, segmentation and entanglement, as well as the relationship between morphological features and MG atrophy were evaluated.Agreement between the two meibographic techniques, bias in symmetry of classification, and association analysis between microscopic changes and MG dropout.Overall agreement for all morphological features was substantial (Cohen kappa coefficient = 0.77; p<0.001, even if, the majority of disagreement occurred for cases with segmentation, where agreement was present in only 108 (81.82% of 132 eyes with adequate images for interpretation, and where SD-OCT tended to diagnose more cases not detected by traditional lid transillumination (McNemar test, p<0.001. Moreover, segmentation and distortion pattern negatively correlated with the degree of drop-out, whereas shortening and entanglement pattern demonstrated only a weak correlation (Spearman's ρ was -0.691, -0.491, -0.359, -0.385, respectively.Each method has its advantages but in general there was close agreement between these meibographic techniques, particularly for MG dropout, which supports the reliability of our novel, simple and patient-friendly SD-OCT approach.

  8. Correlation between morphological characteristics in spectral-domain-optical coherence tomography, different functional tests and a patient's subjective handicap in acute central serous chorioretinopathy.

    Science.gov (United States)

    Gerendas, Bianca S; Kroisamer, Julia-Sophie; Buehl, Wolf; Rezar-Dreindl, Sandra M; Eibenberger, Katharina M; Pablik, Eleonore; Schmidt-Erfurth, Ursula; Sacu, Stefan

    2018-01-16

    The purpose of this study was to identify quantitatively measurable morphologic optical coherence tomography (OCT) characteristics in patients with an acute episode of central serous chorioretinopathy (CSC) and evaluate their correlation to functional and psychological variables for their use in daily clinical practice. Retinal thickness (RT), the height, area and volume of subretinal fluid (SRF)/pigment epithelium detachments were evaluated using the standardized procedures of the Vienna Reading Center. These morphologic characteristics were compared with functional variables [best-corrected visual acuity (BCVA), contrast sensitivity (CS), retinal sensitivity/microperimetry, fixation stability], and patients' subjective handicap from CSC using the National Eye Institute 25-item Visual Function Questionnaire (NEI VFQ-25). Data from 39 CSC patients were included in this analysis. Three different SRF height measures showed a high negative correlation (r = -0.7) to retinal sensitivity within the central 9°, which was also negatively correlated with SRF area and volume (r = -0.6). The CS score and fixation stability (fixation points within 2°) showed a moderate negative correlation (r = -0.4) with SRF height variables. Comparison of the subjective handicap with morphological characteristics in spectral-domain (SD)-OCT showed SRF height had the highest correlation (r = -0.4) with the subjective problems reported and overall NEI VFQ-25 score. In conclusion, SRF height measured in SD-OCT showed the best correlation with functional variables and patients' subjective handicap caused by the disease and therefore seems to be the best variable to look at in daily clinical routine. Even though area and volume also show a correlation, these cannot be so easily measured as height and are therefore not suggested for daily clinical routine. © 2018 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  9. Two- and three-dimensional topographic analysis of pathologically myopic eyes with dome-shaped macula and inferior staphyloma by spectral domain optical coherence tomography.

    Science.gov (United States)

    García-Ben, Antonio; Kamal-Salah, Radua; García-Basterra, Ignacio; Gonzalez Gómez, Ana; Morillo Sanchez, María José; García-Campos, Jose Manuel

    2017-05-01

    To investigate the posterior anatomical structure of pathologically myopic eyes with dome-shaped macula and inferior staphyloma using spectral domain optical coherence tomography (SD-OCT). Our database of 260 pathologically myopic eyes was analyzed retrospectively to identify patients with dome-shaped macula and inferior staphyloma. All patients underwent vertical and horizontal SD-OCT scans across the central fovea, with three-dimensional macular map reconstruction. Best-corrected visual acuity, axial length, and choroidal thickness measurements were recorded. The macular bulge height was also analyzed in eyes with dome-shaped macula. In the three-dimensional images, the symmetry and orientation of the main plane of the inward incurvation of the macula were examined. Twenty-eight (10.7%) of the 260 pathologically myopic eyes had dome-shaped macula of one of three different types: a round radially symmetrical dome (eight eyes, 28.5%), a horizontal axially symmetrical oval-shaped dome (15 eyes, 53.5%), or a vertical axially symmetrical oval-shaped dome (five eyes, 17.8%). The macular bulge height was significantly greater in horizontal oval-shaped dome eyes (p = 0.01, for each comparison). Inferior posterior staphylomas were observed in ten (3.8%) of the 260 pathologically myopic eyes with asymmetrical macular bends. Vertical and horizontal OCT sectional scanning in combination with three-dimensional macular map reconstruction provides important information for understanding the posterior anatomical structure of dome-shaped macula and inferior staphyloma in pathologically myopic eyes.

  10. Measurement of the blood flow rate and velocity in coronary artery stenosis using intracoronary frequency domain optical coherence tomography: Validation against fractional flow reserve.

    Science.gov (United States)

    Zafar, Haroon; Sharif, Faisal; Leahy, Martin J

    2014-12-01

    The main objective of this study was to assess the blood flow rate and velocity in coronary artery stenosis using intracoronary frequency domain optical coherence tomography (FD-OCT). A correlation between fractional flow reserve (FFR) and FD-OCT derived blood flow velocity is also included in this study. A total of 20 coronary stenoses in 15 patients were assessed consecutively by quantitative coronary angiography (QCA), FFR and FD-OCT. A percutaneous coronary intervention (PCI) optimization system was used in this study which combines wireless FFR measurement and FD-OCT imaging in one platform. Stenoses were labelled severe if FFR ≤ 0.8. Blood flow rate and velocity in each stenosis segment were derived from the volumetric analysis of the FD-OCT pull back images. The FFR value was ≤ 0.80 in 5 stenoses (25%). The mean blood flow rate in severe coronary stenosis ( n  = 5) was 2.54 ± 0.55 ml/s as compared to 4.81 ± 1.95 ml/s in stenosis with FFR > 0.8 ( n  = 15). A good and significant correlation between FFR and FD-OCT blood flow velocity in coronary artery stenosis ( r  = 0.74, p  < 0.001) was found. The assessment of stenosis severity using FD-OCT derived blood flow rate and velocity has the ability to overcome many limitations of QCA and intravascular ultrasound (IVUS).

  11. Optic Nerve Head and Retinal Nerve Fiber Layer Analysis in Ocular Hypertension and Early-Stage Glucoma Using Spectral-Domain Optical Coherence Tomography Copernicus

    Directory of Open Access Journals (Sweden)

    Nilgün Solmaz

    2014-01-01

    Full Text Available Objectives: Evaluation of structural alterations of the optic nerve head (ONH and the retinal nerve fiber layer (RNFL in patients with ocular hypertension (OHT and early-stage glaucoma and assessment of the discriminatory diagnostic performance of spectral-domain optical coherence tomography (SD-OCT Copernicus (Optopol Technology S.A.. Materials and Methods: This study included 59 eyes of a total of 59 patients, 29 of whom were diagnosed with OHT (Group 1 and 30 with early-stage glaucoma (Group 2. The differentiation of early-stage glaucoma and OHT was carried out on the basis of standard achromatic visual field test results. Analysis of the ONH and RNFL thickness of all cases was made using SD-OCT. Group 1 and Group 2 were compared with respect to the ONH parameters and RNFL thickness. The diagnostic sensitivity of the OCT parameters was evaluated by the area under the receiver operating characteristics curves (AUC. Results: The average, superior, inferior, and nasal RNFL thicknesses in early-stage glaucoma cases were approximately 10% (12-14 µm less compared to the OHT eyes, with differences being highly significant (p≤0.001. However, there was no statistically significant difference in the temporal RNFL thicknesses. The most sensitive parameter in the early diagnosis of glaucoma was average RNFL thickness corresponding to AUC: 0.852, followed by AUC: 0.816 and AUC: 0.773 values in superior and inferior RNFL thickness, respectively. In localized RNFL defects, the highest sensitivity corresponded to superior and superonasal quadrants (ACU: 0.805 and ACU: 0.781, respectively. There were not any statistically significant differences between the ONH morphological parameters of the two groups. Conclusion: RNFL analysis obtained using SD-OCT Copernicus is able to discriminate early-stage glaucoma eyes from those with OHT. However, ONH morphological parameters do not have the same diagnostic sensitivity. Turk J Ophthalmol 2014; 44: 35-41

  12. EFFECT OF INTRAVITREAL RANIBIZUMAB ON GANGLION CELL COMPLEX AND PERIPAPILLARY RETINAL NERVE FIBER LAYER IN NEOVASCULAR AGE-RELATED MACULAR DEGENERATION USING SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY.

    Science.gov (United States)

    Zucchiatti, Ilaria; Cicinelli, Maria V; Parodi, Maurizio Battaglia; Pierro, Luisa; Gagliardi, Marco; Accardo, Agostino; Bandello, Francesco

    2017-07-01

    To analyze the changes in ganglion cell complex and peripapillary retinal nerve fiber layer thickness, in central macular thickness and choroidal thickness on spectral domain optical coherence tomography in patients with neovascular age-related macular degeneration treated with intravitreal ranibizumab injections. All consecutive patients with untreated neovascular age-related macular degeneration received loading phase of three monthly intravitreal ranibizumab, followed by retreatments on a pro re nata protocol for 12 months. changes in ganglion cell complex and retinal nerve fiber layer at the end of follow-up. Secondary outcome: changes in best-corrected visual acuity, central macular thickness, and choroidal thickness at the end of follow-up. Choroidal thickness was measured at 500 μm, 1000 μm, and 1,500 μm intervals nasally, temporally, superiorly, and inferiorly to the fovea, respectively, on horizontal and vertical line scans centered on the fovea. Twenty-four eyes were included. Ganglion cell complex and peripapillary retinal nerve fiber layer thickness did not show statistically significant changes through 12 months (55.6 ± 18.5 and 81.9 ± 9.9 μm at baseline, 52.7 ± 19.3 and 84.6 ± 15.5 μm at month 12, P > 0.05). Central macular thickness showed progressive decrease from baseline to month 12, with maximum reduction at month 3 (P macular thickness was significantly reduced at the end of treatment. Further studies, with larger sample, longer follow-up, and greater number of injections, are warranted.

  13. Molecular basis of the specific subcellular localization of the C2-like domain of 5-lipoxygenase.

    Science.gov (United States)

    Kulkarni, Shilpa; Das, Sudipto; Funk, Colin D; Murray, Diana; Cho, Wonhwa

    2002-04-12

    The activation of 5-lipoxygenase (5-LO) involves its calcium-dependent translocation to the nuclear envelope, where it catalyzes the two-step transformation of arachidonic acid into leukotriene A(4), leading to the synthesis of various leukotrienes. To understand the mechanism by which 5-LO is specifically targeted to the nuclear envelope, we studied the membrane binding properties of the amino-terminal domain of 5-LO, which has been proposed to have a C2 domain-like structure. The model building, electrostatic potential calculation, and in vitro membrane binding studies of the isolated C2-like domain of 5-LO and selected mutants show that this Ca(2+)-dependent domain selectively binds zwitterionic phosphatidylcholine, which is conferred by tryptophan residues (Trp(13), Trp(75), and Trp(102)) located in the putative Ca(2+)-binding loops. The spatiotemporal dynamics of the enhanced green fluorescence protein-tagged C2-like domain of 5-LO and mutants in living cells also show that the phosphatidylcholine selectivity of the C2-like domain accounts for the specific targeting of 5-LO to the nuclear envelope. Together, these results show that the C2-like domain of 5-LO is a genuine Ca(2+)-dependent membrane-targeting domain and that the subcellular localization of the domain is governed in large part by its membrane binding properties.

  14. Offline fusion of co-registered intravascular ultrasound and frequency domain optical coherence tomography images for the analysis of human atherosclerotic plaques

    DEFF Research Database (Denmark)

    Räber, Lorenz; Heo, Jung Ho; Radu, Maria D

    2012-01-01

    To demonstrate the feasibility and potential usefulness of an offline fusion of matched optical coherence tomography (OCT) and intravascular ultrasound (IVUS)/virtual histology (IVUS-VH) images.......To demonstrate the feasibility and potential usefulness of an offline fusion of matched optical coherence tomography (OCT) and intravascular ultrasound (IVUS)/virtual histology (IVUS-VH) images....

  15. Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications.

    Directory of Open Access Journals (Sweden)

    Jose L Ortega Roldan

    Full Text Available SH3 domains constitute a new type of ubiquitin-binding domains. We previously showed that the third SH3 domain (SH3-C of CD2AP binds ubiquitin in an alternative orientation. We have determined the structure of the complex between first CD2AP SH3 domain and ubiquitin and performed a structural and mutational analysis to decipher the determinants of the SH3-C binding mode to ubiquitin. We found that the Phe-to-Tyr mutation in CD2AP and in the homologous CIN85 SH3-C domain does not abrogate ubiquitin binding, in contrast to previous hypothesis and our findings for the first two CD2AP SH3 domains. The similar alternative binding mode of the SH3-C domains of these related adaptor proteins is characterised by a higher affinity to C-terminal extended ubiquitin molecules. We conclude that CD2AP/CIN85 SH3-C domain interaction with ubiquitin constitutes a new ubiquitin-binding mode involved in a different cellular function and thus changes the previously established mechanism of EGF-dependent CD2AP/CIN85 mono-ubiquitination.

  16. Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions

    International Nuclear Information System (INIS)

    Eibl, Clarissa; Hessenberger, Manuel; Wenger, Julia; Brandstetter, Hans

    2014-01-01

    Pyrin domains (PYDs) recruit downstream effector molecules in NLR signalling. A specific charge-relay system suggests a the formation of a signalling complex involving a PYD dimer. The cytosolic tripartite NLR receptors serve as important signalling platforms in innate immunity. While the C-terminal domains act as sensor and activation modules, the N-terminal death-like domain, e.g. the CARD or pyrin domain, is thought to recruit downstream effector molecules by homotypic interactions. Such homotypic complexes have been determined for all members of the death-domain superfamily except for pyrin domains. Here, crystal structures of human NLRP14 pyrin-domain variants are reported. The wild-type protein as well as the clinical D86V mutant reveal an unexpected rearrangement of the C-terminal helix α6, resulting in an extended α5/6 stem-helix. This reordering mediates a novel symmetric pyrin-domain dimerization mode. The conformational switching is controlled by a charge-relay system with a drastic impact on protein stability. How the identified charge relay allows classification of NLRP receptors with respect to distinct recruitment mechanisms is discussed

  17. Molecular Dynamics Simulations of the STAS Domains of Rat Prestin and Human Pendrin Reveal Conformational Motions in Conserved Flexible Regions

    Directory of Open Access Journals (Sweden)

    Alok K. Sharma

    2014-02-01

    Full Text Available Background: Molecular dynamics (MD simulations provide valuable information on the conformational changes that accompany time-dependent motions in proteins. The reported crystal structure of rat prestin (PDB 3LLO is remarkable for an α1-α2 inter-helical angle that differs substantially from those observed in bacterial STAS domains of SulP anion transporters and anti-sigma factor antagonists. However, NMR data on the rat prestin STAS domain in solution suggests dynamic features at or near the α1-α2 helical region (Pasqualetto et al JMB, 2010. We therefore performed a 100 ns 300K MD simulation study comparing the STAS domains of rat prestin and (modeled human pendrin, to explore possible conformational flexibility in the region of the α1 and α2 helices. Methods: The conformation of the loop missing in the crystal structure of rat prestin STAS (11 amino acids between helix α1 and strand β3 was built using Modeller. MD simulations were performed with GROMACSv4.6 using GROMOS96 53a6 all-atom force field. Results: A subset of secondary structured elements of the STAS domains exhibits significant conformational changes during the simulation time course. The conformationally perturbed segments include the majority of loop regions, as well as the α1 and α2 helices. A significant decrease in the α1-α2 inter-helical angle observed across the simulation trajectory leads to closer helical packing at their C-termini. The end-simulation conformations of the prestin and pendrin STAS domains, including their decreased α1-α2 inter-helical angles, resemble more closely the packing of corresponding helices in the STAS structures of bacterial SulP transporters Rv1739c and ychM, as well as those of the anti-sigma factor antagonists. Several structural segments of the modeled human pendrin STAS domain exhibit larger atomic motions and greater conformational deviations than the corresponding regions of rat prestin, predicting that the human pendrin STAS

  18. The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

    Science.gov (United States)

    Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy. G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Zohar

    2011-01-01

    CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despite its potential role in retinoblastoma. We present the first crystal structure of the human CD147 Ig0 domain and show that the CD147 Ig0 domain is a crystallographic dimer with an I-type domain structure, which is maintained in solution. Furthermore, we have utilized our structural data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6 and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Finally, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation. PMID:21620857

  19. Molecular Mechanisms of SH2- and PTB-Domain-Containing Proteins in Receptor Tyrosine Kinase Signaling

    Science.gov (United States)

    Wagner, Melany J.; Stacey, Melissa M.; Liu, Bernard A.; Pawson, Tony

    2013-01-01

    Intracellular signaling is mediated by reversible posttranslational modifications (PTMs) that include phosphorylation, ubiquitination, and acetylation, among others. In response to extracellular stimuli such as growth factors, receptor tyrosine kinases (RTKs) typically dimerize and initiate signaling through phosphorylation of their cytoplasmic tails and downstream scaffolds. Signaling effectors are recruited to these phosphotyrosine (pTyr) sites primarily through Src homology 2 (SH2) domains and pTyr-binding (PTB) domains. This review describes how these conserved domains specifically recognize pTyr residues and play a major role in mediating precise downstream signaling events. PMID:24296166

  20. Molecular mechanisms of SH2- and PTB-domain-containing proteins in receptor tyrosine kinase signaling.

    Science.gov (United States)

    Wagner, Melany J; Stacey, Melissa M; Liu, Bernard A; Pawson, Tony

    2013-12-01

    Intracellular signaling is mediated by reversible posttranslational modifications (PTMs) that include phosphorylation, ubiquitination, and acetylation, among others. In response to extracellular stimuli such as growth factors, receptor tyrosine kinases (RTKs) typically dimerize and initiate signaling through phosphorylation of their cytoplasmic tails and downstream scaffolds. Signaling effectors are recruited to these phosphotyrosine (pTyr) sites primarily through Src homology 2 (SH2) domains and pTyr-binding (PTB) domains. This review describes how these conserved domains specifically recognize pTyr residues and play a major role in mediating precise downstream signaling events.

  1. Partially coherent isodiffracting pulsed beams

    Science.gov (United States)

    Koivurova, Matias; Ding, Chaoliang; Turunen, Jari; Pan, Liuzhan

    2018-02-01

    We investigate a class of isodiffracting pulsed beams, which are superpositions of transverse modes supported by spherical-mirror laser resonators. By employing modal weights that, for stationary light, produce a Gaussian Schell-model beam, we extend this standard model to pulsed beams. We first construct the two-frequency cross-spectral density function that characterizes the spatial coherence in the space-frequency domain. By assuming a power-exponential spectral profile, we then employ the generalized Wiener-Khintchine theorem for nonstationary light to derive the two-time mutual coherence function that describes the space-time coherence of the ensuing beams. The isodiffracting nature of the laser resonator modes permits all (paraxial-domain) calculations at any propagation distance to be performed analytically. Significant spatiotemporal coupling is revealed in subcycle, single-cycle, and few-cycle domains, where the partial spatial coherence also leads to reduced temporal coherence even though full spectral coherence is assumed.

  2. Molecular LEGO by domain-imprinting of cytochrome P450 BM3.

    Science.gov (United States)

    Jetzschmann, K J; Yarman, A; Rustam, L; Kielb, P; Urlacher, V B; Fischer, A; Weidinger, I M; Wollenberger, U; Scheller, F W

    2018-04-01

    Electrosynthesis of the MIP nano-film after binding of the separated domains or holo-cytochrome BM3 via an engineered anchor should result in domain-specific cavities in the polymer layer. Both the two domains and the holo P450 BM3 have been bound prior polymer deposition via a N-terminal engineered his6-anchor to the electrode surface. Each step of MIP preparation was characterized by cyclic voltammetry of the redox-marker ferricyanide. Rebinding after template removal was evaluated by quantifying the suppression of the diffusive permeability of the signal for ferricyanide and by the NADH-dependent reduction of cytochrome c by the reductase domain (BMR). The working hypothesis is verified by the discrimination of the two domains by the respective MIPs: The holoenzyme P450 BM3 was ca. 5.5 times more effectively recognized by the film imprinted with the oxidase domain (BMO) as compared to the BMR-MIP or the non-imprinted polymer (NIP). Obviously, a cavity is formed during the imprinting process around the his 6 -tag-anchored BMR which cannot accommodate the broader BMO or the P450 BM3. The affinity of the MIP towards P450 BM3 is comparable with that to the monomer in solution. The his 6 -tagged P450 BM3 binds (30 percent) stronger which shows the additive effect of the interaction with the MIP and the binding to the electrode. Copyright © 2018. Published by Elsevier B.V.

  3. Comparison of automated analysis of Cirrus HD OCT spectral-domain optical coherence tomography with stereo photographs of the optic disc.

    Science.gov (United States)

    Sharma, Ashish; Oakley, Jonathan D; Schiffman, Joyce C; Budenz, Donald L; Anderson, Douglas R

    2011-07-01

    To evaluate a new automated analysis of optic disc images obtained by spectral-domain optical coherence tomography (SD OCT). Areas of the optic disc, cup, and neural rim in SD OCT images were compared with these areas from stereoscopic photographs to represent the current traditional optic nerve evaluation. The repeatability of measurements by each method was determined and compared. Evaluation of diagnostic technology. One hundred nineteen healthy eyes, 23 eyes with glaucoma, and 7 glaucoma suspect eyes. Optic disc and cup margins were traced from stereoscopic photographs by 3 individuals independently. Optic disc margins and rim widths were determined automatically in SD OCT. A subset of photographs was examined and traced a second time, and duplicate SD OCT images also were analyzed. Agreement among photograph readers, between duplicate readings, and between SD OCT and photographs were quantified by the intraclass correlation coefficient (ICC), by the root mean square, and by the standard deviation of the differences. Optic disc areas tended to be slightly larger when judged in photographs than by SD OCT, whereas cup areas were similar. Cup and optic disc areas showed good correlation (0.8) between the average photographic reading and SD OCT, but only fair correlation of rim areas (0.4). The SD OCT was highly reproducible (ICC, 0.96-0.99). Each reader also was consistent with himself on duplicate readings of 21 photographs (ICC, 0.80-0.88 for rim area and 0.95-0.98 for all other measurements), but reproducibility was not as good as SD OCT. Measurements derived from SD OCT did not differ from photographic readings more than the readings of photographs by different readers differed from each other. Designation of the cup and optic disc boundaries by an automated analysis of SD OCT was within the range of variable designations by different readers from color stereoscopic photographs, but use of different landmarks typically made the designation of the optic disc

  4. Normative data set identifying properties of the macula across age groups: integration of visual function and retinal structure with microperimetry and spectral-domain optical coherence tomography.

    Science.gov (United States)

    Sabates, Felix N; Vincent, Ryan D; Koulen, Peter; Sabates, Nelson R; Gallimore, Gary

    2011-01-01

    A normative database of functional and structural parameters of the macula from normal subjects was established to identify reference points for the diagnosis of patients with macular disease using microperimetry and scanning laser ophthalmoscope/spectral-domain optical coherence tomography (SD-OCT). This was a community-based, prospective, cross-sectional study of 169 eyes from subjects aged 21 years to 85 years with best-corrected visual acuity of 20/25 or better and without any ocular disease. Full-threshold macular microperimetry combined with the acquisition of structural parameters of the macula with scanning laser ophthalmoscope/SD-OCT was recorded (SD-OCT/scanning laser ophthalmoscope with add-on Microperimetry module; OPKO). Fixation, central, subfield, and mean retinal thickness were acquired together with macular sensitivity function. Thickness and sensitivity as primary outcome measures were mapped and superimposed correlating topographically differentiated macular thickness with sensitivity. Statistical evaluation was performed with age, gender, and ethnicity as covariates. Subfield and mean retinal thickness and sensitivity were measured with macular microperimetry combined with SD-OCT and differentiated by macular topography and subjects' age, gender, and ethnicity. Mean retinal sensitivity and thickness were calculated for 169 healthy eyes (mean age, 48 ± 17 years). A statistically significant decrease in sensitivity was found only in the age group of participants ≥ 70 years and in peripheral portions of the macula in individuals aged ≥60 years and was more pronounced in the area surrounding the fovea than in the center of the macula, while retinal thickness did not change with age. No statistically significant differences in the primary outcome measures or their correlations were found when using gender or ethnicity as a covariate. A database for normal macular thickness and sensitivity was generated with a combined microperimetry SD

  5. The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

    Energy Technology Data Exchange (ETDEWEB)

    Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Z.

    2011-06-18

    CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despite its potential role in retinoblastoma. Thus, here we have extensively characterized the CD147 Ig0 domain by elucidating its three-dimensional structure through crystallography and its solution behavior through several biophysical methods that include nuclear magnetic resonance. Furthermore, we have utilized this data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6, which is a well-known contributor to retinoblastoma and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Furthermore, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation.

  6. The orientation and molecular movement of a k(+) channel voltage-sensing domain.

    Science.gov (United States)

    Gandhi, Chris S; Clark, Eliana; Loots, Eli; Pralle, Arnd; Isacoff, Ehud Y

    2003-10-30

    Voltage-gated channels operate through the action of a voltage-sensing domain (membrane segments S1-S4) that controls the conformation of gates located in the pore domain (membrane segments S5-S6). Recent structural studies on the bacterial K(v)AP potassium channel have led to a new model of voltage sensing in which S4 lies in the lipid at the channel periphery and moves through the membrane as a unit with a portion of S3. Here we describe accessibility probing and disulfide scanning experiments aimed at determining how well the K(v)AP model describes the Drosophila Shaker potassium channel. We find that the S1-S3 helices have one end that is externally exposed, S3 does not undergo a transmembrane motion, and S4 lies in close apposition to the pore domain in the resting and activated state.

  7. Two-dimensional spectroscopy of a molecular dimer unveils the effects of vibronic coupling on exciton coherences

    NARCIS (Netherlands)

    Halpin, Alexei; Johnson, Philip J. M.; Tempelaar, Roel; Murphy, R. Scott; Knoester, Jasper; Jansen, Thomas L. C.; Miller, R. J. Dwayne

    The observation of persistent oscillatory signals in multidimensional spectra of protein-pigment complexes has spurred a debate on the role of coherence-assisted electronic energy transfer as a key operating principle in photosynthesis. Vibronic coupling has recently been proposed as an explanation

  8. Identification of Phytochemicals Targeting c-Met Kinase Domain using Consensus Docking and Molecular Dynamics Simulation Studies.

    Science.gov (United States)

    Aliebrahimi, Shima; Montasser Kouhsari, Shideh; Ostad, Seyed Nasser; Arab, Seyed Shahriar; Karami, Leila

    2018-06-01

    c-Met receptor tyrosine kinase is a proto-oncogene whose aberrant activation is attributed to a lower rate of survival in most cancers. Natural product-derived inhibitors known as "fourth generation inhibitors" constitute more than 60% of anticancer drugs. Furthermore, consensus docking approach has recently been introduced to augment docking accuracy and reduce false positives during a virtual screening. In order to obtain novel small-molecule Met inhibitors, consensus docking approach was performed using Autodock Vina and Autodock 4.2 to virtual screen Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database against active and inactive conformation of c-Met kinase domain structure. Two hit molecules that were in line with drug-likeness criteria, desired docking score, and binding pose were subjected to molecular dynamics simulations to elucidate intermolecular contacts in protein-ligand complexes. Analysis of molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area studies showed that ZINC08234189 is a plausible inhibitor for the active state of c-Met, whereas ZINC03871891 may be more effective toward active c-Met kinase domain compared to the inactive form due to higher binding energy. Our analysis showed that both the hit molecules formed hydrogen bonds with key residues of the hinge region (P1158, M1160) in the active form, which is a hallmark of kinase domain inhibitors. Considering the pivotal role of HGF/c-Met signaling in carcinogenesis, our results propose ZINC08234189 and ZINC03871891 as the therapeutic options to surmount Met-dependent cancers.

  9. Molecular Logic of Neuronal Self-Recognition through Protocadherin Domain Interactions

    DEFF Research Database (Denmark)

    Rubinstein, Rotem; Thu, Chan Aye; Goodman, Kerry Marie

    2015-01-01

    Self-avoidance, a process preventing interactions of axons and dendrites from the same neuron during development, is mediated in vertebrates through the stochastic single-neuron expression of clustered protocadherin protein isoforms. Extracellular cadherin (EC) domains mediate isoform-specific ho...

  10. Structure characterization of the central repetitive domain of high molecular weight gluten proteins .2. Characterization in solution and in the dry state

    NARCIS (Netherlands)

    van Dijk, A.A.; De Boef, E.; Bekkers, A.; van Wijk, L.L.; van Swieten, E.; Hamer, R.J.; Robillard, G.T.

    The structure of the central repetitive domain of high molecular weight (HMW) wheat gluten proteins was characterized in solution and in the dry state using HMW proteins Bx6 and Bx7 and a subcloned, bacterially expressed part of the repetitive domain of HMW Dx5. Model studies of the HMW consensus

  11. Structure characterization of the central repetitive domain of high molecular weight gluten proteins .1. Model studies using cyclic and linear peptides

    NARCIS (Netherlands)

    VanDijk, AA; VanWijk, LL; VanVliet, A; Haris, P; VanSwieten, E; Tesser, GI; Robillard, GT

    The high molecular weight (HMW) proteins from wheat contain a repetitive domain that forms 60-80% of their sequence. The consensus peptides PGQGQQ and GYYPTSPQQ form more than 90% of the domain; both are predicted to adopt beta-turn structure. This paper describes the structural characterization of

  12. Model-free methods of analyzing domain motions in proteins from simulation : A comparison of normal mode analysis and molecular dynamics simulation of lysozyme

    NARCIS (Netherlands)

    Hayward, S.; Kitao, A.; Berendsen, H.J.C.

    Model-free methods are introduced to determine quantities pertaining to protein domain motions from normal mode analyses and molecular dynamics simulations, For the normal mode analysis, the methods are based on the assumption that in low frequency modes, domain motions can be well approximated by

  13. Sarcocystis neurona: molecular characterization of enolase domain I region and a comparison to other protozoa.

    Science.gov (United States)

    Bolten, K E; Marsh, A E; Reed, S M; Dubey, J P; Toribio, R E; Saville, W J A

    2008-09-01

    Sarcocystis neurona causes protozoal myeloencephalitis and has the ability to infect a wide host range in contrast to other Sarcocystis species. In the current study, five S. neurona isolates from a variety of sources, three Sarcocystis falcatula, one Sarcocystis dasypi/S. neurona-like isolate, and one Besnoitia darlingi isolate were used to compare the enolase 2 gene segment containing the domain I region to previously sequenced enolase genes from Neospora caninum, Neospora hughesi, Toxoplasma gondii, Plasmodium falciparum, and Trypanosoma cruzi; enolase 2 segment containing domain I region is highly conserved amongst these parasites of veterinary and medical importance. Immunohistochemistry results indicates reactivity of T. gondii enolase 1 and 2 antibodies to S. neurona merozoites and metrocytes, but no reactivity of anti-enolase 1 to the S. neurona bradyzoite stage despite reactivity to T. gondii bradyzoites, suggesting expression differences between organisms.

  14. Ultrasonic force microscopy: detection and imaging of ultra-thin molecular domains.

    Science.gov (United States)

    Dinelli, Franco; Albonetti, Cristiano; Kolosov, Oleg V

    2011-03-01

    The analysis of the formation of ultra-thin organic films is a very important issue. In fact, it is known that the properties of organic light emitting diodes and field effect transistors are strongly affected by the early growth stages. For instance, in the case of sexithiophene, the presence of domains made of molecules with the backbone parallel to the substrate surface has been indirectly evidenced by photoluminescence spectroscopy and confocal microscopy. On the contrary, conventional scanning force microscopy both in contact and intermittent contact modes have failed to detect such domains. In this paper, we show that Ultrasonic Force Microscopy (UFM), sensitive to nanomechanical properties, allows one to directly identify the structure of sub-monolayer thick films. Sexithiophene flat domains have been imaged for the first time with nanometer scale spatial resolution. A comparison with lateral force and intermittent contact modes has been carried out in order to explain the origins of the UFM contrast and its advantages. In particular, it indicates that UFM is highly suitable for investigations where high sensitivity to material properties, low specimen damage and high spatial resolution are required. Copyright © 2010 Elsevier B.V. All rights reserved.

  15. Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies.

    Directory of Open Access Journals (Sweden)

    Shannon E Hill

    Full Text Available Olfactomedin (OLF domains are found within extracellular, multidomain proteins in numerous tissues of multicellular organisms. Even though these proteins have been implicated in human disorders ranging from cancers to attention deficit disorder to glaucoma, little is known about their structure(s and function(s. Here we biophysically, biochemically, and structurally characterize OLF domains from H. sapiens olfactomedin-1 (npoh-OLF, also called noelin, pancortin, OLFM1, and hOlfA, and M. musculus gliomedin (glio-OLF, also called collomin, collmin, and CRG-L2, and compare them with available structures of myocilin (myoc-OLF recently reported by us and R. norvegicus glio-OLF and M. musculus latrophilin-3 (lat3-OLF by others. Although the five-bladed β-propeller architecture remains unchanged, numerous physicochemical characteristics differ among these OLF domains. First, npoh-OLF and glio-OLF exhibit prominent, yet distinct, positive surface charges and copurify with polynucleotides. Second, whereas npoh-OLF and myoc-OLF exhibit thermal stabilities typical of human proteins near 55°C, and most myoc-OLF variants are destabilized and highly prone to aggregation, glio-OLF is nearly 20°C more stable and significantly more resistant to chemical denaturation. Phylogenetically, glio-OLF is most similar to primitive OLFs, and structurally, glio-OLF is missing distinguishing features seen in OLFs such as the disulfide bond formed by N- and C- terminal cysteines, the sequestered Ca2+ ion within the propeller central hydrophilic cavity, and a key loop-stabilizing cation-π interaction on the top face of npoh-OLF and myoc-OLF. While deciphering the explicit biological functions, ligands, and binding partners for OLF domains will likely continue to be a challenging long-term experimental pursuit, we used structural insights gained here to generate a new antibody selective for myoc-OLF over npoh-OLF and glio-OLF as a first step in overcoming the impasse in

  16. Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome.

    Science.gov (United States)

    Rzhetsky, A; Gomez, S M

    2001-10-01

    Current growth in the field of genomics has provided a number of exciting approaches to the modeling of evolutionary mechanisms within the genome. Separately, dynamical and statistical analyses of networks such as the World Wide Web and the social interactions existing between humans have shown that these networks can exhibit common fractal properties-including the property of being scale-free. This work attempts to bridge these two fields and demonstrate that the fractal properties of molecular networks are linked to the fractal properties of their underlying genomes. We suggest a stochastic model capable of describing the evolutionary growth of metabolic or signal-transduction networks. This model generates networks that share important statistical properties (so-called scale-free behavior) with real molecular networks. In particular, the frequency of vertices connected to exactly k other vertices follows a power-law distribution. The shape of this distribution remains invariant to changes in network scale: a small subgraph has the same distribution as the complete graph from which it is derived. Furthermore, the model correctly predicts that the frequencies of distinct DNA and protein domains also follow a power-law distribution. Finally, the model leads to a simple equation linking the total number of different DNA and protein domains in a genome with both the total number of genes and the overall network topology. MatLab (MathWorks, Inc.) programs described in this manuscript are available on request from the authors. ar345@columbia.edu.

  17. MOLECULAR PATHOPHYSIOLOGY AND PHARMACOLOGY OF THE VOLTAGE-SENSING DOMAIN OF NEURONAL ION CHANNELS

    Directory of Open Access Journals (Sweden)

    Francesco eMiceli

    2015-07-01

    Full Text Available Voltage-gated ion channels (VGIC are membrane proteins that switch from a closed to open state in response to changes in membrane potential, thus enabling ion fluxes across the cell membranes. The mechanism that regulate the structural rearrangements occurring in VGIC in response to changes in membrane potential still remains one of the most challenging topic of modern biophysics. Na+, Ca2+ and K+ voltage-gated channels are structurally formed by the assembly of four similar domains, each comprising six transmembrane segments. Each domain can be divided in two main regions: the Pore Module (PM and the Voltage-Sensing Module (VSM. The PM (helices S5 and S6 and intervening linker is responsible for gate opening and ion selectivity; by contrast, the VSM, comprising the first four transmembrane helices (S1-S4, undergoes the first conformational changes in response to membrane voltage. In particular, the S4 segment of each domain, which contains several positively charged residues interspersed with hydrophobic amino acids, is located within the membrane electric field and plays an essential role in voltage sensing. In neurons, specific gating properties of each channel subtype underlie a variety of biological events, ranging from the generation and propagation of electrical impulses, to the secretion of neurotransmitters, to the regulation of gene expression. Given the important functional role played by the VSM in neuronal VGICs, it is not surprising that various VSM mutations affecting the gating process of these channels are responsible for human diseases, and that compounds acting on the VSM have emerged as important investigational tools with great therapeutic potential. In the present review we will briefly describe the most recent discoveries concerning how the VSM exerts its function, how genetically inherited diseases caused by mutations occurring in the VSM affects gating in VGICs, and how several classes of drugs and toxins selectively

  18. The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

    OpenAIRE

    Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy. G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Zohar

    2011-01-01

    CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues a...

  19. Data-Aided Frequency-Domain 2×2 MIMO Equalizer for 112 Gbit/s PDM-QPSK Coherent Transmission Systems

    DEFF Research Database (Denmark)

    Pittalà, Fabio; Hauske, Fabian N.; Ye, Yabin

    2012-01-01

    Benefits of a low-complexity adaptive 32-tap 2×2 MIMO frequency-domain filter update by data-aided channel estimation over a time-domain filter with DD-LMS are shown. Superior stability and convergence speed is demonstrated with identical impairment tolerance....

  20. Molecular cloning and functional characterization of duck nucleotide-binding oligomerization domain 1 (NOD1).

    Science.gov (United States)

    Li, Huilin; Jin, Hui; Li, Yaqian; Liu, Dejian; Foda, Mohamed Frahat; Jiang, Yunbo; Luo, Rui

    2017-09-01

    Nucleotide-binding oligomerization domain 1 (NOD1) is an imperative cytoplasmic pattern recognition receptor (PRR) and considered as a key member of the NOD-like receptor (NLR) family which plays a critical role in innate immunity through sensing microbial components derived from bacterial peptidoglycan. In the current study, the full-length of duck NOD1 (duNOD1) cDNA from duck embryo fibroblasts (DEFs) was cloned. Multiple sequence alignment and phylogenetic analysis demonstrated that duNOD1 exhibited a strong evolutionary relationship with chicken and rock pigeon NOD1. Tissue-specific expression analysis showed that duNOD1 was widely distributed in various organs, with the highest expression observed in the liver. Furthermore, duNOD1 overexpression induced NF-κB activation in DEFs and the CARD domain is crucial for duNOD1-mediated NF-κB activation. In addition, silencing the duNOD1 decreased the activity of NF-κB in DEFs stimulated by iE-DAP. Overexpression of duNOD1 significantly increased the expression of TNF-α, IL-6, and RANTES in DEFs. These findings highlight the crucial role of duNOD1 as an intracellular sensor in duck innate immune system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Molecular architecture of the nucleoprotein C-terminal domain from the Ebola and Marburg viruses.

    Science.gov (United States)

    Baker, Laura E; Ellena, Jeffrey F; Handing, Katarzyna B; Derewenda, Urszula; Utepbergenov, Darkhan; Engel, Daniel A; Derewenda, Zygmunt S

    2016-01-01

    The Filoviridae family of negative-sense, single-stranded RNA (ssRNA) viruses is comprised of two species of Marburgvirus (MARV and RAVV) and five species of Ebolavirus, i.e. Zaire (EBOV), Reston (RESTV), Sudan (SUDV), Taï Forest (TAFV) and Bundibugyo (BDBV). In each of these viruses the ssRNA encodes seven distinct proteins. One of them, the nucleoprotein (NP), is the most abundant viral protein in the infected cell and within the viral nucleocapsid. It is tightly associated with the viral RNA in the nucleocapsid, and during the lifecycle of the virus is essential for transcription, RNA replication, genome packaging and nucleocapsid assembly prior to membrane encapsulation. The structure of the unique C-terminal globular domain of the NP from EBOV has recently been determined and shown to be structurally unrelated to any other known protein [Dziubańska et al. (2014), Acta Cryst. D70, 2420-2429]. In this paper, a study of the C-terminal domains from the NP from the remaining four species of Ebolavirus, as well as from the MARV strain of Marburgvirus, is reported. As expected, the crystal structures of the BDBV and TAFV proteins show high structural similarity to that from EBOV, while the MARV protein behaves like a molten globule with a core residual structure that is significantly different from that of the EBOV protein.

  2. Comparative molecular dynamics study of neuromyelitis optica-immunoglobulin G binding to aquaporin-4 extracellular domains.

    Science.gov (United States)

    Alberga, Domenico; Trisciuzzi, Daniela; Lattanzi, Gianluca; Bennett, Jeffrey L; Verkman, Alan S; Mangiatordi, Giuseppe Felice; Nicolotti, Orazio

    2017-08-01

    Neuromyelitis optica (NMO) is an inflammatory demyelinating disease of the central nervous system in which most patients have serum autoantibodies (called NMO-IgG) that bind to astrocyte water channel aquaporin-4 (AQP4). A potential therapeutic strategy in NMO is to block the interaction of NMO-IgG with AQP4. Building on recent observation that some single-point and compound mutations of the AQP4 extracellular loop C prevent NMO-IgG binding, we carried out comparative Molecular Dynamics (MD) investigations on three AQP4 mutants, TP 137-138 AA, N 153 Q and V 150 G, whose 295-ns long trajectories were compared to that of wild type human AQP4. A robust conclusion of our modeling is that loop C mutations affect the conformation of neighboring extracellular loop A, thereby interfering with NMO-IgG binding. Analysis of individual mutations suggested specific hydrogen bonding and other molecular interactions involved in AQP4-IgG binding to AQP4. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Simultaneous measurements of global vibrational spectra and dephasing times of molecular vibrational modes by broadband time-resolved coherent anti-Stokes Raman scattering spectrography

    International Nuclear Information System (INIS)

    Yin Jun; Yu Ling-Yao; Liu Xing; Wan Hui; Lin Zi-Yang; Niu Han-Ben

    2011-01-01

    In broadband coherent anti-Stokes Raman scattering (CARS) spectroscopy with supercontinuum (SC), the simultaneously detectable spectral coverage is limited by the spectral continuity and the simultaneity of various spectral components of SC in an enough bandwidth. By numerical simulations, the optimal experimental conditions for improving the SC are obtained. The broadband time-resolved CARS spectrography based on the SC with required temporal and spectral distributions is realised. The global molecular vibrational spectrum with well suppressed nonresonant background noise can be obtained in a single measurement. At the same time, the measurements of dephasing times of various molecular vibrational modes can be conveniently achieved from intensities of a sequence of time-resolved CARS signals. It will be more helpful to provide a complete picture of molecular vibrations, and to exhibit a potential to understand not only both the solvent dynamics and the solute-solvent interactions, but also the mechanisms of chemical reactions in the fields of biology, chemistry and material science. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  4. Coherence-driven argumentation to norm consensus

    NARCIS (Netherlands)

    Joseph, S.; Prakken, H.

    2009-01-01

    In this paper coherence-based models are proposed as an alternative to logic-based BDI and argumentation models for the reasoning of normative agents. A model is provided for how two coherence-based agents can deliberate on how to regulate a domain of interest. First a deductive coherence model

  5. Real-time monitoring of disintegration activity of catalytic core domain of HIV-1 integrase using molecular beacon.

    Science.gov (United States)

    Zhang, Da-wei; Zhao, Ming-ming; He, Hong-qiu; Guo, Shun-xing

    2013-09-15

    HIV-1 integrase, an essential enzyme for retroviral replication, is a validated target for anti-HIV therapy development. The catalytic core domain of integrase (IN-CCD) is capable of catalyzing disintegration reaction. In this work, a hairpin-shaped disintegration substrate was designed and validated by enzyme-linked immunosorbent assay; a molecular beacon-based assay was developed for disintegration reaction of IN-CCD. Results showed that the disintegration substrate could be recognized and catalyzed by IN-CCD, and the disintegration reaction can be monitored according to the increase of fluorescent signal. The assay can be applied to real-time detection of disintegration with advantages of simplicity, high sensitivity, and excellent specificity. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. A synthetic prestin reveals protein domains and molecular operation of outer hair cell piezoelectricity.

    Science.gov (United States)

    Schaechinger, Thorsten J; Gorbunov, Dmitry; Halaszovich, Christian R; Moser, Tobias; Kügler, Sebastian; Fakler, Bernd; Oliver, Dominik

    2011-06-24

    Prestin, a transporter-like protein of the SLC26A family, acts as a piezoelectric transducer that mediates the fast electromotility of outer hair cells required for cochlear amplification and auditory acuity in mammals. Non-mammalian prestin orthologues are anion transporters without piezoelectric activity. Here, we generated synthetic prestin (SynPres), a chimera of mammalian and non-mammalian prestin exhibiting both, piezoelectric properties and anion transport. SynPres delineates two distinct domains in the protein's transmembrane core that are necessary and sufficient for generating electromotility and associated non-linear charge movement (NLC). Functional analysis of SynPres showed that the amplitude of NLC and hence electromotility are determined by the transport of monovalent anions. Thus, prestin-mediated electromotility is a dual-step process: transport of anions by an alternate access cycle, followed by an anion-dependent transition generating electromotility. The findings define structural and functional determinants of prestin's piezoelectric activity and indicate that the electromechanical process evolved from the ancestral transport mechanism.

  7. On the Role of the SP1 Domain in HIV-1 Particle Assembly: a Molecular Switch?▿

    Science.gov (United States)

    Datta, Siddhartha A. K.; Temeselew, Lakew G.; Crist, Rachael M.; Soheilian, Ferri; Kamata, Anne; Mirro, Jane; Harvin, Demetria; Nagashima, Kunio; Cachau, Raul E.; Rein, Alan

    2011-01-01

    Expression of a retroviral protein, Gag, in mammalian cells is sufficient for assembly of immature virus-like particles (VLPs). VLP assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We have investigated the role of SP1, a spacer between CA and NC in HIV-1 Gag, in VLP assembly. Mutational analysis showed that even subtle changes in the first 4 residues of SP1 destroy the ability of Gag to assemble correctly, frequently leading to formation of tubes or other misassembled structures rather than proper VLPs. We also studied the conformation of the CA-SP1 junction region in solution, using both molecular dynamics simulations and circular dichroism. Consonant with nuclear magnetic resonance (NMR) studies from other laboratories, we found that SP1 is nearly unstructured in aqueous solution but undergoes a concerted change to an α-helical conformation when the polarity of the environment is reduced by addition of dimethyl sulfoxide (DMSO), trifluoroethanol, or ethanol. Remarkably, such a coil-to-helix transition is also recapitulated in an aqueous medium at high peptide concentrations. The exquisite sensitivity of SP1 to mutational changes and its ability to undergo a concentration-dependent structural transition raise the possibility that SP1 could act as a molecular switch to prime HIV-1 Gag for VLP assembly. We suggest that changes in the local environment of SP1 when Gag oligomerizes on nucleic acid might trigger this switch. PMID:21325421

  8. Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study.

    Directory of Open Access Journals (Sweden)

    Musa Ozboyaci

    Full Text Available BACKGROUND: Histone demethylase, JMJD2A, specifically recognizes and binds to methylated lysine residues at histone H3 and H4 tails (especially trimethylated H3K4 (H3K4me3, trimethylated H3K9 (H3K9me3 and di,trimethylated H4K20 (H4K20me2, H4K20me3 via its tandem tudor domains. Crystal structures of JMJD2A-tudor binding to H3K4me3 and H4K20me3 peptides are available whereas the others are not. Complete picture of the recognition of the four histone peptides by the tandem tudor domains yet remains to be clarified. METHODOLOGY/PRINCIPAL FINDINGS: We report a detailed molecular dynamics simulation and binding energy analysis of the recognition of JMJD2A-tudor with four different histone tails. 25 ns fully unrestrained molecular dynamics simulations are carried out for each of the bound and free structures. We investigate the important hydrogen bonds and electrostatic interactions between the tudor domains and the peptide molecules and identify the critical residues that stabilize the complexes. Our binding free energy calculations show that H4K20me2 and H3K9me3 peptides have the highest and lowest affinity to JMJD2A-tudor, respectively. We also show that H4K20me2 peptide adopts the same binding mode with H4K20me3 peptide, and H3K9me3 peptide adopts the same binding mode with H3K4me3 peptide. Decomposition of the enthalpic and the entropic contributions to the binding free energies indicate that the recognition of the histone peptides is mainly driven by favourable van der Waals interactions. Residue decomposition of the binding free energies with backbone and side chain contributions as well as their energetic constituents identify the hotspots in the binding interface of the structures. CONCLUSION: Energetic investigations of the four complexes suggest that many of the residues involved in the interactions are common. However, we found two receptor residues that were related to selective binding of the H3 and H4 ligands. Modifications or mutations

  9. Genomic, RNAseq, and Molecular Modeling Evidence Suggests That the Major Allergen Domain in Insects Evolved from a Homodimeric Origin

    Science.gov (United States)

    Randall, Thomas A.; Perera, Lalith; London, Robert E.; Mueller, Geoffrey A.

    2013-01-01

    The major allergen domain (MA) is widely distributed in insects. The crystal structure of a single Bla g 1 MA revealed a novel protein fold in which the fundamental structure was a duplex of two subsequences (monomers), which had diverged over time. This suggested that the evolutionary origin of the MA structure may have been a homodimer of this smaller subsequence. Using publicly available genomic data, the distribution of the basic unit of this class of proteins was determined to better understand its evolutionary history. The duplication and divergence is examined at three distinct levels of resolution: 1) within the orders Diptera and Hymenoptera, 2) within one genus Drosophila, and 3) within one species Aedes aegypti. Within the family Culicidae, we have found two separate occurrences of monomers as independent genes. The organization of the gene family in A. aegypti shows a common evolutionary origin for its monomer and several closely related MAs. Molecular modeling of the A. aegypti monomer with the unique Bla g 1 fold confirms the distant evolutionary relationship and supports the feasibility of homodimer formation from a single monomer. RNAseq data for A. aegypti confirms that the monomer is expressed in the mosquito similar to other A. aegypti MAs after a blood meal. Together, these data support the contention that the detected monomer shares similar functional characteristics to related MAs in other insects. An extensive search for this domain outside of Insecta confirms that the MAs are restricted to insects. PMID:24253356

  10. Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1

    Science.gov (United States)

    Musselman, Catherine A.; Avvakumov, Nikita; Watanabe, Reiko; Abraham, Christopher G.; Lalonde, Marie-Eve; Hong, Zehui; Allen, Christopher; Roy, Siddhartha; Nuñez, James K.; Nickoloff, Jac; Kulesza, Caroline A.; Yasui, Akira; Côté, Jacques; Kutateladze, Tatiana G.

    2013-01-01

    The PHD finger protein 1 (PHF1) is essential in epigenetic regulation and genome maintenance. Here, we demonstrate that the Tudor domain of human PHF1 binds to histone H3 trimethylated at Lys36 (H3K36me3). We report a 1.9 Å resolution crystal structure of the Tudor domain in complex with H3K36me3 and describe the molecular mechanism of H3K36me3 recognition using NMR analysis. Binding of PHF1 to H3K36me3 inhibits the ability of the Polycomb PRC2 complex to methylate H3K27 in vitro and in vivo. Laser micro-irradiation data reveal that PHF1 is transiently recruited to DNA double-strand breaks (DSBs), and PHF1 mutants impaired in the H3K36me3 interaction exhibit reduced retention at DSB sites. Together, our findings suggest that PHF1 can mediate deposition of the repressive H3K27me3 mark and acts as an early DNA damage response cofactor. PMID:23142980

  11. Localization and Molecular Determinants of the Hanatoxin Receptors on the Voltage-Sensing Domains of a K+ Channel

    Science.gov (United States)

    Li-Smerin, Yingying; Swartz, Kenton J.

    2000-01-01

    Hanatoxin inhibits voltage-gated K+ channels by modifying the energetics of activation. We studied the molecular determinants and physical location of the Hanatoxin receptors on the drk1 voltage-gated K+ channel. First, we made multiple substitutions at three previously identified positions in the COOH terminus of S3 to examine whether these residues interact intimately with the toxin. We also examined a region encompassing S1–S3 using alanine-scanning mutagenesis to identify additional determinants of the toxin receptors. Finally, guided by the structure of the KcsA K+ channel, we explored whether the toxin interacts with the peripheral extracellular surface of the pore domain in the drk1 K+ channel. Our results argue for an intimate interaction between the toxin and the COOH terminus of S3 and suggest that the Hanatoxin receptors are confined within the voltage-sensing domains of the channel, at least 20–25 Å away from the central pore axis. PMID:10828242

  12. Computational Studies of the Active and Inactive Regulatory Domains of Response Regulator PhoP Using Molecular Dynamics Simulations.

    Science.gov (United States)

    Qing, Xiao-Yu; Steenackers, Hans; Venken, Tom; De Maeyer, Marc; Voet, Arnout

    2017-11-01

    The response regulator PhoP is part of the PhoP/PhoQ two-component system, which is responsible for regulating the expression of multiple genes involved in controlling virulence, biofilm formation, and resistance to antimicrobial peptides. Therefore, modulating the transcriptional function of the PhoP protein is a promising strategy for developing new antimicrobial agents. There is evidence suggesting that phosphorylation-mediated dimerization in the regulatory domain of PhoP is essential for its transcriptional function. Disruption or stabilization of protein-protein interactions at the dimerization interface may inhibit or enhance the expression of PhoP-dependent genes. In this study, we performed molecular dynamics simulations on the active and inactive dimers and monomers of the PhoP regulatory domains, followed by pocket-detecting screenings and a quantitative hot-spot analysis in order to assess the druggability of the protein. Consistent with prior hypothesis, the calculation of the binding free energy shows that phosphorylation enhances dimerization of PhoP. Furthermore, we have identified two different putative binding sites at the dimerization active site (the α4-β5-α5 face) with energetic "hot-spot" areas, which could be used to search for modulators of protein-protein interactions. This study delivers insight into the dynamics and druggability of the dimerization interface of the PhoP regulatory domain, and may serve as a basis for the rational identification of new antimicrobial drugs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Preliminary Molecular Dynamic Simulations of the Estrogen Receptor Alpha Ligand Binding Domain from Antagonist to Apo

    Directory of Open Access Journals (Sweden)

    Adrian E. Roitberg

    2008-06-01

    Full Text Available Estrogen receptors (ER are known as nuclear receptors. They exist in the cytoplasm of human cells and serves as a DNA binding transcription factor that regulates gene expression. However the estrogen receptor also has additional functions independent of DNA binding. The human estrogen receptor comes in two forms, alpha and beta. This work focuses on the alpha form of the estrogen receptor. The ERα is found in breast cancer cells, ovarian stroma cells, endometrium, and the hypothalamus. It has been suggested that exposure to DDE, a metabolite of DDT, and other pesticides causes conformational changes in the estrogen receptor. Before examining these factors, this work examines the protein unfolding from the antagonist form found in the 3ERT PDB crystal structure. The 3ERT PDB crystal structure has the estrogen receptor bound to the cancer drug 4-hydroxytamoxifen. The 4-hydroxytamoxifen ligand was extracted before the simulation, resulting in new conformational freedom due to absence of van der Waals contacts between the ligand and the receptor. The conformational changes that result expose the binding clef of the co peptide beside Helix 12 of the receptor forming an apo conformation. Two key conformations in the loops at either end of the H12 are produced resulting in the antagonist to apo conformation transformation. The results were produced over a 42ns Molecular Dynamics simulation using the AMBER FF99SB force field.

  14. Molecular interactions of prodiginines with the BH3 domain of anti-apoptotic Bcl-2 family members.

    Directory of Open Access Journals (Sweden)

    Ali Hosseini

    Full Text Available Prodigiosin and obatoclax, members of the prodiginines family, are small molecules with anti-cancer properties that are currently under preclinical and clinical trials. The molecular target(s of these agents, however, is an open question. Combining experimental and computational techniques we find that prodigiosin binds to the BH3 domain in some BCL-2 protein families, which play an important role in the apoptotic programmed cell death. In particular, our results indicate a large affinity of prodigiosin for MCL-1, an anti-apoptotic member of the BCL-2 family. In melanoma cells, we demonstrate that prodigiosin activates the mitochondrial apoptotic pathway by disrupting MCL-1/BAK complexes. Computer simulations with the PELE software allow the description of the induced fit process, obtaining a detailed atomic view of the molecular interactions. These results provide new data to understand the mechanism of action of these molecules, and assist in the development of more specific inhibitors of anti-apoptotic BCL-2 proteins.

  15. Alterations of the outer retina in non-arteritic anterior ischaemic optic neuropathy detected using spectral-domain optical coherence tomography.

    Science.gov (United States)

    Ackermann, Philipp; Brachert, Maike; Albrecht, Philipp; Ringelstein, Marius; Finis, David; Geerling, Gerd; Aktas, Orhan; Guthoff, Rainer

    2017-07-01

    A characteristic disease pattern may be reflected by retinal layer thickness changes in non-arteritic anterior ischaemic optic neuropathy measured using spectraldomain optical coherence tomography. Retinal layer segmentation is enabled by advanced software. In this study, retinal layer thicknesses in acute and chronic non-arteritic anterior ischaemic optic neuropathy were compared. A single-centre cross-sectional analysis was used. A total of 27 patients (20 age-matched healthy eyes) were included: 14 with acute (optic neuropathy. Macular volume and 12° peripapillary ring optical coherence tomography scans were used. The peripapillary thicknesses of the following layers were determined by manual segmentation: retinal nerve fibres, ganglion cells + inner plexiform layer, inner nuclear layer + outer plexiform layer, outer nuclear layer + inner segments of the photoreceptors and outer segments of the photoreceptors to Bruch's membrane. Macular retinal layer thicknesses were automatically determined in volume cubes centred on the fovea. Peripapillary retinal swelling in acute nonarteritic anterior ischaemic optic neuropathy was attributable to retinal nerve fibre layer, ganglion cell layer/inner plexiform layer and outer nuclear layer/segments of the photoreceptors thickening. In chronic cases, peripapillary retinal nerve fibre layer, macular ganglion cell layer and inner plexiform layer thinning were observed. In acute non-arteritic anterior ischaemic optic neuropathy, the inner and outer peripapillary retinal layers are affected by thickness changes. In chronic cases, atrophy of the ganglion cells and their axons and dendrites is evident by inner retinal layer thinning. © 2017 Royal Australian and New Zealand College of Ophthalmologists.

  16. Molecular modeling and structural analysis of two-pore domain potassium channels TASK1 interactions with the blocker A1899

    Directory of Open Access Journals (Sweden)

    David Mauricio Ramirez

    2015-03-01

    Full Text Available A1899 is a potent and highly selective blocker of the Two-pore domain potassium (K2P channel TASK-1, it acts as an antagonist blocking the K+ flux and binds to TASK-1 in the inner cavity and shows an activity in nanomolar order. This drug travels through the central cavity and finally binds in the bottom of the selectivity filter with some threonines and waters molecules forming a H-bond network and several hydrophobic interactions. Using alanine mutagenesis screens the binding site was identify involving residues in the P1 and P2 pore loops, the M2 and M4 transmembrane segments, and the halothane response element; mutations were introduced in the human TASK-1 (KCNK3, NM_002246 expressed in Oocytes from anesthetized Xenopus laevis frogs. Based in molecular modeling and structural analysis as such as molecular docking and binding free energy calculations a pose was suggested using a TASK-1 homology models. Recently, various K2P crystal structures have been obtained. We want redefined – from a structural point of view – the binding mode of A1899 in TASK-1 homology models using as a template the K2P crystal structures. By computational structural analysis we describe the molecular basis of the A1899 binding mode, how A1899 travel to its binding site and suggest an interacting pose (Figure 1. after 100 ns of molecular dynamics simulation (MDs we found an intra H-Bond (80% of the total MDs, a H-Bond whit Thr93 (42% of the total MDs, a pi-pi stacking interaction between a ring and Phe125 (88% of the total MDs and several water bridges. Our experimental and computational results allow the molecular understanding of the structural binding mechanism of the selective blocker A1899 to TASK-1 channels. We identified the structural common and divergent features of TASK-1 channel through our theoretical and experimental studies of A1899 drug action.

  17. Interactive domains in the molecular chaperone human alphaB crystallin modulate microtubule assembly and disassembly.

    Directory of Open Access Journals (Sweden)

    Joy G Ghosh

    2007-06-01

    Full Text Available Small heat shock proteins regulate microtubule assembly during cell proliferation and in response to stress through interactions that are poorly understood.Novel functions for five interactive sequences in the small heat shock protein and molecular chaperone, human alphaB crystallin, were investigated in the assembly/disassembly of microtubules and aggregation of tubulin using synthetic peptides and mutants of human alphaB crystallin.The interactive sequence (113FISREFHR(120 exposed on the surface of alphaB crystallin decreased microtubule assembly by approximately 45%. In contrast, the interactive sequences, (131LTITSSLSSDGV(142 and (156ERTIPITRE(164, corresponding to the beta8 strand and the C-terminal extension respectively, which are involved in complex formation, increased microtubule assembly by approximately 34-45%. The alphaB crystallin peptides, (113FISREFHR(120 and (156ERTIPITRE(164, inhibited microtubule disassembly by approximately 26-36%, and the peptides (113FISREFHR(120 and (131LTITSSLSSDGV(142 decreased the thermal aggregation of tubulin by approximately 42-44%. The (131LTITSSLSSDGV(142 and (156ERTIPITRE(164 peptides were more effective than the widely used anti-cancer drug, Paclitaxel, in modulating tubulinmicrotubule dynamics. Mutagenesis of these interactive sequences in wt human alphaB crystallin confirmed the effects of the alphaB crystallin peptides on microtubule assembly/disassembly and tubulin aggregation. The regulation of microtubule assembly by alphaB crystallin varied over a narrow range of concentrations. The assembly of microtubules was maximal at alphaB crystallin to tubulin molar ratios between 1:4 and 2:1, while molar ratios >2:1 inhibited microtubule assembly.Interactive sequences on the surface of human alphaB crystallin collectively modulate microtubule assembly through a dynamic subunit exchange mechanism that depends on the concentration and ratio of alphaB crystallin to tubulin. These are the first

  18. Structure characterization of the central repetitive domain of high molecular weight gluten proteins. II. Characterization in solution and in the dry state

    OpenAIRE

    Dijk, Alard A. van; Boef, Esther de; Bekkers, August; Wijk, Lourens L. van; Swieten, Eric van; Hamer, Rob J.; Robillard, George T.

    1997-01-01

    The structure of the central repetitive domain of high molecular weight HMW) wheat gluten proteins was characterized in solution and in the dry state using HMW proteins Bx6 and Bx7 and a subcloned, bacterially expressed part of the repetitive domain of HMW Dx5. Model studies of the HMW consensus peptides PGQGQQ and GYYPTSPQQ formed the basis for the data analysis (van Dijk AA et al., 1997, Protein Sci 6:637-648). In solution, the repetitive domain contained a continuous nonoverlapping series ...

  19. Insight into the adsorption profiles of the Saprolegnia monoica chitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studies.

    Science.gov (United States)

    Kuang, Guanglin; Liang, Lijun; Brown, Christian; Wang, Qi; Bulone, Vincent; Tu, Yaoquan

    2016-02-21

    The critical role of chitin synthases in oomycete hyphal tip growth has been established. A microtubule interacting and trafficking (MIT) domain was discovered in the chitin synthases of the oomycete model organism, Saprolegnia monoica. MIT domains have been identified in diverse proteins and may play a role in intracellular trafficking. The structure of the Saprolegnia monoica chitin synthase 1 (SmChs1) MIT domain has been recently determined by our group. However, although our in vitro assay identified increased strength in interactions between the MIT domain and phosphatidic acid (PA) relative to other phospholipids including phosphatidylcholine (PC), the mechanism used by the MIT domain remains unknown. In this work, the adsorption behavior of the SmChs1 MIT domain on POPA and POPC membranes was systematically investigated by molecular dynamics simulations. Our results indicate that the MIT domain can adsorb onto the tested membranes in varying orientations. Interestingly, due to the specific interactions between MIT residues and lipid molecules, the binding affinity to the POPA membrane is much higher than that to the POPC membrane. A binding hotspot, which is critical for the adsorption of the MIT domain onto the POPA membrane, was also identified. The lower binding affinity to the POPC membrane can be attributed to the self-saturated membrane surface, which is unfavorable for hydrogen-bond and electrostatic interactions. The present study provides insight into the adsorption profile of SmChs1 and additionally has the potential to improve our understanding of other proteins containing MIT domains.

  20. Ribonucleocapsid Formation of SARS-COV Through Molecular Action of the N-Terminal Domain of N Protein

    Energy Technology Data Exchange (ETDEWEB)

    Saikatendu, K.S.; Joseph, J.S.; Subramanian, V.; Neuman, B.W.; Buchmeier, M.J.; Stevens, R.C.; Kuhn, P.; /Scripps Res. Inst.

    2007-07-12

    Conserved amongst all coronaviruses are four structural proteins, the matrix (M), small envelope (E) and spike (S) that are embedded in the viral membrane and the nucleocapsid phosphoprotein (N), which exists in a ribonucleoprotein complex in their lumen. The N terminal domain of coronaviral N proteins (N-NTD) provides a scaffold for RNA binding while the C-terminal domain (N-CTD) mainly acts as oligomerization modules during assembly. The C-terminus of N protein anchors it to the viral membrane by associating with M protein. We characterized the structures of N-NTD from severe acute respiratory syndrome coronavirus (SARS-CoV) in two crystal forms, at 1.17A (monoclinic) and 1.85 A (cubic) respectively, solved by molecular replacement using the homologous avian infectious bronchitis virus (IBV) structure. Flexible loops in the solution structure of SARS-CoV N-NTD are now shown to be well ordered around the beta-sheet core. The functionally important positively charged beta-hairpin protrudes out of the core and is oriented similar to that in the IBV N-NTD and is involved in crystal packing in the monoclinic form. In the cubic form, the monomers form trimeric units that stack in a helical array. Comparison of crystal packing of SARS-CoV and IBV N-NTDs suggest a common mode of RNA recognition, but probably associate differently in vivo during the formation of the ribonucleoprotein complex. Electrostatic potential distribution on the surface of homology models of related coronaviral N-NTDs hints that they employ different modes of both RNA recognition as well as oligomeric assembly, perhaps explaining why their nucleocapsids have different morphologies.

  1. Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation.

    Directory of Open Access Journals (Sweden)

    Matteo eLambrughi

    2012-11-01

    Full Text Available Cyclin-dependent kinase inhibitors (CKIs are key regulatory proteins of the eukaryotic cell cycle, which modulate cyclin-dependent kinase (Cdk activity. CKIs perform their inhibitory effect by the formation of ternary complexes with a target kinase and its cognate cyclin. These regulators generally belong to the class of intrinsically disordered proteins (IDPs, which lack a well-defined and organized three-dimensional structure in their free state, undergoing folding upon binding to specific partners. Unbound IDPs are not merely random-coil structures, but can present intrinsically folded structural units (IFSUs and collapsed conformations. These structural features can be relevant to protein function in vivo.The yeast CKI Sic1 is a 284-amino acid IDP that binds to Cdk1 in complex with the Clb5,6 cyclins, preventing phosphorylation of G1 substrates and, therefore, entrance to the S phase. Sic1 degradation, triggered by multiple phosphorylation events, promotes cell-cycle progression. Previous experimental studies pointed out a propensity of Sic1 and its isolated domains to populate both extended and compact conformations. The present contribution provides models of the compact conformations of the Sic1 kinase-inhibitory domain (KID by all-atom molecular-dynamics simulations in explicit solvent and in the absence of interactors. The results are integrated by spectroscopic and spectrometric data. Helical IFSUs are identified, along with networks of intramolecular interactions. The results identify a group of hub residues and electrostatic interactions which are likely to be involved in the stabilization of globular states.

  2. High-resolution retinal swept source optical coherence tomography with an ultra-wideband Fourier-domain mode-locked laser at MHz A-scan rates.

    Science.gov (United States)

    Kolb, Jan Philip; Pfeiffer, Tom; Eibl, Matthias; Hakert, Hubertus; Huber, Robert

    2018-01-01

    We present a new 1060 nm Fourier domain mode locked laser (FDML laser) with a record 143 nm sweep bandwidth at 2∙ 417 kHz  =  834 kHz and 120 nm at 1.67 MHz, respectively. We show that not only the bandwidth alone, but also the shape of the spectrum is critical for the resulting axial resolution, because of the specific wavelength-dependent absorption of the vitreous. The theoretical limit of our setup lies at 5.9 µm axial resolution. In vivo MHz-OCT imaging of human retina is performed and the image quality is compared to the previous results acquired with 70 nm sweep range, as well as to existing spectral domain OCT data with 2.1 µm axial resolution from literature. We identify benefits of the higher resolution, for example the improved visualization of small blood vessels in the retina besides several others.

  3. Coherent and incoherent giant dipole resonance γ-ray emission induced by heavy ion collisions: Study of the 40Ca+48Ca system by means of the constrained molecular dynamics model

    International Nuclear Information System (INIS)

    Papa, Massimo; Cardella, Giuseppe; Bonanno, Antonio; Pappalardo, Giuseppe; Rizzo, Francesca; Amorini, Francesca; Bonasera, Aldo; Di Pietro, Alessia; Figuera, Pier Paolo; Tudisco, Salvatore; Maruyama, Toshiki

    2003-01-01

    Coherent and incoherent dipolar γ-ray emission is studied in a fully dynamical approach by means of the constrained molecular dynamics model. The study is focused on the system 40 Ca+ 48 Ca for which recently experimental data have been collected at 25 MeV/nucleon. The approach allows us to explain the experimental results in a self-consistent way without using statistical or hybrid models. Moreover, calculations performed at higher energy show interesting correlations between the fragment formation process, the degree of collectivity, and the coherence degree of the γ-ray emission process

  4. [The Detection of Ultra-Broadband Terahertz Spectroscopy of InP Wafer by Using Coherent Heterodyne Time-Domain Spectrometer].

    Science.gov (United States)

    Zhang, Liang-liang; Zhang, Rui; Xu, Xiao-yan; Zhang, Cun-lin

    2016-02-01

    Indium Phosphide (InP) has attracted great physical interest because of its unique characteristics and is indispensable to both optical and electronic devices. However, the optical property of InP in the terahertz range (0. 110 THz) has not yet been fully characterized and systematically studied. The former researches about the properties of InP concentrated on the terahertz frequency between 0.1 and 4 THz. The terahertz optical properties of the InP in the range of 4-10 THz are still missing. It is fairly necessary to fully understand its properties in the entire terahertz range, which results in a better utilization as efficient terahertz devices. In this paper, we study the optical properties of undoped (100) InP wafer in the ultra-broad terahertz frequency range (0.5-18 THz) by using air-biased-coherent-detection (ABCD) system, enabling the coherent detection of terahertz wave in gases, which leads to a significant improvement on the dynamic range and sensitivity of the system. The advantage of this method is broad frequency bandwidth from 0.2 up to 18 THz which is only mainly limited by laser pulse duration since it uses ionized air as terahertz emitter and detector instead of using an electric optical crystal or photoconductive antenna. The terahertz pulse passing through the InP wafer is delayed regarding to the reference pulse and has much lower amplitude. In addition, the frequency spectrum amplitude of the terahertz sample signal drops to the noise floor level from 6.7 to 12.1 THz. At the same time InP wafer is opaque at the frequencies spanning from 6.7 to 12.1 THz. In the frequency regions of 0.8-6.7 and 12.1-18 THz it has relativemy low absorption coefficient. Meanwhile, the refractive index increases monotonously in the 0.8-6.7 THz region and 12.1-18 THz region. These findings will contribute to the design of InP based on nonlinear terahertz devices.

  5. Comparative Study of Anterior Eye Segment Measurements with Spectral Swept-Source and Time-Domain Optical Coherence Tomography in Eyes with Corneal Dystrophies.

    Science.gov (United States)

    Nowinska, Anna K; Teper, Sławomir J; Janiszewska, Dominika A; Lyssek-Boron, Anita; Dobrowolski, Dariusz; Koprowski, Robert; Wylegala, Edward

    2015-01-01

    To compare anterior eye segment measurements and morphology obtained with two optical coherence tomography systems (TD OCT, SS OCT) in eyes with corneal dystrophies (CDs). Fifty healthy volunteers (50 eyes) and 54 patients (96 eyes) diagnosed with CD (epithelial basement membrane dystrophy, EBMD = 12 eyes; Thiel-Behnke CD = 6 eyes; lattice CD TGFBI type = 15 eyes; granular CD type 1 = 7 eyes, granular CD type 2 = 2 eyes; macular CD = 23 eyes; and Fuchs endothelial CD = 31 eyes) were recruited for the study. Automated and manual central corneal thickness (aCCT, mCCT), anterior chamber depth (ACD), and nasal and temporal trabecular iris angle (nTIA, tTIA) were measured and compared with Bland-Altman plots. Good agreement between the TD and SS OCT measurements was demonstrated for mCCT and aCCT in normal individuals and for mCCT in the CDs group. The ACD, nTIA, and tTIA measurements differed significantly in both groups. TBCD, LCD, and FECD caused increased CCT. MCD caused significant corneal thinning. FECD affected all analyzed parameters. Better agreement between SS OCT and TD OCT measurements was demonstrated in normal individuals compared to the CDs group. OCT provides comprehensive corneal deposits analysis and demonstrates the association of CD with CCT, ACD, and TIA measurements.

  6. Comparative Study of Anterior Eye Segment Measurements with Spectral Swept-Source and Time-Domain Optical Coherence Tomography in Eyes with Corneal Dystrophies

    Directory of Open Access Journals (Sweden)

    Anna K. Nowinska

    2015-01-01

    Full Text Available Purpose. To compare anterior eye segment measurements and morphology obtained with two optical coherence tomography systems (TD OCT, SS OCT in eyes with corneal dystrophies (CDs. Methods. Fifty healthy volunteers (50 eyes and 54 patients (96 eyes diagnosed with CD (epithelial basement membrane dystrophy, EBMD = 12 eyes; Thiel-Behnke CD = 6 eyes; lattice CD TGFBI type = 15 eyes; granular CD type 1 = 7 eyes, granular CD type 2 = 2 eyes; macular CD = 23 eyes; and Fuchs endothelial CD = 31 eyes were recruited for the study. Automated and manual central corneal thickness (aCCT, mCCT, anterior chamber depth (ACD, and nasal and temporal trabecular iris angle (nTIA, tTIA were measured and compared with Bland-Altman plots. Results. Good agreement between the TD and SS OCT measurements was demonstrated for mCCT and aCCT in normal individuals and for mCCT in the CDs group. The ACD, nTIA, and tTIA measurements differed significantly in both groups. TBCD, LCD, and FECD caused increased CCT. MCD caused significant corneal thinning. FECD affected all analyzed parameters. Conclusions. Better agreement between SS OCT and TD OCT measurements was demonstrated in normal individuals compared to the CDs group. OCT provides comprehensive corneal deposits analysis and demonstrates the association of CD with CCT, ACD, and TIA measurements.

  7. Resolving Hot Spots in the C-Terminal Dimerization Domain that Determine the Stability of the Molecular Chaperone Hsp90

    Science.gov (United States)

    Reimann, Sven; Smits, Sander H. J.; Schmitt, Lutz; Groth, Georg; Gohlke, Holger

    2014-01-01

    Human heat shock protein of 90 kDa (hHsp90) is a homodimer that has an essential role in facilitating malignant transformation at the molecular level. Inhibiting hHsp90 function is a validated approach for treating different types of tumors. Inhibiting the dimerization of hHsp90 via its C-terminal domain (CTD) should provide a novel way to therapeutically interfere with hHsp90 function. Here, we predicted hot spot residues that cluster in the CTD dimerization interface by a structural decomposition of the effective energy of binding computed by the MM-GBSA approach and confirmed these predictions using in silico alanine scanning with DrugScorePPI. Mutation of these residues to alanine caused a significant decrease in the melting temperature according to differential scanning fluorimetry experiments, indicating a reduced stability of the mutant hHsp90 complexes. Size exclusion chromatography and multi-angle light scattering studies demonstrate that the reduced stability of the mutant hHsp90 correlates with a lower complex stoichiometry due to the disruption of the dimerization interface. These results suggest that the identified hot spot residues can be used as a pharmacophoric template for identifying and designing small-molecule inhibitors of hHsp90 dimerization. PMID:24760083

  8. Interaction of the transactivation domain of B-Myb with the TAZ2 domain of the coactivator p300: molecular features and properties of the complex.

    Directory of Open Access Journals (Sweden)

    Ojore Oka

    Full Text Available The transcription factor B-Myb is a key regulator of the cell cycle in vertebrates, with activation of transcription involving the recognition of specific DNA target sites and the recruitment of functional partner proteins, including the coactivators p300 and CBP. Here we report the results of detailed studies of the interaction between the transactivation domain of B-Myb (B-Myb TAD and the TAZ2 domain of p300. The B-Myb TAD was characterized using circular dichroism, fluorescence and NMR spectroscopy, which revealed that the isolated domain exists as a random coil polypeptide. Pull-down and spectroscopic experiments clearly showed that the B-Myb TAD binds to p300 TAZ2 to form a moderately tight (K(d ~1.0-10 µM complex, which results in at least partial folding of the B-Myb TAD. Significant changes in NMR spectra of p300 TAZ2 suggest that the B-Myb TAD binds to a relatively large patch on the surface of the domain (~1200 Å(2. The apparent B-Myb TAD binding site on p300 TAZ2 shows striking similarity to the surface of CBP TAZ2 involved in binding to the transactivation domain of the transcription factor signal transducer and activator of transcription 1 (STAT1, which suggests that the structure of the B-Myb TAD-p300 TAZ2 complex may share many features with that reported for STAT1 TAD-p300 TAZ2.

  9. Coherent detectors

    International Nuclear Information System (INIS)

    Lawrence, C R; Church, S; Gaier, T; Lai, R; Ruf, C; Wollack, E

    2009-01-01

    Coherent systems offer significant advantages in simplicity, testability, control of systematics, and cost. Although quantum noise sets the fundamental limit to their performance at high frequencies, recent breakthroughs suggest that near-quantum-limited noise up to 150 or even 200 GHz could be realized within a few years. If the demands of component separation can be met with frequencies below 200 GHz, coherent systems will be strong competitors for a space CMB polarization mission. The rapid development of digital correlator capability now makes space interferometers with many hundreds of elements possible. Given the advantages of coherent interferometers in suppressing systematic effects, such systems deserve serious study.

  10. Coherent detectors

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, C R [M/C 169-327, Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Church, S [Room 324 Varian Physics Bldg, 382 Via Pueblo Mall, Stanford, CA 94305-4060 (United States); Gaier, T [M/C 168-314, Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Lai, R [Northrop Grumman Corporation, Redondo Beach, CA 90278 (United States); Ruf, C [1533 Space Research Building, The University of Michigan, Ann Arbor, MI 48109-2143 (United States); Wollack, E, E-mail: charles.lawrence@jpl.nasa.go [NASA/GSFC, Code 665, Observational Cosmology Laboratory, Greenbelt, MD 20771 (United States)

    2009-03-01

    Coherent systems offer significant advantages in simplicity, testability, control of systematics, and cost. Although quantum noise sets the fundamental limit to their performance at high frequencies, recent breakthroughs suggest that near-quantum-limited noise up to 150 or even 200 GHz could be realized within a few years. If the demands of component separation can be met with frequencies below 200 GHz, coherent systems will be strong competitors for a space CMB polarization mission. The rapid development of digital correlator capability now makes space interferometers with many hundreds of elements possible. Given the advantages of coherent interferometers in suppressing systematic effects, such systems deserve serious study.

  11. Optimally cloned binary coherent states

    Science.gov (United States)

    Müller, C. R.; Leuchs, G.; Marquardt, Ch.; Andersen, U. L.

    2017-10-01

    Binary coherent state alphabets can be represented in a two-dimensional Hilbert space. We capitalize this formal connection between the otherwise distinct domains of qubits and continuous variable states to map binary phase-shift keyed coherent states onto the Bloch sphere and to derive their quantum-optimal clones. We analyze the Wigner function and the cumulants of the clones, and we conclude that optimal cloning of binary coherent states requires a nonlinearity above second order. We propose several practical and near-optimal cloning schemes and compare their cloning fidelity to the optimal cloner.

  12. Ultrabroadband THz time-domain spectroscopy of biomolecular crystals

    DEFF Research Database (Denmark)

    Kaltenecker, Korbinian J.; Engelbrecht, Sebastian; Iwaszczuk, Krzysztof

    2016-01-01

    Ultrabroadband THz time-domain spectroscopy based on two-color plasma generation and air biased coherent detection is used for the investigation of molecular dynamics of crystalline materials in the frequency range from 0.3 THz to 20 THz. We show that the spectral features in this extended...... frequency range are a result of inter- and intramolecular vibrations which are identified by means of simulations of the crystalline materials....

  13. Quantum Mechanics and Molecular Mechanics Study of the Catalytic Mechanism of Human AMSH-LP Domain Deubiquitinating Enzymes.

    Science.gov (United States)

    Zhu, Wenyou; Liu, Yongjun; Ling, Baoping

    2015-08-25

    Deubiquitinating enzymes (DUBs) catalyze the cleavage of the isopeptide bond in polyubiquitin chains to control and regulate the deubiquitination process in all known eukaryotic cells. The human AMSH-LP DUB domain specifically cleaves the isopeptide bonds in the Lys63-linked polyubiquitin chains. In this article, the catalytic mechanism of AMSH-LP has been studied using a combined quantum mechanics and molecular mechanics method. Two possible hydrolysis processes (Path 1 and Path 2) have been considered. Our calculation results reveal that the activation of Zn(2+)-coordinated water molecule is the essential step for the hydrolysis of isopeptide bond. In Path 1, the generated hydroxyl first attacks the carbonyl group of Gly76, and then the amino group of Lys63 is protonated, which is calculated to be the rate limiting step with an energy barrier of 13.1 kcal/mol. The energy barrier of the rate limiting step and the structures of intermediate and product are in agreement with the experimental results. In Path 2, the protonation of amino group of Lys63 is prior to the nucleophilic attack of activated hydroxyl. The two proton transfer processes in Path 2 correspond to comparable overall barriers (33.4 and 36.1 kcal/mol), which are very high for an enzymatic reaction. Thus, Path 2 can be ruled out. During the reaction, Glu292 acts as a proton transfer mediator, and Ser357 mainly plays a role in stabilizing the negative charge of Gly76. Besides acting as a Lewis acid, Zn(2+) also influences the reaction by coordinating to the reaction substrates (W1 and Gly76).

  14. Factor VII deficiency: Unveiling the cellular and molecular mechanisms underlying three model alterations of the enzyme catalytic domain.

    Science.gov (United States)

    Chollet, Maria Eugenia; Andersen, Elisabeth; Skarpen, Ellen; Myklebust, Christiane F; Koehler, Christian; Morth, Jens Preben; Chuansumrit, Ampaiwan; Pinotti, Mirko; Bernardi, Francesco; Thiede, Bernd; Sandset, Per Morten; Skretting, Grethe

    2018-03-01

    Activated factor (F) VII is a vitamin K-dependent glycoprotein that initiates blood coagulation upon interaction with tissue factor. FVII deficiency is the most common of the rare congenital bleeding disorders. While the mutational pattern has been extensively characterized, the pathogenic molecular mechanisms of mutations, particularly at the intracellular level, have been poorly defined. Here, we aimed at elucidating the mechanisms underlying altered FVII biosynthesis in the presence of three mutation types in the catalytic domain: a missense change, a microdeletion and a frameshift/elongation, associated with severe or moderate to severe phenotypes. Using CHO-K1 cells transiently transfected with expression vectors containing the wild-type FVII cDNA (FVIIwt) or harboring the p.I289del, p.G420V or p.A354V-p.P464Hfs mutations, we found that the secretion of the FVII mutants was severely decreased compared to FVIIwt. The synthesis rate of the mutants was slower than the FVIIwt and delayed, and no degradation of the FVII mutants by proteasomes, lysosomes or cysteine proteases was observed. Confocal immunofluorescence microscopy studies showed that FVII variants were localized into the endoplasmic reticulum (ER) but were not detectable within the Golgi apparatus. These findings suggested that a common pathogenic mechanism, possibly a defective folding of the mutant proteins, was triggered by the FVII mutations. The misfolded state led to impaired trafficking of these proteins causing ER retention, which would explain the low to very low FVII plasma levels observed in patients carrying these mutations. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Intra- and interobserver reliability and intra-catheter reproducibility using frequency domain optical coherence tomography for the evaluation of morphometric stent parameters and qualitative assessment of stent strut coverage

    International Nuclear Information System (INIS)

    Antonsen, Lisbeth; Thayssen, Per; Junker, Anders; Veien, Karsten Tange; Hansen, Henrik Steen; Hansen, Knud Nørregaard; Hougaard, Mikkel; Jensen, Lisette Okkels

    2015-01-01

    Purpose: Frequency-domain optical coherence tomography (FD-OCT) is a high-resolution imaging tool (~ 10–15 μm), which enables near-histological in-vivo images of the coronary vessel wall. The use of the technique is increasing, both for research- and clinical purposes. This study sought to investigate the intra- and interobserver reliability, as well as the intra-catheter reproducibility of quantitative FD-OCT-assessment of morphometric stent parameters and qualitative FD-OCT-evaluation of strut coverage in 10 randomly selected 6-month follow-up Nobori® biolimus-eluting stents (N-BESs). Methods: Ten N-BESs (213 cross sectional areas (CSAs) and 1897 struts) imaged with OCT 6 months post-implantation were randomly selected and analyzed by 2 experienced analysts, and the same 10 N-BESs were analyzed by one of the analysts 3 months later. Further, 2 consecutive pullbacks randomly performed in another 10 N-BESs (219 CSAs and 1860 struts) were independently assessed by one of the analysts. Results: The intraobserver variability with regard to relative difference of mean luminal area and mean stent area at the CSA-level was very low: 0.1% ± 1.4% and 0.5% ± 3.2%. Interobserver variability also proved to be low: − 2.1% ± 3.3% and 2.1% ± 4.6%, and moreover, very restricted intra-catheter variation was observed: 0.02% ± 6.8% and − 0.18% ± 5.2%. The intraobserver-, interobserver- and intra-catheter reliability for the qualitative evaluation of strut coverage was found to be: kappa (κ) = 0.91 (95% confidence interval (CI): 0.88–0.93, p < 0.01), κ = 0.88 (95% CI: 0.85–0.91, p < 0.01), and κ = 0.73 (95% CI: 0.68–0.78, p < 0.01), respectively. Conclusions: FD-OCT is a reproducible and reliable imaging tool for quantitative evaluation of stented coronary segments, and for qualitative assessment of strut coverage. - Highlights: • Frequency-domain optical coherence tomography (FD-OCT) is increasingly adopted in the catherization laboratories. • This

  16. Intra- and interobserver reliability and intra-catheter reproducibility using frequency domain optical coherence tomography for the evaluation of morphometric stent parameters and qualitative assessment of stent strut coverage

    Energy Technology Data Exchange (ETDEWEB)

    Antonsen, Lisbeth, E-mail: Lisbeth.antonsen@rsyd.dk; Thayssen, Per; Junker, Anders; Veien, Karsten Tange; Hansen, Henrik Steen; Hansen, Knud Nørregaard; Hougaard, Mikkel; Jensen, Lisette Okkels

    2015-12-15

    Purpose: Frequency-domain optical coherence tomography (FD-OCT) is a high-resolution imaging tool (~ 10–15 μm), which enables near-histological in-vivo images of the coronary vessel wall. The use of the technique is increasing, both for research- and clinical purposes. This study sought to investigate the intra- and interobserver reliability, as well as the intra-catheter reproducibility of quantitative FD-OCT-assessment of morphometric stent parameters and qualitative FD-OCT-evaluation of strut coverage in 10 randomly selected 6-month follow-up Nobori® biolimus-eluting stents (N-BESs). Methods: Ten N-BESs (213 cross sectional areas (CSAs) and 1897 struts) imaged with OCT 6 months post-implantation were randomly selected and analyzed by 2 experienced analysts, and the same 10 N-BESs were analyzed by one of the analysts 3 months later. Further, 2 consecutive pullbacks randomly performed in another 10 N-BESs (219 CSAs and 1860 struts) were independently assessed by one of the analysts. Results: The intraobserver variability with regard to relative difference of mean luminal area and mean stent area at the CSA-level was very low: 0.1% ± 1.4% and 0.5% ± 3.2%. Interobserver variability also proved to be low: − 2.1% ± 3.3% and 2.1% ± 4.6%, and moreover, very restricted intra-catheter variation was observed: 0.02% ± 6.8% and − 0.18% ± 5.2%. The intraobserver-, interobserver- and intra-catheter reliability for the qualitative evaluation of strut coverage was found to be: kappa (κ) = 0.91 (95% confidence interval (CI): 0.88–0.93, p < 0.01), κ = 0.88 (95% CI: 0.85–0.91, p < 0.01), and κ = 0.73 (95% CI: 0.68–0.78, p < 0.01), respectively. Conclusions: FD-OCT is a reproducible and reliable imaging tool for quantitative evaluation of stented coronary segments, and for qualitative assessment of strut coverage. - Highlights: • Frequency-domain optical coherence tomography (FD-OCT) is increasingly adopted in the catherization laboratories. • This

  17. Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation.

    Directory of Open Access Journals (Sweden)

    David J Huggins

    2010-08-01

    Full Text Available The Polo-Like Kinase 1 (PLK1 acts as a central regulator of mitosis and is over-expressed in a wide range of human tumours where high levels of expression correlate with a poor prognosis. PLK1 comprises two structural elements, a kinase domain and a polo-box domain (PBD. The PBD binds phosphorylated substrates to control substrate phosphorylation by the kinase domain. Although the PBD preferentially binds to phosphopeptides, it has a relatively broad sequence specificity in comparison with other phosphopeptide binding domains. We analysed the molecular determinants of recognition by performing molecular dynamics simulations of the PBD with one of its natural substrates, CDC25c. Predicted binding free energies were calculated using a molecular mechanics, Poisson-Boltzmann surface area approach. We calculated the per-residue contributions to the binding free energy change, showing that the phosphothreonine residue and the mainchain account for the vast majority of the interaction energy. This explains the very broad sequence specificity with respect to other sidechain residues. Finally, we considered the key role of bridging water molecules at the binding interface. We employed inhomogeneous fluid solvation theory to consider the free energy of water molecules on the protein surface with respect to bulk water molecules. Such an analysis highlights binding hotspots created by elimination of water molecules from hydrophobic surfaces. It also predicts that a number of water molecules are stabilized by the presence of the charged phosphate group, and that this will have a significant effect on the binding affinity. Our findings suggest a molecular rationale for the promiscuous binding of the PBD and highlight a role for bridging water molecules at the interface. We expect that this method of analysis will be very useful for probing other protein surfaces to identify binding hotspots for natural binding partners and small molecule inhibitors.

  18. Reliability and reproducibility of spectral and time domain optical coherence tomography images before and after correction for patients with age-related macular degeneration [v2; ref status: indexed, http://f1000r.es/50m

    Directory of Open Access Journals (Sweden)

    Mohammad A. Sadiq

    2015-03-01

    Full Text Available Purpose: To evaluate the reproducibility and reliability of optical coherence tomography scans obtained using the time domain (TD-OCT StratusTM OCT, and the Spectral Domain (SD-OCT SpectralisTM and CirrusTM OCT devices before and after manual correction in eyes with either Neovascular (NV-AMD or Non-Neovascular (NNV-AMD age-related macular degeneration. Design: Prospective observational study. Methods: Setting: University-based retina practice. Patients: Thirty-six patients (50 eyes with NV-AMD or NNV-AMD. Procedure: OCT scans were taken simultaneously using one TD-OCT and two SD-OCT devices. Main Outcome Measures: Macular thickness measurements were assessed before and after correction of the algorithm by constructing Bland-Altman plots for agreement and calculating intraclass correlation coefficients (ICCs and coefficients of repeatability (COR to evaluate intraclass repeatability. Results: Spectralis had the highest number of images needing manual correction.  All machines had high ICCs, with Spectralis having the highest.  Also, Bland-Altman plots indicated that there was low agreement between Cirrus™ and Stratus™, Spectralis™ and Stratus™, while there was good agreement between the Cirrus™ and Spectralis™.  The CORs were lowest for SpectralisTM and similar and higher for CirrusTM and StratusTM.  Agreement, CORs, and ICCs generally improved after manual correction, but only minimally.  Conclusion: Agreement is low between devices, except between both SD-OCT machines.  Manual correction tends to improve results.

  19. The molecular basis of FHA domain:phosphopeptide binding specificity and implications for phospho-dependent signaling mechanisms.

    Science.gov (United States)

    Durocher, D; Taylor, I A; Sarbassova, D; Haire, L F; Westcott, S L; Jackson, S P; Smerdon, S J; Yaffe, M B

    2000-11-01

    Forkhead-associated (FHA) domains are a class of ubiquitous signaling modules that appear to function through interactions with phosphorylated target molecules. We have used oriented peptide library screening to determine the optimal phosphopeptide binding motifs recognized by several FHA domains, including those within a number of DNA damage checkpoint kinases, and determined the X-ray structure of Rad53p-FHA1, in complex with a phospho-threonine peptide, at 1.6 A resolution. The structure reveals a striking similarity to the MH2 domains of Smad tumor suppressor proteins and reveals a mode of peptide binding that differs from SH2, 14-3-3, or PTB domain complexes. These results have important implications for DNA damage signaling and CHK2-dependent tumor suppression, and they indicate that FHA domains play important and unsuspected roles in S/T kinase signaling mechanisms in prokaryotes and eukaryotes.

  20. Domain activities of PapC usher reveal the mechanism of action of an Escherichia coli molecular machine.

    Science.gov (United States)

    Volkan, Ender; Ford, Bradley A; Pinkner, Jerome S; Dodson, Karen W; Henderson, Nadine S; Thanassi, David G; Waksman, Gabriel; Hultgren, Scott J

    2012-06-12

    P pili are prototypical chaperone-usher pathway-assembled pili used by Gram-negative bacteria to adhere to host tissues. The PapC usher contains five functional domains: a transmembrane β-barrel, a β-sandwich Plug, an N-terminal (periplasmic) domain (NTD), and two C-terminal (periplasmic) domains, CTD1 and CTD2. Here, we delineated usher domain interactions between themselves and with chaperone-subunit complexes and showed that overexpression of individual usher domains inhibits pilus assembly. Prior work revealed that the Plug domain occludes the pore of the transmembrane domain of a solitary usher, but the chaperone-adhesin-bound usher has its Plug displaced from the pore, adjacent to the NTD. We demonstrate an interaction between the NTD and Plug domains that suggests a biophysical basis for usher gating. Furthermore, we found that the NTD exhibits high-affinity binding to the chaperone-adhesin (PapDG) complex and low-affinity binding to the major tip subunit PapE (PapDE). We also demonstrate that CTD2 binds with lower affinity to all tested chaperone-subunit complexes except for the chaperone-terminator subunit (PapDH) and has a catalytic role in dissociating the NTD-PapDG complex, suggesting an interplay between recruitment to the NTD and transfer to CTD2 during pilus initiation. The Plug domain and the NTD-Plug complex bound all of the chaperone-subunit complexes tested including PapDH, suggesting that the Plug actively recruits chaperone-subunit complexes to the usher and is the sole recruiter of PapDH. Overall, our studies reveal the cooperative, active roles played by periplasmic domains of the usher to initiate, grow, and terminate a prototypical chaperone-usher pathway pilus.

  1. Comparison of diagnostic capability of macular ganglion cell complex and retinal nerve fiber layer among primary open angle glaucoma, ocular hypertension, and normal population using Fourier-domain optical coherence tomography and determining their functional correlation in Indian population

    Directory of Open Access Journals (Sweden)

    Nabanita Barua

    2016-01-01

    Full Text Available Context: Analysis of diagnostic ability of macular ganglionic cell complex and retinal nerve fiber layer (RNFL in glaucoma. Aim: To correlate functional and structural parameters and comparing predictive value of each of the structural parameters using Fourier-domain (FD optical coherence tomography (OCT among primary open angle glaucoma (POAG and ocular hypertension (OHT versus normal population. Setting and Design: Single centric, cross-sectional study done in 234 eyes. Materials and Methods: Patients were enrolled in three groups: POAG, ocular hypertensive and normal (40 patients in each group. After comprehensive ophthalmological examination, patients underwent standard automated perimetry and FD-OCT scan in optic nerve head and ganglion cell mode. The relationship was assessed by correlating ganglion cell complex (GCC parameters with mean deviation. Results were compared with RNFL parameters. Statistical Analysis: Data were analyzed with SPSS, analysis of variance, t-test, Pearson′s coefficient, and receiver operating curve. Results: All parameters showed strong correlation with visual field (P 0.5 when compared with other parameters. None of the parameters showed significant diagnostic capability to detect OHT from normal population. In diagnosing early glaucoma from OHT and normal population, only inferior GCC had statistically significant AUC value (0.715. Conclusion: In this study, GCC and RNFL parameters showed equal predictive capability in perimetric versus normal group. In early stage, inferior GCC was the best parameter. In OHT population, single day cross-sectional imaging was not valuable.

  2. Quantitative Characteristics of Spectral-Domain Optical Coherence Tomography in Corresponding Areas of Increased Autofluorescence at the Margin of Geographic Atrophy in Patients With Age-Related Macular Degeneration.

    Science.gov (United States)

    Hariri, Amir H; Nittala, Muneeswar G; Sadda, SriniVas R

    2016-06-01

    To evaluate the spectral-domain optical coherence tomography (SD-OCT) characteristics of the junctional zone corresponding to areas of increased autofluorescence (IAF) at the margin of geographic atrophy (GA) in patients with age-related macular degeneration (AMD). SD-OCT and fundus autofluorescence (FAF) images from untreated eyes with GA available from archived studies at Doheny Image Reading Center were evaluated. Areas of definite decreased autofluorescence (DDAF) corresponding to GA, and areas of IAF at the margins of the GA were manually segmented. Eyes with evidence of IAF were selected. Following manual registration of FAF and OCT data, areas of IAF and normal fluorescence were correlated with OCT features at these locations. Thirty eyes were included. The mean retinal pigment epithelium (RPE) thickness in areas of IAF was 40.6 µm ± 7.69 µm, compared to 28.8 µm ± 7.09 µm in normal adjacent areas (P Retina. 2016;47:523-527.]. Copyright 2016, SLACK Incorporated.

  3. Generalized hypergeometric coherent states

    International Nuclear Information System (INIS)

    Appl, Thomas; Schiller, Diethard H

    2004-01-01

    We introduce a large class of holomorphic quantum states by choosing their normalization functions to be given by generalized hypergeometric functions. We call them generalized hypergeometric states in general, and generalized hypergeometric coherent states in particular, if they allow a resolution of unity. Depending on the domain of convergence of the generalized hypergeometric functions, we distinguish generalized hypergeometric states on the plane, the open unit disc and the unit circle. All states are eigenstates of suitably defined lowering operators. We then study their photon number statistics and phase properties as revealed by the Husimi and Pegg-Barnett phase distributions. On the basis of the generalized hypergeometric coherent states we introduce new analytic representations of arbitrary quantum states in Bargmann and Hardy spaces as well as generalized hypergeometric Husimi distributions and corresponding phase distributions

  4. Cellulase linkers are optimized based on domain type and function: insights from sequence analysis, biophysical measurements, and molecular simulation.

    Directory of Open Access Journals (Sweden)

    Deanne W Sammond

    Full Text Available Cellulase enzymes deconstruct cellulose to glucose, and are often comprised of glycosylated linkers connecting glycoside hydrolases (GHs to carbohydrate-binding modules (CBMs. Although linker modifications can alter cellulase activity, the functional role of linkers beyond domain connectivity remains unknown. Here we investigate cellulase linkers connecting GH Family 6 or 7 catalytic domains to Family 1 or 2 CBMs, from both bacterial and eukaryotic cellulases to identify conserved characteristics potentially related to function. Sequence analysis suggests that the linker lengths between structured domains are optimized based on the GH domain and CBM type, such that linker length may be important for activity. Longer linkers are observed in eukaryotic GH Family 6 cellulases compared to GH Family 7 cellulases. Bacterial GH Family 6 cellulases are found with structured domains in either N to C terminal order, and similar linker lengths suggest there is no effect of domain order on length. O-glycosylation is uniformly distributed across linkers, suggesting that glycans are required along entire linker lengths for proteolysis protection and, as suggested by simulation, for extension. Sequence comparisons show that proline content for bacterial linkers is more than double that observed in eukaryotic linkers, but with fewer putative O-glycan sites, suggesting alternative methods for extension. Conversely, near linker termini where linkers connect to structured domains, O-glycosylation sites are observed less frequently, whereas glycines are more prevalent, suggesting the need for flexibility to achieve proper domain orientations. Putative N-glycosylation sites are quite rare in cellulase linkers, while an N-P motif, which strongly disfavors the attachment of N-glycans, is commonly observed. These results suggest that linkers exhibit features that are likely tailored for optimal function, despite possessing low sequence identity. This study suggests

  5. Molecular Dissection of the Homotrimeric Sliding Clamp of T4 Phage: Two Domains of a Subunit Display Asymmetric Characteristics.

    Science.gov (United States)

    Singh, Manika Indrajit; Jain, Vikas

    2016-01-26

    Sliding clamp proteins are circular dimers or trimers that encircle DNA and serve as processivity factors during DNA replication. Their presence in all the three domains of life and in bacteriophages clearly indicates their high level of significance. T4 gp45, besides functioning as the DNA polymerase processivity factor, also moonlights as the late promoter transcription determinant. Here we report a detailed biophysical analysis of gp45. The chemical denaturation of gp45 probed by circular dichroism spectroscopy, tryptophan fluorescence anisotropy, and blue-native polyacrylamide gel electrophoresis suggests that the protein follows a three-state denaturation profile and displays an intermediate molten globule-like state. The three-state transition was found to be the result of the sequential unfolding of the two domains, the N-terminal domain (NTD) and the C-terminal domain (CTD), of gp45. The experiments involving Trp fluorescence quenching by acrylamide demonstrate that the CTD undergoes substantial changes in conformation during formation of the intermediate state. Further biophysical dissection of the individual domain reveals contrasting properties of the two domains. The NTD unfolds at low urea concentrations and is also susceptible to protease cleavage, whereas the CTD resists urea-mediated denaturation and is not amenable to protease digestion even at higher urea concentrations. These experiments allow us to conclude that the two domains of gp45 differ in their dynamics. While the CTD shows stability and rigidity, we find that the NTD is unstable and flexible. We believe that the asymmetric characteristics of the two domains and the interface they form hold significance in gp45 structure and function.

  6. Molecular dissection of the interaction between the SH3 domain and the SH2-Kinase Linker region in PTK6.

    Science.gov (United States)

    Kim, Han Ie; Jung, Jinwon; Lee, Eun-Saem; Kim, Yong-Chul; Lee, Weontae; Lee, Seung-Taek

    2007-11-03

    PTK6 (also known as Brk) is an intracellular tyrosine kinase that contains SH3, SH2, and tyrosine kinase catalytic (Kinase) domains. The SH3 domain of PTK6 interacts with the N-terminal half of the linker (Linker) region between the SH2 and Kinase domains. Site-directed mutagenesis and surface plasmon resonance studies showed that a tryptophan residue (Trp44) in the SH3 domain and proline residues in the Linker region, in the order of Pro177, Pro175, and Pro179, contribute to the interaction. The three-dimensional modeled structure of the SH3-Linker complex was in agreement with the biochemical data. Disruption of the intramolecular interaction between the SH3 domain and the Linker region by mutation of Trp44, Pro175, Pro177, and Pro179 markedly increased the catalytic activity of PTK6 in HEK 293 cells. These results demonstrate that Trp44 in the SH3 domain and Pro177, Pro175, and Pro179 in the N-terminal half of the Linker region play important roles in the SH3-Linker interaction to maintain the protein in an inactive conformation along with the phosphorylated Tyr447-SH2 interaction.

  7. Molecular dynamics simulations of site point mutations in the TPR domain of cyclophilin 40 identify conformational states with distinct dynamic and enzymatic properties

    Science.gov (United States)

    Gur, Mert; Blackburn, Elizabeth A.; Ning, Jia; Narayan, Vikram; Ball, Kathryn L.; Walkinshaw, Malcolm D.; Erman, Burak

    2018-04-01

    Cyclophilin 40 (Cyp40) is a member of the immunophilin family that acts as a peptidyl-prolyl-isomerase enzyme and binds to the heat shock protein 90 (Hsp90). Its structure comprises an N-terminal cyclophilin domain and a C-terminal tetratricopeptide (TPR) domain. Cyp40 is overexpressed in prostate cancer and certain T-cell lymphomas. The groove for Hsp90 binding on the TPR domain includes residues Lys227 and Lys308, referred to as the carboxylate clamp, and is essential for Cyp40-Hsp90 binding. In this study, the effect of two mutations, K227A and K308A, and their combinative mutant was investigated by performing a total of 5.76 μs of all-atom molecular dynamics (MD) simulations in explicit solvent. All simulations, except the K308A mutant, were found to adopt two distinct (extended or compact) conformers defined by different cyclophilin-TPR interdomain distances. The K308A mutant was only observed in the extended form which is observed in the Cyp40 X-ray structure. The wild-type, K227A, and combined mutant also showed bimodal distributions. The experimental melting temperature, Tm, values of the mutants correlate with the degree of compactness with the K308A extended mutant having a marginally lower melting temperature. Another novel measure of compactness determined from the MD data, the "coordination shell volume," also shows a direct correlation with Tm. In addition, the MD simulations show an allosteric effect with the mutations in the remote TPR domain having a pronounced effect on the molecular motions of the enzymatic cyclophilin domain which helps rationalise the experimentally observed increase in enzyme activity measured for all three mutations.

  8. Insights into the folding and unfolding processes of wild-type and mutated SH3 domain by molecular dynamics and replica exchange molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Wen-Ting Chu

    Full Text Available Src-homology regions 3 (SH3 domain is essential for the down-regulation of tyrosine kinase activity. Mutation A39V/N53P/V55L of SH3 is found to be relative to the urgent misfolding diseases. To gain insight, the human and gallus SH3 domains (PDB ID: 1NYG and 2LP5, including 58 amino acids in each protein, were selected for MD simulations (Amber11, ff99SB force field and cluster analysis to investigate the influence of mutations on the spatial structure of the SH3 domain. It is found that the large conformational change of mutations mainly exists in three areas in the vicinity of protein core: RT loop, N-src loop, distal β-hairpin to 310 helix. The C-terminus of the mutated gallus SH3 is disordered after simulation, which represents the intermediate state of aggregation. The disappeared strong Hbond net in the mutated human and gallus systems will make these mutated proteins looser than the wild-type proteins. Additionally, by performing the REMD simulations on the gallus SH3 domain, the mutated domain is found to have an obvious effect on the unfolding process. These studies will be helpful for further aggregation mechanisms investigations on SH3 family.

  9. Coherence and Sense of Coherence

    DEFF Research Database (Denmark)

    Dau, Susanne

    2014-01-01

    Constraints in the implementation of models of blended learning can be explained by several causes, but in this paper, it is illustrated that lack of sense of coherence is a major factor of these constraints along with the referential whole of the perceived learning environments. The question exa...

  10. Ultrahigh Molecular Weight Linear Block Copolymers: Rapid Access by Reversible-Deactivation Radical Polymerization and Self- Assembly into Large Domain Nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Mapas, Jose Kenneth D.; Thomay, Tim; Cartwright, Alexander N.; Ilavsky, Jan; Rzayev, Javid

    2016-05-05

    Block copolymer (BCP) derived periodic nanostructures with domain sizes larger than 150 nm present a versatile platform for the fabrication of photonic materials. So far, the access to such materials has been limited to highly synthetically involved protocols. Herein, we report a simple, “user-friendly” method for the preparation of ultrahigh molecular weight linear poly(solketal methacrylate-b-styrene) block copolymers by a combination of Cu-wire-mediated ATRP and RAFT polymerizations. The synthesized copolymers with molecular weights up to 1.6 million g/mol and moderate dispersities readily assemble into highly ordered cylindrical or lamella microstructures with domain sizes as large as 292 nm, as determined by ultra-small-angle x-ray scattering and scanning electron microscopy analyses. Solvent cast films of the synthesized block copolymers exhibit stop bands in the visible spectrum correlated to their domain spacings. The described method opens new avenues for facilitated fabrication and the advancement of fundamental understanding of BCP-derived photonic nanomaterials for a variety of applications.

  11. Coherent dynamics in semiconductors

    DEFF Research Database (Denmark)

    Hvam, Jørn Märcher

    1998-01-01

    enhanced in quantum confined lower-dimensional systems, where exciton and biexciton effects dominate the spectra even at room temperature. The coherent dynamics of excitons are at modest densities well described by the optical Bloch equations and a number of the dynamical effects known from atomic......Ultrafast nonlinear optical spectroscopy is used to study the coherent dynamics of optically excited electron-hole pairs in semiconductors. Coulomb interaction implies that the optical inter-band transitions are dominated, at least at low temperatures, by excitonic effects. They are further...... and molecular systems are found and studied in the exciton-biexciton system of semiconductors. At densities where strong exciton interactions, or many-body effects, become dominant, the semiconductor Bloch equations present a more rigorous treatment of the phenomena Ultrafast degenerate four-wave mixing is used...

  12. Molecular determinants of transport stimulation of EAAT2 are located at interface between the trimerization and substrate transport domains.

    Science.gov (United States)

    Mortensen, Ole V; Liberato, José L; Coutinho-Netto, Joaquim; Dos Santos, Wagner F; Fontana, Andréia C K

    2015-04-01

    Excitatory amino acid transporters (EAATs) regulate glutamatergic signal transmission by clearing extracellular glutamate. Dysfunction of these transporters has been implicated in the pathogenesis of various neurological disorders. Previous studies have shown that venom from the spider Parawixia bistriata and a purified compound (Parawixin1) stimulate EAAT2 activity and protect retinal tissue from ischemic damage. In the present study, the EAAT2 subtype specificity of this compound was explored, employing chimeric proteins between EAAT2 and EAAT3 transporter subtypes and mutants to characterize the structural region targeted by the compound. This identified a critical residue (Histidine-71 in EAAT2 and Serine-45 in EAAT3) in transmembrane domain 2 (TM2) to be important for the selectivity between EAAT2 and EAAT3 and for the activity of the venom. Using the identified residue in TM2 as a structural anchor, several neighboring amino acids within TM5 and TM8 were identified to also be important for the activity of the venom. This structural domain of the transporter lies at the interface of the rigid trimerization domain and the central substrate-binding transport domain. Our studies suggest that the mechanism of glutamate transport enhancement involves an interaction with the transporter that facilitates the movement of the transport domain. We identified a domain (purple star) in the glutamate transporter EAAT2 that is important for transport stimulation through a spider venom, and suggest a mechanism for enhanced transporter function through facilitated substrate translocation (arrow). Because the dysfunction of glutamate transporters is implicated in the pathogenesis of neurological disorders, understanding the mechanisms of enhanced transport could have therapeutic implications. © 2015 International Society for Neurochemistry.

  13. THICKNESS OF THE MACULA, RETINAL NERVE FIBER LAYER, AND GANGLION CELL-INNER PLEXIFORM LAYER IN THE AGE-RELATED MACULAR DEGENERATION: The Repeatability Study of Spectral Domain Optical Coherence Tomography.

    Science.gov (United States)

    Shin, Il-Hwan; Lee, Woo-Hyuk; Lee, Jong-Joo; Jo, Young-Joon; Kim, Jung-Yeul

    2018-02-01

    To determine the repeatability of measuring the thickness of the central macula, retinal nerve fiber layer, and ganglion cell-inner plexiform layer (GC-IPL) using spectral domain optical coherence tomography (Cirrus HD-OCT) in eyes with age-related macular degeneration. One hundred and thirty-four eyes were included. The measurement repeatability was assessed by an experienced examiner who performed two consecutive measurements using a 512 × 128 macular cube scan and a 200 × 200 optic disk cube scan. To assess changes in macular morphology in patients with age-related macular degeneration, the patients were divided into the following three groups according to the central macular thickness (CMT): A group, CMT 300 μm. Measurement repeatability was assessed using test-retest variability, a coefficient of variation, and an intraclass correlation coefficient. The mean measurement repeatability for the central macular, retinal nerve fiber layer, and GC-IPL thickness was high in the B group. The mean measurement repeatability for both the central macula and retinal nerve fiber layer thickness was high in the A and C groups, but was lower for the GC-IPL thickness. The measurement repeatability for GC-IPL thickness was high in the B group, but low in the A group and in the C group. The automated measurement repeatability for GC-IPL thickness was significantly lower in patients with age-related macular degeneration with out of normal CMT range. The effect of changes in macular morphology should be considered when analyzing GC-IPL thicknesses in a variety of ocular diseases.

  14. Interacting mechanism of ID3 HLH domain towards E2A/E12 transcription factor – An Insight through molecular dynamics and docking approach

    Directory of Open Access Journals (Sweden)

    Nishith Saurav Topno

    2016-03-01

    Full Text Available Inhibitor of DNA binding protein 3 (ID3 has long been characterized as an oncogene that implicates its functional role through its Helix–Loop–Helix (HLH domain upon protein–protein interaction. An insight into the dimerization brought by this domain helps in identifying the key residues that favor the mechanism behind it. Molecular dynamics (MD simulations were performed for the HLH proteins ID3 and Transcription factor E2-alpha (E2A/E12 and their ensemble complex (ID3-E2A/E12 to gather information about the HLH domain region and its role in the interaction process. Further evaluation of the results by Principal Component Analysis (PCA and Free Energy Landscape (FEL helped in revealing residues of E2A/E12: Lys570, Ala595, Val598, and Ile599 and ID3: Glu53, Gln63, and Gln66 buried in their HLH motifs imparting key roles in dimerization process. Furthermore the T-pad analysis results helped in identifying the key fluctuations and conformational transitions using the intrinsic properties of the residues present in the domain region of the proteins thus specifying their crucial role towards molecular recognition. The study provides an insight into the interacting mechanism of the ID3-E2A/E12 complex and maps the structural transitions arising in the essential conformational space indicating the key structural changes within the helical regions of the motif. It thereby describes how the internal dynamics of the proteins might regulate their intrinsic structural features and its subsequent functionality.

  15. Using molecular principal axes for structural comparison: determining the tertiary changes of a FAB antibody domain induced by antigenic binding

    Directory of Open Access Journals (Sweden)

    Silverman B David

    2007-11-01

    Full Text Available Abstract Background Comparison of different protein x-ray structures has previously been made in a number of different ways; for example, by visual examination, by differences in the locations of secondary structures, by explicit superposition of structural elements, e.g. α-carbon atom locations, or by procedures that utilize a common symmetry element or geometrical feature of the structures to be compared. Results A new approach is applied to determine the structural changes that an antibody protein domain experiences upon its interaction with an antigenic target. These changes are determined with the use of two different, however comparable, sets of principal axes that are obtained by diagonalizing the second-order tensors that yield the moments-of-geometry as well as an ellipsoidal characterization of domain shape, prior to and after interaction. Determination of these sets of axes for structural comparison requires no internal symmetry features of the domains, depending solely upon their representation in three-dimensional space. This representation may involve atomic, Cα, or residue centroid coordinates. The present analysis utilizes residue centroids. When the structural changes are minimal, the principal axes of the domains, prior to and after interaction, are essentially comparable and consequently may be used for structural comparison. When the differences of the axes cannot be neglected, but are nevertheless slight, a smaller relatively invariant substructure of the domains may be utilized for comparison. The procedure yields two distance metrics for structural comparison. First, the displacements of the residue centroids due to antigenic binding, referenced to the ellipsoidal principal axes, are noted. Second, changes in the ellipsoidal distances with respect to the non-interacting structure provide a direct measure of the spatial displacements of the residue centroids, towards either the interior or exterior of the domain

  16. Impairment of different protein domains causes variable clinical presentation within Pitt-Hopkins syndrome and suggests intragenic molecular syndromology of TCF4.

    Science.gov (United States)

    Bedeschi, Maria Francesca; Marangi, Giuseppe; Calvello, Maria Rosaria; Ricciardi, Stefania; Leone, Francesca Pia Chiara; Baccarin, Marco; Guerneri, Silvana; Orteschi, Daniela; Murdolo, Marina; Lattante, Serena; Frangella, Silvia; Keena, Beth; Harr, Margaret H; Zackai, Elaine; Zollino, Marcella

    2017-11-01

    Pitt-Hopkins syndrome is a neurodevelopmental disorder characterized by severe intellectual disability and a distinctive facial gestalt. It is caused by haploinsufficiency of the TCF4 gene. The TCF4 protein has different functional domains, with the NLS (nuclear localization signal) domain coded by exons 7-8 and the bHLH (basic Helix-Loop-Helix) domain coded by exon 18. Several alternatively spliced TCF4 variants have been described, allowing for translation of variable protein isoforms. Typical PTHS patients have impairment of at least the bHLH domain. To which extent impairment of the remaining domains contributes to the final phenotype is not clear. There is recent evidence that certain loss-of-function variants disrupting TCF4 are associated with mild ID, but not with typical PTHS. We describe a frameshift-causing partial gene deletion encompassing exons 4-6 of TCF4 in an adult patient with mild ID and nonspecific facial dysmorphisms but without the typical features of PTHS, and a c.520C > T nonsense variant within exon 8 in a child presenting with a severe phenotype largely mimicking PTHS, but lacking the typical facial dysmorphism. Investigation on mRNA, along with literature review, led us to suggest a preliminary phenotypic map of loss-of-function variants affecting TCF4. An intragenic phenotypic map of loss-of-function variants in TCF4 is suggested here for the first time: variants within exons 1-4 and exons 4-6 give rise to a recurrent phenotype with mild ID not in the spectrum of Pitt-Hopkins syndrome (biallelic preservation of both the NLS and bHLH domains); variants within exons 7-8 cause a severe phenotype resembling PTHS but in absence of the typical facial dysmorphism (impairment limited to the NLS domain); variants within exons 9-19 cause typical Pitt-Hopkins syndrome (impairment of at least the bHLH domain). Understanding the TCF4 molecular syndromology can allow for proper nosology in the current era of whole genomic investigations. Copyright

  17. Coherent Baryogenesis

    CERN Document Server

    Garbrecht, B; Schmidt, M G; Garbrecht, Bjorn; Prokopec, Tomislav; Schmidt, Michael G.

    2004-01-01

    We propose a new baryogenesis scenario based on coherent production and mixing of different fermionic species. The mechanism is operative during phase transitions, at which the fermions acquire masses via Yukawa couplings to scalar fields. Baryon production is efficient when the mass matrix is nonadiabatically varying, nonsymmetric and when it violates CP and B-L directly, or some other charges that are eventually converted to B-L. We first consider a toy model, which involves two mixing fermionic species, and then a hybrid inflationary scenario embedded in a supersymmetric Pati-Salam GUT. We show that, quite generically, a baryon excess in accordance with observation can result.

  18. Coherent states: a contemporary panorama Coherent states: a contemporary panorama

    Science.gov (United States)

    Twareque Ali, S.; Antoine, Jean-Pierre; Bagarello, Fabio; Gazeau, Jean-Pierre

    2012-06-01

    Coherent states (CS) of the harmonic oscillator (also called canonical CS) were introduced in 1926 by Schrödinger in answer to a remark by Lorentz on the classical interpretation of the wave function. They were rediscovered in the early 1960s, first (somewhat implicitly) by Klauder in the context of a novel representation of quantum states, then by Glauber and Sudarshan for the description of coherence in lasers. Since then, CS have grown into an extremely rich domain that pervades almost every corner of physics and have also led to the development of several flourishing topics in mathematics. Along the way, a number of review articles have appeared in the literature, devoted to CS, notably the 1985 reprint volume of Klauder and Skagerstam [1], the 1990 review paper by Zhang et al [2], the 1993 Oak Ridge Conference [3] and the 1995 review paper by Ali et al [4]. Textbooks also have been published, among which one might mention the ground breaking text of Perelomov [5] focusing on the group-theoretical aspects, that of Ali et al [6]1 analyzing systematically the mathematical structure beyond the group-theoretical approach and also the relation to wavelet analysis, that of Dodonov and Man'ko [7] mostly devoted to quantum optics, that of Gazeau [8] more oriented towards the physical, probabilistic and quantization aspects, and finally the very recent one by Combescure and Robert [9]. In retrospect, one can see that the development of CS has gone through a two-phase transition. First, the (simultaneous) discovery in 1972 by Gilmore and Perelomov that CS were rooted in group theory, then the realization that CS can be defined in a purely algebraic way, as an eigenvalue problem or by a series expansion (Malkin and Man'ko 1969, Barut and Girardello 1971, Gazeau and Klauder 1999; references to the original articles may be found in the textbooks quoted above). Both facts resulted in an explosive expansion of the CS literature. We thought, therefore, that the time was ripe

  19. Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations.

    Science.gov (United States)

    Subbotina, Julia; Yarov-Yarovoy, Vladimir; Lees-Miller, James; Durdagi, Serdar; Guo, Jiqing; Duff, Henry J; Noskov, Sergei Yu

    2010-11-01

    The hERG1 gene (Kv11.1) encodes a voltage-gated potassium channel. Mutations in this gene lead to one form of the Long QT Syndrome (LQTS) in humans. Promiscuous binding of drugs to hERG1 is known to alter the structure/function of the channel leading to an acquired form of the LQTS. Expectably, creation and validation of reliable 3D model of the channel have been a key target in molecular cardiology and pharmacology for the last decade. Although many models were built, they all were limited to pore domain. In this work, a full model of the hERG1 channel is developed which includes all transmembrane segments. We tested a template-driven de-novo design with ROSETTA-membrane modeling using side-chain placements optimized by subsequent molecular dynamics (MD) simulations. Although backbone templates for the homology modeled parts of the pore and voltage sensors were based on the available structures of KvAP, Kv1.2 and Kv1.2-Kv2.1 chimera channels, the missing parts are modeled de-novo. The impact of several alignments on the structure of the S4 helix in the voltage-sensing domain was also tested. Herein, final models are evaluated for consistency to the reported structural elements discovered mainly on the basis of mutagenesis and electrophysiology. These structural elements include salt bridges and close contacts in the voltage-sensor domain; and the topology of the extracellular S5-pore linker compared with that established by toxin foot-printing and nuclear magnetic resonance studies. Implications of the refined hERG1 model to binding of blockers and channels activators (potent new ligands for channel activations) are discussed. © 2010 Wiley-Liss, Inc.

  20. Simultaneous optical coherence tomography and lipofuscin autofluorescence imaging of the retina with a single broadband light source at 480nm

    OpenAIRE

    Jiang, Minshan; Liu, Tan; Liu, Xiaojing; Jiao, Shuliang

    2014-01-01

    We accomplished spectral domain optical coherence tomography and auto-fluorescence microscopy for imaging the retina with a single broadband light source centered at 480 nm. This technique is able to provide simultaneous structural imaging and lipofuscin molecular contrast of the retina. Since the two imaging modalities are provided by the same group of photons, their images are intrinsically registered. To test the capabilities of the technique we periodically imaged the retinas of the same ...

  1. The Voltage-Sensing Domain of Kv7.2 Channels as a Molecular Target for Epilepsy-Causing Mutations and Anticonvulsants

    Science.gov (United States)

    Miceli, Francesco; Soldovieri, Maria Virginia; Iannotti, Fabio Arturo; Barrese, Vincenzo; Ambrosino, Paolo; Martire, Maria; Cilio, Maria Roberta; Taglialatela, Maurizio

    2010-01-01

    Understanding the molecular mechanisms underlying voltage-dependent gating in voltage-gated ion channels (VGICs) has been a major effort over the last decades. In recent years, changes in the gating process have emerged as common denominators for several genetically determined channelopathies affecting heart rhythm (arrhythmias), neuronal excitability (epilepsy, pain), or skeletal muscle contraction (periodic paralysis). Moreover, gating changes appear as the main molecular mechanism by which several natural toxins from a variety of species affect ion channel function. In this work, we describe the pathophysiological and pharmacological relevance of the gating process in voltage-gated K+ channels encoded by the Kv7 gene family. After reviewing the current knowledge on the molecular mechanisms and on the structural models of voltage-dependent gating in VGICs, we describe the physiological relevance of these channels, with particular emphasis on those formed by Kv7.2–Kv7.5 subunits having a well-established role in controlling neuronal excitability in humans. In fact, genetically determined alterations in Kv7.2 and Kv7.3 genes are responsible for benign familial neonatal convulsions, a rare seizure disorder affecting newborns, and the pharmacological activation of Kv7.2/3 channels can exert antiepileptic activity in humans. Both mutation-triggered channel dysfunction and drug-induced channel activation can occur by impeding or facilitating, respectively, channel sensitivity to membrane voltage and can affect overlapping molecular sites within the voltage-sensing domain of these channels. Thus, understanding the molecular steps involved in voltage-sensing in Kv7 channels will allow to better define the pathogenesis of rare human epilepsy, and to design innovative pharmacological strategies for the treatment of epilepsies and, possibly, other human diseases characterized by neuronal hyperexcitability. PMID:21687499

  2. The voltage-sensing domain of kv7.2 channels as a molecular target for epilepsy-causing mutations and anticonvulsants

    Directory of Open Access Journals (Sweden)

    Francesco eMiceli

    2011-02-01

    Full Text Available Understanding the molecular mechanisms underlying voltage-dependent gating in voltage-gated ion channels (VGICs has been a major effort over the last decades. In recent years, changes in the gating process have emerged as common denominators for several genetically-determined channelopathies affecting heart rhythm (arrhythmias, neuronal excitability (epilepsy, pain or skeletal muscle contraction (periodic paralysis. Moreover, gating changes appear as the main molecular mechanism by which several natural toxins from a variety of species affect ion channel function.In this work, we describe the pathophysiological and pharmacological relevance of the gating process in voltage-gated K+ channels encoded by the Kv7 gene family. After reviewing the current knowledge on the molecular mechanisms and on the structural models of voltage-dependent gating in VGICs, we describe the physiological relevance of these channels, with particular emphasis on those formed by Kv7.2-5 subunits having a well-established role in controlling neuronal excitability in humans. In fact, genetically-determined alterations in Kv7.2 and Kv7.3 genes are responsible for benign familial neonatal convulsions, a rare seizure disorder affecting newborns, and the pharmacological activation of Kv7.2/3 channels can exert antiepileptic activity in humans. Both mutation-triggered channel dysfunction and drug-induced channel activation can occur by impeding or facilitating, respectively, channel sensitivity to membrane voltage and can affect overlapping molecular sites within the voltage-sensing domain of these channels. Thus, understanding the molecular steps involved in voltage-sensing in Kv7 channels will allow to better define the pathogenesis of rare human epilepsy, and to design innovative pharmacological strategies for the treatment of epilepsies and, possibly, other human diseases characterized by neuronal hyperexcitability.

  3. The Voltage-Sensing Domain of K(v)7.2 Channels as a Molecular Target for Epilepsy-Causing Mutations and Anticonvulsants.

    Science.gov (United States)

    Miceli, Francesco; Soldovieri, Maria Virginia; Iannotti, Fabio Arturo; Barrese, Vincenzo; Ambrosino, Paolo; Martire, Maria; Cilio, Maria Roberta; Taglialatela, Maurizio

    2011-01-01

    Understanding the molecular mechanisms underlying voltage-dependent gating in voltage-gated ion channels (VGICs) has been a major effort over the last decades. In recent years, changes in the gating process have emerged as common denominators for several genetically determined channelopathies affecting heart rhythm (arrhythmias), neuronal excitability (epilepsy, pain), or skeletal muscle contraction (periodic paralysis). Moreover, gating changes appear as the main molecular mechanism by which several natural toxins from a variety of species affect ion channel function. In this work, we describe the pathophysiological and pharmacological relevance of the gating process in voltage-gated K(+) channels encoded by the K(v)7 gene family. After reviewing the current knowledge on the molecular mechanisms and on the structural models of voltage-dependent gating in VGICs, we describe the physiological relevance of these channels, with particular emphasis on those formed by K(v)7.2-K(v)7.5 subunits having a well-established role in controlling neuronal excitability in humans. In fact, genetically determined alterations in K(v)7.2 and K(v)7.3 genes are responsible for benign familial neonatal convulsions, a rare seizure disorder affecting newborns, and the pharmacological activation of K(v)7.2/3 channels can exert antiepileptic activity in humans. Both mutation-triggered channel dysfunction and drug-induced channel activation can occur by impeding or facilitating, respectively, channel sensitivity to membrane voltage and can affect overlapping molecular sites within the voltage-sensing domain of these channels. Thus, understanding the molecular steps involved in voltage-sensing in K(v)7 channels will allow to better define the pathogenesis of rare human epilepsy, and to design innovative pharmacological strategies for the treatment of epilepsies and, possibly, other human diseases characterized by neuronal hyperexcitability.

  4. Challenges in analysing and visualizing large-scale molecular dynamics simulations: domain and defect formation in lung surfactant monolayers

    International Nuclear Information System (INIS)

    Mendez-Villuendas, E; Baoukina, S; Tieleman, D P

    2012-01-01

    Molecular dynamics simulations have rapidly grown in size and complexity, as computers have become more powerful and molecular dynamics software more efficient. Using coarse-grained models like MARTINI system sizes of the order of 50 nm × 50 nm × 50 nm can be simulated on commodity clusters on microsecond time scales. For simulations of biological membranes and monolayers mimicking lung surfactant this enables large-scale transformation and complex mixtures of lipids and proteins. Here we use a simulation of a monolayer with three phospholipid components, cholesterol, lung surfactant proteins, water, and ions on a ten microsecond time scale to illustrate some current challenges in analysis. In the simulation, phase separation occurs followed by formation of a bilayer fold in which lipids and lung surfactant protein form a highly curved structure in the aqueous phase. We use Voronoi analysis to obtain detailed physical properties of the different components and phases, and calculate local mean and Gaussian curvatures of the bilayer fold.

  5. Extrapolation of Inter Domain Communications and Substrate Binding Cavity of Camel HSP70 1A: A Molecular Modeling and Dynamics Simulation Study.

    Directory of Open Access Journals (Sweden)

    Saurabh Gupta

    Full Text Available Heat shock protein 70 (HSP70 is an important chaperone, involved in protein folding, refolding, translocation and complex remodeling reactions under normal as well as stress conditions. However, expression of HSPA1A gene in heat and cold stress conditions associates with other chaperons and perform its function. Experimental structure for Camel HSP70 protein (cHSP70 has not been reported so far. Hence, we constructed 3D models of cHSP70 through multi- template comparative modeling with HSP110 protein of S. cerevisiae (open state and with HSP70 protein of E. coli 70kDa DnaK (close state and relaxed them for 100 nanoseconds (ns using all-atom Molecular Dynamics (MD Simulation. Two stable conformations of cHSP70 with Substrate Binding Domain (SBD in open and close states were obtained. The collective mode analysis of different transitions of open state to close state and vice versa was examined via Principal Component Analysis (PCA and Minimum Distance Matrix (MDM. The results provide mechanistic representation of the communication between Nucleotide Binding Domain (NBD and SBD to identify the role of sub domains in conformational change mechanism, which leads the chaperone cycle of cHSP70. Further, residues present in the chaperon functioning site were also identified through protein-peptide docking. This study provides an overall insight into the inter domain communication mechanism and identification of the chaperon binding cavity, which explains the underlying mechanism involved during heat and cold stress conditions in camel.

  6. Structural models of zebrafish (Danio rerio NOD1 and NOD2 NACHT domains suggest differential ATP binding orientations: insights from computational modeling, docking and molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Jitendra Maharana

    Full Text Available Nucleotide-binding oligomerization domain-containing protein 1 (NOD1 and NOD2 are cytosolic pattern recognition receptors playing pivotal roles in innate immune signaling. NOD1 and NOD2 recognize bacterial peptidoglycan derivatives iE-DAP and MDP, respectively and undergoes conformational alternation and ATP-dependent self-oligomerization of NACHT domain followed by downstream signaling. Lack of structural adequacy of NACHT domain confines our understanding about the NOD-mediated signaling mechanism. Here, we predicted the structure of NACHT domain of both NOD1 and NOD2 from model organism zebrafish (Danio rerio using computational methods. Our study highlighted the differential ATP binding modes in NOD1 and NOD2. In NOD1, γ-phosphate of ATP faced toward the central nucleotide binding cavity like NLRC4, whereas in NOD2 the cavity was occupied by adenine moiety. The conserved 'Lysine' at Walker A formed hydrogen bonds (H-bonds and Aspartic acid (Walker B formed electrostatic interaction with ATP. At Sensor 1, Arg328 of NOD1 exhibited an H-bond with ATP, whereas corresponding Arg404 of NOD2 did not. 'Proline' of GxP motif (Pro386 of NOD1 and Pro464 of NOD2 interacted with adenine moiety and His511 at Sensor 2 of NOD1 interacted with γ-phosphate group of ATP. In contrast, His579 of NOD2 interacted with the adenine moiety having a relatively inverted orientation. Our findings are well supplemented with the molecular interaction of ATP with NLRC4, and consistent with mutagenesis data reported for human, which indicates evolutionary shared NOD signaling mechanism. Together, this study provides novel insights into ATP binding mechanism, and highlights the differential ATP binding modes in zebrafish NOD1 and NOD2.

  7. A Molecular Staple: D-Loops in the I Domain of Bacteriophage P22 Coat Protein Make Important Intercapsomer Contacts Required for Procapsid Assembly

    Science.gov (United States)

    D'Lima, Nadia G.

    2015-01-01

    ABSTRACT Bacteriophage P22, a double-stranded DNA (dsDNA) virus, has a nonconserved 124-amino-acid accessory domain inserted into its coat protein, which has the canonical HK97 protein fold. This I domain is involved in virus capsid size determination and stability, as well as protein folding. The nuclear magnetic resonance (NMR) solution structure of the I domain revealed the presence of a D-loop, which was hypothesized to make important intersubunit contacts between coat proteins in adjacent capsomers. Here we show that amino acid substitutions of residues near the tip of the D-loop result in aberrant assembly products, including tubes and broken particles, highlighting the significance of the D-loops in proper procapsid assembly. Using disulfide cross-linking, we showed that the tips of the D-loops are positioned directly across from each other both in the procapsid and the mature virion, suggesting their importance in both states. Our results indicate that D-loop interactions act as “molecular staples” at the icosahedral 2-fold symmetry axis and significantly contribute to stabilizing the P22 capsid for DNA packaging. IMPORTANCE Many dsDNA viruses have morphogenic pathways utilizing an intermediate capsid, known as a procapsid. These procapsids are assembled from a coat protein having the HK97 fold in a reaction driven by scaffolding proteins or delta domains. Maturation of the capsid occurs during DNA packaging. Bacteriophage HK97 uniquely stabilizes its capsid during maturation by intercapsomer cross-linking, but most virus capsids are stabilized by alternate means. Here we show that the I domain that is inserted into the coat protein of bacteriophage P22 is important in the process of proper procapsid assembly. Specifically, the I domain allows for stabilizing interactions across the capsid 2-fold axis of symmetry via a D-loop. When amino acid residues at the tip of the D-loop are mutated, aberrant assembly products, including tubes, are formed instead

  8. Inherent dynamics of head domain correlates with ATP-recognition of P2X4 receptors: insights gained from molecular simulations.

    Directory of Open Access Journals (Sweden)

    Li-Dong Huang

    Full Text Available P2X receptors are ATP-gated ion channels involved in many physiological functions, and determination of ATP-recognition (AR of P2X receptors will promote the development of new therapeutic agents for pain, inflammation, bladder dysfunction and osteoporosis. Recent crystal structures of the zebrafish P2X4 (zfP2X4 receptor reveal a large ATP-binding pocket (ABP located at the subunit interface of zfP2X4 receptors, which is occupied by a conspicuous cluster of basic residues to recognize triphosphate moiety of ATP. Using the engineered affinity labeling and molecular modeling, at least three sites (S1, S2 and S3 within ABP have been identified that are able to recognize the adenine ring of ATP, implying the existence of at least three distinct AR modes in ABP. The open crystal structure of zfP2X4 confirms one of three AR modes (named AR1, in which the adenine ring of ATP is buried into site S1 while the triphosphate moiety interacts with clustered basic residues. Why architecture of ABP favors AR1 not the other two AR modes still remains unexplored. Here, we examine the potential role of inherent dynamics of head domain, a domain involved in ABP formation, in AR determinant of P2X4 receptors. In silico docking and binding free energy calculation revealed comparable characters of three distinct AR modes. Inherent dynamics of head domain, especially the downward motion favors the preference of ABP for AR1 rather than AR2 and AR3. Along with the downward motion of head domain, the closing movement of loop139-146 and loop169-183, and structural rearrangements of K70, K72, R298 and R143 enabled ABP to discriminate AR1 from other AR modes. Our observations suggest the essential role of head domain dynamics in determining AR of P2X4 receptors, allowing evaluation of new strategies aimed at developing specific blockers/allosteric modulators by preventing the dynamics of head domain associated with both AR and channel activation of P2X4 receptors.

  9. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    politicians and in the media, especially in the discussion whether some languages undergo ‘domain loss’ vis-à-vis powerful international languages like English. An objection that has been raised here is that domains, as originally conceived, are parameters of language choice and not properties of languages...

  10. MOLECULAR OUTFLOWS IN THE SUBSTELLAR DOMAIN: MILLIMETER OBSERVATIONS OF YOUNG VERY LOW MASS OBJECTS IN TAURUS AND ρ OPHIUCHI

    International Nuclear Information System (INIS)

    Ngoc Phan-Bao; Lee, Chin-Fei; Ho, Paul T. P.; Tang, Ya-Wen

    2011-01-01

    We report here our search for molecular outflows from young very low mass stars and brown dwarfs in Taurus and ρ Ophiuchi. Using the Submillimeter Array and the Combined Array for Research in Millimeter-wave Astronomy, we have observed four targets at 1.3 mm wavelength (230 GHz) to search for CO J = 2 → 1 outflows. A young very low mass star MHO 5 (in Taurus) with an estimated mass of 90 M J , which is just above the hydrogen-burning limit, shows two gas lobes that are likely outflows. While the CO map of MHO 5 does not show a clear structure of outflow, possibly due to environment gas, its position-velocity diagram indicates two distinct blue- and redshifted components. We therefore conclude that they are components of a bipolar molecular outflow from MHO 5. We estimate an outflow mass of 7.0 x 10 -5 M sun and a mass-loss rate of 9.0 x 10 -10 M sun . These values are over two orders of magnitude smaller than the typical ones for T Tauri stars and somewhat weaker than those we have observed in the young brown dwarf ISO-Oph 102 of 60 M J in ρ Ophiuchi. This makes MHO 5 the first young very low mass star showing a bipolar molecular outflow in Taurus. The detection boosts the scenario that very low mass objects form like low-mass stars but in a version scaled down by a factor of over 100.

  11. Identification of Novel Molecular Targets for Pleckstrin Homology (PH) Domains Found in Oncogenes Implicated in Breast Cancer

    Science.gov (United States)

    2008-03-01

    roles as a positive regulator of IL- 2 gene induction in T cells (Deckert et al, 1998), NK cell-mediated cytotoxicity (Jevremovic et al, 2001), and FcRI...Identification of a gene encoding a human oxysterol-binding protein-homologue: a potential general molecular marker for blood dissemination of solid...Biol. 6(5), 384-385. Scanlan, MJ, Gout , I, Gordon, CM, Williamson, B, Stockert, E, Gure, AO, Jager, D, Chen, YT, Mackay, A, O’Hare, MJ, and Old LJ

  12. Coherent states in quantum physics

    CERN Document Server

    Gazeau, Jean-Pierre

    2009-01-01

    This self-contained introduction discusses the evolution of the notion of coherent states, from the early works of Schrödinger to the most recent advances, including signal analysis. An integrated and modern approach to the utility of coherent states in many different branches of physics, it strikes a balance between mathematical and physical descriptions.Split into two parts, the first introduces readers to the most familiar coherent states, their origin, their construction, and their application and relevance to various selected domains of physics. Part II, mostly based on recent original results, is devoted to the question of quantization of various sets through coherent states, and shows the link to procedures in signal analysis. Title: Coherent States in Quantum Physics Print ISBN: 9783527407095 Author(s): Gazeau, Jean-Pierre eISBN: 9783527628292 Publisher: Wiley-VCH Dewey: 530.12 Publication Date: 23 Sep, 2009 Pages: 360 Category: Science, Science: Physics LCCN: Language: English Edition: N/A LCSH:

  13. Dynamical coupling of plasmons and molecular excitations by hybrid quantum/classical calculations: time-domain approach

    International Nuclear Information System (INIS)

    Sakko, Arto; Rossi, Tuomas P; Nieminen, Risto M

    2014-01-01

    The presence of plasmonic material influences the optical properties of nearby molecules in untrivial ways due to the dynamical plasmon-molecule coupling. We combine quantum and classical calculation schemes to study this phenomenon in a hybrid system that consists of a Na 2 molecule located in the gap between two Au/Ag nanoparticles. The molecule is treated quantum-mechanically with time-dependent density-functional theory, and the nanoparticles with quasistatic classical electrodynamics. The nanoparticle dimer has a plasmon resonance in the visible part of the electromagnetic spectrum, and the Na 2 molecule has an electron-hole excitation in the same energy range. Due to the dynamical interaction of the two subsystems the plasmon and the molecular excitations couple, creating a hybridized molecular-plasmon excited state. This state has unique properties that yield e.g. enhanced photoabsorption compared to the freestanding Na 2 molecule. The computational approach used enables decoupling of the mutual plasmon-molecule interaction, and our analysis verifies that it is not legitimate to neglect the backcoupling effect when describing the dynamical interaction between plasmonic material and nearby molecules. Time-resolved analysis shows nearly instantaneous formation of the coupled state, and provides an intuitive picture of the underlying physics. (paper)

  14. Dissection of the IgNAR V domain: molecular scanning and orthologue database mining define novel IgNAR hallmarks and affinity maturation mechanisms.

    Science.gov (United States)

    Fennell, B J; Darmanin-Sheehan, A; Hufton, S E; Calabro, V; Wu, L; Müller, M R; Cao, W; Gill, D; Cunningham, O; Finlay, W J J

    2010-07-09

    The shark antigen-binding V(NAR) domain has the potential to provide an attractive alternative to traditional biotherapeutics based on its small size, advantageous physiochemical properties, and unusual ability to target clefts in enzymes or cell surface molecules. The V(NAR) shares many of the properties of the well-characterised single-domain camelid V(H)H but is much less understood at the molecular level. We chose the hen-egg-lysozyme-specific archetypal Type I V(NAR) 5A7 and used ribosome display in combination with error-prone mutagenesis to interrogate the entire sequence space. We found a high level of mutational plasticity across the V(NAR) domain, particularly within the framework 2 and hypervariable region 2 regions. A number of residues important for affinity were identified, and a triple mutant combining A1D, S61R, and G62R resulted in a K(D) of 460 pM for hen egg lysozyme, a 20-fold improvement over wild-type 5A7, and the highest K(D) yet reported for V(NAR)-antigen interactions. These findings were rationalised using structural modelling and indicate the importance of residues outside the classical complementarity determining regions in making novel antigen contacts that modulate affinity. We also located two solvent-exposed residues (G15 and G42), distant from the V(NAR) paratope, which retain function upon mutation to cysteine and have the potential to be exploited as sites for targeted covalent modification. Our findings with 5A7 were extended to all known NAR structures using an in-depth bioinformatic analysis of sequence data available in the literature and a newly generated V(NAR) database. This study allowed us to identify, for the first time, both V(NAR)-specific and V(NAR)/Ig V(L)/TCR V(alpha) overlapping hallmark residues, which are critical for the structural and functional integrity of the single domain. Intriguingly, each of our designated V(NAR)-specific hallmarks align precisely with previously defined mutational 'cold spots' in

  15. Molecular Docking Characterization of a Four-Domain Segment of Human Fibronectin Encompassing the RGD Loop with Hydroxyapatite

    Directory of Open Access Journals (Sweden)

    Tailin Guo

    2013-12-01

    Full Text Available Fibronectin adsorption on biomaterial surfaces plays a key role in the biocompatibility of biomedical implants. In the current study, the adsorption behavior of the 7–10th type III modules of fibronectin (FN-III7–10 in the presence of hydroxyapatite (HAP was systematically investigated by using molecular docking approach. It was revealed that the FN-III10 is the most important module among FN-III7–10 in promoting fibronectin binding to HAP by optimizing the interaction energy; the arginine residues were observed to directly interact with the hydroxyl group of HAP through electrostatic forces and hydrogen bonding. Moreover, it was found that the HAP-binding sites on FN-III10 are mainly located at the RGD loop region, which does not affect the interaction between the fibronectin protein and its cognate receptors on the cell surface.

  16. Molecular cloning and functional analysis of nucleotide-binding oligomerization domain-containing protein 1 in rainbow trout, Oncorhynchus mykiss.

    Science.gov (United States)

    Jang, Ju Hye; Kim, Hyun; Kim, Yu Jin; Cho, Ju Hyun

    2016-04-01

    NOD1 has important roles in innate immunity as sensor of microbial components derived from bacterial peptidoglycan. In this study, we identified genes encoding components of the NOD1 signaling pathway, including NOD1 (OmNOD1) and RIP2 (OmRIP2) from rainbow trout, Oncorhynchus mykiss, and investigated whether OmNOD1 has immunomodulating activity in a rainbow trout hepatoma cell line RTH-149 treated with NOD1-specific ligand (iE-DAP). The deduced amino acid sequence of OmNOD1 contained conserved CARD, NOD and LRR domains. Loss-of-function and gain-of-function experiments indicated that OmNOD1 is involved in the expression of pro-inflammatory cytokines. Silencing of OmNOD1 in RTH-149 cells treated with iE-DAP decreased the expression of IL-1β, IL-6, IL-8 and TNF-α. Conversely, overexpression of OmNOD1 resulted in up-regulation of IL-1β, IL-6, IL-8 and TNF-α expression. In addition, RIP2 inhibitor (gefitinib) significantly decreased the expression of these pro-inflammatory cytokines induced by iE-DAP in RTH-149 cells. These findings highlight the important role of NOD1 signaling pathway in fish in eliciting innate immune response. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Digital processing optical transmission and coherent receiving techniques

    CERN Document Server

    Binh, Le Nguyen

    2013-01-01

    With coherent mixing in the optical domain and processing in the digital domain, advanced receiving techniques employing ultra-high speed sampling rates have progressed tremendously over the last few years. These advances have brought coherent reception systems for lightwave-carried information to the next stage, resulting in ultra-high capacity global internetworking. Digital Processing: Optical Transmission and Coherent Receiving Techniques describes modern coherent receiving techniques for optical transmission and aspects of modern digital optical communications in the most basic lines. The

  18. Molecular dynamics simulation reveals insights into the mechanism of unfolding by the A130T/V mutations within the MID1 zinc-binding Bbox1 domain.

    Directory of Open Access Journals (Sweden)

    Yunjie Zhao

    Full Text Available The zinc-binding Bbox1 domain in protein MID1, a member of the TRIM family of proteins, facilitates the ubiquitination of the catalytic subunit of protein phosphatase 2A and alpha4, a protein regulator of PP2A. The natural mutation of residue A130 to a valine or threonine disrupts substrate recognition and catalysis. While NMR data revealed the A130T mutant Bbox1 domain failed to coordinate both structurally essential zinc ions and resulted in an unfolded structure, the unfolding mechanism is unknown. Principle component analysis revealed that residue A130 served as a hinge point between the structured β-strand-turn-β-strand (β-turn-β and the lasso-like loop sub-structures that constitute loop1 of the ββα-RING fold that the Bbox1 domain adopts. Backbone RMSD data indicate significant flexibility and departure from the native structure within the first 5 ns of the molecular dynamics (MD simulation for the A130V mutant (>6 Å and after 30 ns for A130T mutant (>6 Å. Overall RMSF values were higher for the mutant structures and showed increased flexibility around residues 125 and 155, regions with zinc-coordinating residues. Simulated pKa values of the sulfhydryl group of C142 located near A130 suggested an increased in value to ~9.0, paralleling the increase in the apparent dielectric constants for the small cavity near residue A130. Protonation of the sulfhydryl group would disrupt zinc-coordination, directly contributing to unfolding of the Bbox1. Together, the increased motion of residues of loop 1, which contains four of the six zinc-binding cysteine residues, and the increased pKa of C142 could destabilize the structure of the zinc-coordinating residues and contribute to the unfolding.

  19. Molecular characterization of the 30-AA N-terminal mineral interaction domain of the biomineralization protein AP7.

    Science.gov (United States)

    Kim, Il Won; Morse, Daniel E; Evans, John Spencer

    2004-12-21

    The AP7 protein is one of several mollusk shell proteins which are responsible for aragonite polymorph formation and stabilization within the nacre layer of the Pacific red abalone, H. rufescens. Previously, we demonstrated that the 30-AA N-terminal domain of AP7, denoted as AP7-1, exists as an unfolded sequence and possesses the capability of inhibiting calcium carbonate crystal growth in vitro via growth step frustration or interruption. However, very little is known with regard to the interactive capabilities of this sequence with Ca(II) and with calcium carbonates. Using multidisciplinary techniques, we determine that the AP7-1 polypeptide interacts with Ca(II) ions at the -DD- sequence clusters, yet retains its unfolded, conformationally labile structure in the presence of Ca(II) ions. Further, NMR experiments reveal that the extended structured sequence blocks, -GNGM-, -SVRTQG-, and -ISYL, exhibit motional, chemical exchange, and/or backbone geometry perturbations in response to Ca(II) interactions with AP7-1. Solid-state NMR magic angle spinning studies verify that during the course of in vitro calcium carbonate crystal growth, AP7-1 becomes bound to calcite fragments and cannot be entirely displaced from the mineral fragments using competitive Ca(II) washing. Finally, using a scrambled sequence version of the AP7-1 polypeptide, we observe that sequence scrambling does not adversely affect the crystal growth inhibitory activity of AP7-1, suggesting that the amino acid composition of AP7-1 may be more critical to growth step inhibition than the linear ordering of amino acids.

  20. Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics

    Directory of Open Access Journals (Sweden)

    Thérèse E Malliavin

    2017-06-01

    Full Text Available Although CyaA has been studied for over three decades and revealed itself to be a very good prototype for developing various biotechnological applications, only a little is known about its functional dynamics and about the conformational landscape of this protein. Molecular dynamics simulations helped to clarify the view on these points in the following way. First, the model of interaction between AC and calmodulin (CaM has evolved from an interaction centered on the surface between C-CaM hydrophobic patch and the α helix H of AC, to a more balanced view, in which the C-terminal tail of AC along with the C-CaM Calcium loops play an important role. This role has been confirmed by the reduction of the affinity of AC for calmodulin in the presence of R338, D360 and N347 mutations. In addition, enhanced sampling studies have permitted to propose a representation of the conformational space for the isolated AC. It remains to refine this representation using structural low resolution information measured on the inactive state of AC. Finally, due to a virtual screening study on another adenyl cyclase from Bacillus anthracis, weak inhibitors of AC have been discovered.

  1. Molecular mechanisms of protein-cholesterol interactions in plasma membranes: Functional distinction between topological (tilted) and consensus (CARC/CRAC) domains.

    Science.gov (United States)

    Fantini, Jacques; Di Scala, Coralie; Baier, Carlos J; Barrantes, Francisco J

    2016-09-01

    The molecular mechanisms that control the multiple possible modes of protein association with membrane cholesterol are remarkably convergent. These mechanisms, which include hydrogen bonding, CH-π stacking and dispersion forces, are used by a wide variety of extracellular proteins (e.g. microbial or amyloid) and membrane receptors. Virus fusion peptides penetrate the membrane of host cells with a tilted orientation that is compatible with a transient interaction with cholesterol; this tilted orientation is also characteristic of the process of insertion of amyloid proteins that subsequently form oligomeric pores in the plasma membrane of brain cells. Membrane receptors that are associated with cholesterol generally display linear consensus binding motifs (CARC and CRAC) characterized by a triad of basic (Lys/Arg), aromatic (Tyr/phe) and aliphatic (Leu/Val) amino acid residues. In some cases, the presence of both CARC and CRAC within the same membrane-spanning domain allows the simultaneous binding of two cholesterol molecules, one in each membrane leaflet. In this review the molecular basis and the functional significance of the different modes of protein-cholesterol interactions in plasma membranes are discussed. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. Molecular dynamics simulations of Hsp40 J-domain mutants identifies disruption of the critical HPD-motif as the key factor for impaired curing in vivo of the yeast prion [URE3].

    Science.gov (United States)

    Xue, You-Lin; Wang, Hao; Riedy, Michael; Roberts, Brittany-Lee; Sun, Yuna; Song, Yong-Bo; Jones, Gary W; Masison, Daniel C; Song, Youtao

    2018-05-01

    Genetic screens using Saccharomyces cerevisiae have identified an array of Hsp40 (Ydj1p) J-domain mutants that are impaired in the ability to cure the yeast [URE3] prion through disrupting functional interactions with Hsp70. However, biochemical analysis of some of these Hsp40 J-domain mutants has so far failed to provide major insight into the specific functional changes in Hsp40-Hsp70 interactions. To explore the detailed structural and dynamic properties of the Hsp40 J-domain, 20 ns molecular dynamic simulations of 4 mutants (D9A, D36A, A30T, and F45S) and wild-type J-domain were performed, followed by Hsp70 docking simulations. Results demonstrated that although the Hsp70 interaction mechanism of the mutants may vary, the major structural change was targeted to the critical HPD motif of the J-domain. Our computational analysis fits well with previous yeast genetics studies regarding highlighting the importance of J-domain function in prion propagation. During the molecular dynamics simulations several important residues were identified and predicted to play an essential role in J-domain structure. Among these residues, Y26 and F45 were confirmed, using both in silico and in vivo methods, as being critical for Ydj1p function.

  3. Nanoparticles of [Fe(NH2-trz)3]Br2.3H2O (NH2-trz=2-amino-1,2,4-triazole) prepared by the reverse micelle technique: influence of particle and coherent domain sizes on spin-crossover properties.

    Science.gov (United States)

    Forestier, Thibaut; Kaiba, Abdellah; Pechev, Stanislav; Denux, Dominique; Guionneau, Philippe; Etrillard, Céline; Daro, Nathalie; Freysz, Eric; Létard, Jean-François

    2009-06-15

    This paper describes the synthesis of iron(II) spin-crossover nanoparticles prepared by the reverse micelle technique by using the non-ionic surfactant Lauropal (Ifralan D0205) from the polyoxyethylenic family. By changing the surfactant/water ratio, the size of the particles of [Fe(NH2-trz)3]Br2.3H2O (with NH2trz=4-amino-1,2,4-triazole) can be controlled. On the macroscopic scale this complex exhibits cooperative thermal spin crossovers at 305 and 320 K. We find that when the size is reduced down to 50 nm, the spin transition becomes gradual and no hysteresis can be detected. For our data it seems that the critical size, for which the existence of a thermal hysteresis can be detected, is around 50 nm. Interestingly, the change of the particle size induces almost no change in the temperature of the thermal spin transition. A systematic determination of coherent domain size carried out on the nanoparticles by powder X-ray diffraction indicates that at approximately 30 nm individual particles consist of one coherent domain.

  4. Molecular basis of perinatal hypophosphatasia with tissue-nonspecific alkaline phosphatase bearing a conservative replacement of valine by alanine at position 406. Structural importance of the crown domain.

    Science.gov (United States)

    Numa, Natsuko; Ishida, Yoko; Nasu, Makiko; Sohda, Miwa; Misumi, Yoshio; Noda, Tadashi; Oda, Kimimitsu

    2008-06-01

    Hypophosphatasia, a congenital metabolic disease related to the tissue-nonspecific alkaline phosphatase gene (TNSALP), is characterized by reduced serum alkaline phosphatase levels and defective mineralization of hard tissues. A replacement of valine with alanine at position 406, located in the crown domain of TNSALP, was reported in a perinatal form of hypophosphatasia. To understand the molecular defect of the TNSALP (V406A) molecule, we examined this missense mutant protein in transiently transfected COS-1 cells and in stable CHO-K1 Tet-On cells. Compared with the wild-type enzyme, the mutant protein showed a markedly reduced alkaline phosphatase activity. This was not the result of defective transport and resultant degradation of TNSALP (V406A) in the endoplasmic reticulum, as the majority of newly synthesized TNSALP (V406A) was conveyed to the Golgi apparatus and incorporated into a cold detergent insoluble fraction (raft) at a rate similar to that of the wild-type TNSALP. TNSALP (V406A) consisted of a dimer, as judged by sucrose gradient centrifugation, suggestive of its proper folding and correct assembly, although this mutant showed increased susceptibility to digestion by trypsin or proteinase K. When purified as a glycosylphosphatidylinositol-anchorless soluble form, the mutant protein exhibited a remarkably lower Kcat/Km value compared with that of the wild-type TNSALP. Interestingly, leucine and isoleucine, but not phenylalanine, were able to substitute for valine, pointing to the indispensable role of residues with a longer aliphatic side chain at position 406 of TNSALP. Taken together, this particular mutation highlights the structural importance of the crown domain with respect to the catalytic function of TNSALP.

  5. Molecular mimicry of human tRNALys anti-codon domain by HIV-1 RNA genome facilitates tRNA primer annealing.

    Science.gov (United States)

    Jones, Christopher P; Saadatmand, Jenan; Kleiman, Lawrence; Musier-Forsyth, Karin

    2013-02-01

    The primer for initiating reverse transcription in human immunodeficiency virus type 1 (HIV-1) is tRNA(Lys3). Host cell tRNA(Lys) is selectively packaged into HIV-1 through a specific interaction between the major tRNA(Lys)-binding protein, human lysyl-tRNA synthetase (hLysRS), and the viral proteins Gag and GagPol. Annealing of the tRNA primer onto the complementary primer-binding site (PBS) in viral RNA is mediated by the nucleocapsid domain of Gag. The mechanism by which tRNA(Lys3) is targeted to the PBS and released from hLysRS prior to annealing is unknown. Here, we show that hLysRS specifically binds to a tRNA anti-codon-like element (TLE) in the HIV-1 genome, which mimics the anti-codon loop of tRNA(Lys) and is located proximal to the PBS. Mutation of the U-rich sequence within the TLE attenuates binding of hLysRS in vitro and reduces the amount of annealed tRNA(Lys3) in virions. Thus, LysRS binds specifically to the TLE, which is part of a larger LysRS binding domain in the viral RNA that includes elements of the Psi packaging signal. Our results suggest that HIV-1 uses molecular mimicry of the anti-codon of tRNA(Lys) to increase the efficiency of tRNA(Lys3) annealing to viral RNA.

  6. Coherent Raman scattering: Applications in imaging and sensing

    Science.gov (United States)

    Cui, Meng

    In this thesis, I discuss the theory, implementation and applications of coherent Raman scattering to imaging and sensing. A time domain interferometric method has been developed to collect high resolution shot-noise-limited Raman spectra over the Raman fingerprint regime and completely remove the electronic background signal in coherent Raman scattering. Compared with other existing coherent Raman microscopy methods, this time domain approach is proved to be simpler and more robust in rejecting background signal. We apply this method to image polymers and biological samples and demonstrate that the same setup can be used to collect two photon fluorescence and self phase modulation signals. A signal to noise ratio analysis is performed to show that this time domain method has a comparable signal to noise ratio to spectral domain methods, which we confirm experimentally. The coherent Raman method is also compared with spontaneous Raman scattering. The conditions under which coherent methods provide signal enhancement are discussed and experiments are performed to compare coherent Raman scattering with spontaneous Raman scattering under typical biological imaging conditions. A critical power, above which coherent Raman scattering is more sensitive than spontaneous Raman scattering, is experimentally determined to be ˜1mW in samples of high molecule concentration with a 75MHz laser system. This finding is contrary to claims that coherent methods provide many orders of magnitude enhancement under comparable conditions. In addition to the far field applications, I also discuss the combination of our time domain coherent Raman method with near field enhancement to explore the possibility of sensing and near field imaging. We report the first direct time-resolved coherent Raman measurement performed on a nanostructured substrate for molecule sensing. The preliminary results demonstrate that sub 20 fs pulses can be used to obtain coherent Raman spectra from a small number

  7. Cohering power of quantum operations

    Energy Technology Data Exchange (ETDEWEB)

    Bu, Kaifeng, E-mail: bkf@zju.edu.cn [School of Mathematical Sciences, Zhejiang University, Hangzhou 310027 (China); Kumar, Asutosh, E-mail: asukumar@hri.res.in [Harish-Chandra Research Institute, Chhatnag Road, Jhunsi, Allahabad 211019 (India); Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094 (India); Zhang, Lin, E-mail: linyz@zju.edu.cn [Institute of Mathematics, Hangzhou Dianzi University, Hangzhou 310018 (China); Wu, Junde, E-mail: wjd@zju.edu.cn [School of Mathematical Sciences, Zhejiang University, Hangzhou 310027 (China)

    2017-05-18

    Highlights: • Quantum coherence. • Cohering power: production of quantum coherence by quantum operations. • Study of cohering power and generalized cohering power, and their comparison for differentmeasures of quantum coherence. • Operational interpretation of cohering power. • Bound on cohering power of a generic quantum operation. - Abstract: Quantum coherence and entanglement, which play a crucial role in quantum information processing tasks, are usually fragile under decoherence. Therefore, the production of quantum coherence by quantum operations is important to preserve quantum correlations including entanglement. In this paper, we study cohering power–the ability of quantum operations to produce coherence. First, we provide an operational interpretation of cohering power. Then, we decompose a generic quantum operation into three basic operations, namely, unitary, appending and dismissal operations, and show that the cohering power of any quantum operation is upper bounded by the corresponding unitary operation. Furthermore, we compare cohering power and generalized cohering power of quantum operations for different measures of coherence.

  8. Image Inpainting Based on Coherence Transport with Adapted Distance Functions

    KAUST Repository

    Mä rz, Thomas

    2011-01-01

    We discuss an extension of our method image inpainting based on coherence transport. For the latter method the pixels of the inpainting domain have to be serialized into an ordered list. Until now, to induce the serialization we have used

  9. Partially coherent imaging and spatial coherence wavelets

    International Nuclear Information System (INIS)

    Castaneda, Roman

    2003-03-01

    A description of spatially partially coherent imaging based on the propagation of second order spatial coherence wavelets and marginal power spectra (Wigner distribution functions) is presented. In this dynamics, the spatial coherence wavelets will be affected by the system through its elementary transfer function. The consistency of the model with the both extreme cases of full coherent and incoherent imaging was proved. In the last case we obtained the classical concept of optical transfer function as a simple integral of the elementary transfer function. Furthermore, the elementary incoherent response function was introduced as the Fourier transform of the elementary transfer function. It describes the propagation of spatial coherence wavelets form each object point to each image point through a specific point on the pupil planes. The point spread function of the system was obtained by a simple integral of the elementary incoherent response function. (author)

  10. Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

    Science.gov (United States)

    Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

    2018-03-22

    Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

  11. Quantum superchemistry in an output coupler of coherent matter waves

    International Nuclear Information System (INIS)

    Jing, H.; Cheng, J.

    2006-01-01

    We investigate the quantum superchemistry or Bose-enhanced atom-molecule conversions in a coherent output coupler of matter waves, as a simple generalization of the two-color photoassociation. The stimulated effects of molecular output step and atomic revivals are exhibited by steering the rf output couplings. The quantum noise-induced molecular damping occurs near a total conversion in a levitation trap. This suggests a feasible two-trap scheme to make a stable coherent molecular beam

  12. On Longitudinal Spectral Coherence

    DEFF Research Database (Denmark)

    Kristensen, Leif

    1979-01-01

    It is demonstrated that the longitudinal spectral coherence differs significantly from the transversal spectral coherence in its dependence on displacement and frequency. An expression for the longitudinal coherence is derived and it is shown how the scale of turbulence, the displacement between ...... observation sites and the turbulence intensity influence the results. The limitations of the theory are discussed....

  13. Reflective type objective based spectral-domain phase-sensitive optical coherence tomography for high-sensitive structural and functional imaging of cochlear microstructures through intact bone of an excised guinea pig cochlea

    Science.gov (United States)

    Subhash, Hrebesh M.; Wang, Ruikang K.; Chen, Fangyi; Nuttall, Alfred L.

    2013-03-01

    Most of the optical coherence tomographic (OCT) systems for high resolution imaging of biological specimens are based on refractive type microscope objectives, which are optimized for specific wave length of the optical source. In this study, we present the feasibility of using commercially available reflective type objective for high sensitive and high resolution structural and functional imaging of cochlear microstructures of an excised guinea pig through intact temporal bone. Unlike conventional refractive type microscopic objective, reflective objective are free from chromatic aberrations due to their all-reflecting nature and can support a broadband of spectrum with very high light collection efficiency.

  14. Molecular characterization of the haptoglobin.hemoglobin receptor CD163. Ligand binding properties of the scavenger receptor cysteine-rich domain region

    DEFF Research Database (Denmark)

    Madsen, Mette; Møller, Holger J; Nielsen, Marianne Jensby

    2004-01-01

    binding to SRCR domain 3 exhibited effective inhibition of ligand binding. Furthermore, analysis of purified native CD163 revealed that proteolytic cleavage in SRCR domain 3 inactivates ligand binding. Calcium protects against cleavage in this domain. Analysis of the calcium sensitivity of ligand binding...... to CD163 demonstrated that optimal ligand binding requires physiological plasma calcium concentrations, and an immediate ligand release occurs at the low calcium concentrations measured in acidifying endosomes. In conclusion, SRCR domain 3 of CD163 is an exposed domain and a critical determinant...... for the calcium-sensitive coupling of haptoglobin.hemoglobin complexes....

  15. Domain analysis

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

    The domain-analytic approach to knowledge organization (KO) (and to the broader field of library and information science, LIS) is outlined. The article reviews the discussions and proposals on the definition of domains, and provides an example of a domain-analytic study in the field of art studies....... Varieties of domain analysis as well as criticism and controversies are presented and discussed....

  16. Solution Structure of the N-Terminal Domain of Mediator Subunit MED26 and Molecular Characterization of Its Interaction with EAF1 and TAF7.

    Science.gov (United States)

    Lens, Zoé; Cantrelle, François-Xavier; Peruzzini, Riccardo; Hanoulle, Xavier; Dewitte, Frédérique; Ferreira, Elisabeth; Baert, Jean-Luc; Monté, Didier; Aumercier, Marc; Villeret, Vincent; Verger, Alexis; Landrieu, Isabelle

    2017-10-13

    MED26 is a subunit of Mediator, a large complex central to the regulation of gene transcription by RNA Polymerase II. MED26 plays a role in the switch between the initiation and elongation phases of RNA Polymerase II-mediated transcription process. Regulation of these steps requires successive binding of MED26 N-terminal domain (NTD) to TATA-binding protein-associated factor 7 (TAF7) and Eleven-nineteen lysine-rich in leukemia-Associated Factor 1 (EAF1). In order to investigate the mechanism of regulation by MED26, MED26-NTD structure was solved by NMR, revealing a 4-helix bundle. EAF1 (239-268) and TAF7 (205-235) peptide interactions were both mapped to the same groove formed by H3 and H4 helices of MED26-NTD. Both interactions are characterized by dissociation constants in the 10-μM range. Further experiments revealed a folding-upon-binding mechanism that leads to the formation of EAF1 (N247-S260) and TAF7 (L214-S227) helices. Chemical shift perturbations and nuclear Overhauser enhancement contacts support the involvement of residues I222/F223 in anchoring TAF7 helix to a hydrophobic pocket of MED26-NTD, including residues L48, W80 and I84. In addition, Ala mutations of charged residues located in the C-terminal disordered part of TAF7 and EAF1 peptides affected the binding, with a loss of affinity characterized by a 10-time increase of dissociation constants. A structural model of MED26-NTD/TAF7 complex shows bi-partite components, combining ordered and disordered segments, as well as hydrophobic and electrostatic contributions to the binding. This study provides molecular detail that will help to decipher the mechanistic basis for the initiation to elongation switch-function mediated by MED26-NTD. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Haruki Nakamura

    2012-02-01

    Full Text Available The phosphorylated kinase-inducible activation domain (pKID adopts a helix–loop–helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, αA and αB. We performed all-atom multicanonical molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensembles. Although the unbound pKID was disordered overall, αA and αB exhibited a nascent helix propensity; the propensity of αA was stronger than that of αB, which agrees with experimental results. In the bound state, the free-energy landscape of αB involved two low free-energy fractions: native-like and non-native fractions. This result suggests that αB folds according to the induced-fit mechanism. The αB-helix direction was well aligned as in the NMR complex structure, although the αA helix exhibited high flexibility. These results also agree quantitatively with experimental observations. We have detected that the αB helix can bind to another site of KIX, to which another protein MLL also binds with the adopting helix. Consequently, MLL can facilitate pKID binding to the pKID-binding site by blocking the MLL-binding site. This also supports experimentally obtained results.

  18. Molecular basis of calcium-sensitizing and desensitizing mutations of the human cardiac troponin C regulatory domain: a multi-scale simulation study.

    Directory of Open Access Journals (Sweden)

    Peter Michael Kekenes-Huskey

    Full Text Available Troponin C (TnC is implicated in the initiation of myocyte contraction via binding of cytosolic Ca²⁺ and subsequent recognition of the Troponin I switch peptide. Mutations of the cardiac TnC N-terminal regulatory domain have been shown to alter both calcium binding and myofilament force generation. We have performed molecular dynamics simulations of engineered TnC variants that increase or decrease Ca²⁺ sensitivity, in order to understand the structural basis of their impact on TnC function. We will use the distinction for mutants that are associated with increased Ca²⁺ affinity and for those mutants with reduced affinity. Our studies demonstrate that for GOF mutants V44Q and L48Q, the structure of the physiologically-active site II Ca²⁺ binding site in the Ca²⁺-free (apo state closely resembled the Ca²⁺-bound (holo state. In contrast, site II is very labile for LOF mutants E40A and V79Q in the apo form and bears little resemblance with the holo conformation. We hypothesize that these phenomena contribute to the increased association rate, k(on, for the GOF mutants relative to LOF. Furthermore, we observe significant positive and negative positional correlations between helices in the GOF holo mutants that are not found in the LOF mutants. We anticipate these correlations may contribute either directly to Ca²⁺ affinity or indirectly through TnI association. Our observations based on the structure and dynamics of mutant TnC provide rationale for binding trends observed in GOF and LOF mutants and will guide the development of inotropic drugs that target TnC.

  19. Quantum Mechanical Calculations of Vibrational Sum-Frequency-Generation (SFG) Spectra of Cellulose: Dependence of the CH and OH Peak Intensity on the Polarity of Cellulose Chains within the SFG Coherence Domain.

    Science.gov (United States)

    Lee, Christopher M; Chen, Xing; Weiss, Philip A; Jensen, Lasse; Kim, Seong H

    2017-01-05

    Vibrational sum-frequency-generation (SFG) spectroscopy is capable of selectively detecting crystalline biopolymers interspersed in amorphous polymer matrices. However, the spectral interpretation is difficult due to the lack of knowledge on how spatial arrangements of crystalline segments influence SFG spectra features. Here we report time-dependent density functional theory (TD-DFT) calculations of cellulose crystallites in intimate contact with two different polarities: parallel versus antiparallel. TD-DFT calculations reveal that the CH/OH intensity ratio is very sensitive to the polarity of the crystallite packing. Theoretical calculations of hyperpolarizability tensors (β abc ) clearly show the dependence of SFG intensities on the polarity of crystallite packing within the SFG coherence length, which provides the basis for interpretation of the empirically observed SFG features of native cellulose in biological systems.

  20. Ligand binding by PDZ domains

    DEFF Research Database (Denmark)

    Chi, Celestine N.; Bach, Anders; Strømgaard, Kristian

    2012-01-01

    , for example, are particularly rich in these domains. The general function of PDZ domains is to bring proteins together within the appropriate cellular compartment, thereby facilitating scaffolding, signaling, and trafficking events. The many functions of PDZ domains under normal physiological as well...... as pathological conditions have been reviewed recently. In this review, we focus on the molecular details of how PDZ domains bind their protein ligands and their potential as drug targets in this context....

  1. Concrete domains

    OpenAIRE

    Kahn, G.; Plotkin, G.D.

    1993-01-01

    This paper introduces the theory of a particular kind of computation domains called concrete domains. The purpose of this theory is to find a satisfactory framework for the notions of coroutine computation and sequentiality of evaluation.

  2. Domain Engineering

    Science.gov (United States)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  3. New class of uncertainty relations for partially coherent light

    NARCIS (Netherlands)

    Bastiaans, M.J.

    1984-01-01

    A class of uncertainty relations for partially coherent light is derived; the uncertainty relations in this class express the fact that the product of the effective widths of the space-domain intensity and the spatial-frequency-domain intensity of the light has a lower bound and that this lower

  4. Reproducing Kernels and Coherent States on Julia Sets

    Energy Technology Data Exchange (ETDEWEB)

    Thirulogasanthar, K., E-mail: santhar@cs.concordia.ca; Krzyzak, A. [Concordia University, Department of Computer Science and Software Engineering (Canada)], E-mail: krzyzak@cs.concordia.ca; Honnouvo, G. [Concordia University, Department of Mathematics and Statistics (Canada)], E-mail: g_honnouvo@yahoo.fr

    2007-11-15

    We construct classes of coherent states on domains arising from dynamical systems. An orthonormal family of vectors associated to the generating transformation of a Julia set is found as a family of square integrable vectors, and, thereby, reproducing kernels and reproducing kernel Hilbert spaces are associated to Julia sets. We also present analogous results on domains arising from iterated function systems.

  5. Reproducing Kernels and Coherent States on Julia Sets

    International Nuclear Information System (INIS)

    Thirulogasanthar, K.; Krzyzak, A.; Honnouvo, G.

    2007-01-01

    We construct classes of coherent states on domains arising from dynamical systems. An orthonormal family of vectors associated to the generating transformation of a Julia set is found as a family of square integrable vectors, and, thereby, reproducing kernels and reproducing kernel Hilbert spaces are associated to Julia sets. We also present analogous results on domains arising from iterated function systems

  6. Coherent scattering of electromagnetic radiation by a polarized particle system

    International Nuclear Information System (INIS)

    Agre, M.Ya.; Rapoport, L.P.

    1996-01-01

    The paper deals with the development of the theory of coherent scattering of electromagnetic waves by a polarized atom or molecular system. Peculiarities of the angular distribution and polarization peculiarities of scattered radiation are discussed

  7. Text Coherence in Translation

    Science.gov (United States)

    Zheng, Yanping

    2009-01-01

    In the thesis a coherent text is defined as a continuity of senses of the outcome of combining concepts and relations into a network composed of knowledge space centered around main topics. And the author maintains that in order to obtain the coherence of a target language text from a source text during the process of translation, a translator can…

  8. Coherent Multistatic ISAR Imaging

    NARCIS (Netherlands)

    Dorp, Ph. van; Otten, M.P.G.; Verzeilberg, J.M.M.

    2012-01-01

    This paper presents methods for Coherent Multistatic Radar Imaging for Non Cooperative Target Recognition (NCTR) with a network of radar sensors. Coherent Multistatic Radar Imaging is based on an extension of existing monostatic ISAR algorithms to the multistatic environment. The paper describes the

  9. VCSEL Based Coherent PONs

    DEFF Research Database (Denmark)

    Jensen, Jesper Bevensee; Rodes, Roberto; Caballero Jambrina, Antonio

    2014-01-01

    We present a review of research performed in the area of coherent access technologies employing vertical cavity surface emitting lasers (VCSELs). Experimental demonstrations of optical transmission over a passive fiber link with coherent detection using VCSEL local oscillators and directly modula...

  10. Cellulose binding domain proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  11. Scalable coherent interface

    International Nuclear Information System (INIS)

    Alnaes, K.; Kristiansen, E.H.; Gustavson, D.B.; James, D.V.

    1990-01-01

    The Scalable Coherent Interface (IEEE P1596) is establishing an interface standard for very high performance multiprocessors, supporting a cache-coherent-memory model scalable to systems with up to 64K nodes. This Scalable Coherent Interface (SCI) will supply a peak bandwidth per node of 1 GigaByte/second. The SCI standard should facilitate assembly of processor, memory, I/O and bus bridge cards from multiple vendors into massively parallel systems with throughput far above what is possible today. The SCI standard encompasses two levels of interface, a physical level and a logical level. The physical level specifies electrical, mechanical and thermal characteristics of connectors and cards that meet the standard. The logical level describes the address space, data transfer protocols, cache coherence mechanisms, synchronization primitives and error recovery. In this paper we address logical level issues such as packet formats, packet transmission, transaction handshake, flow control, and cache coherence. 11 refs., 10 figs

  12. Molecular characterization of the haptoglobin.hemoglobin receptor CD163. Ligand binding properties of the scavenger receptor cysteine-rich domain region

    DEFF Research Database (Denmark)

    Madsen, Mette; Møller, Holger J; Nielsen, Marianne Jensby

    2004-01-01

    CD163 is the macrophage receptor for endocytosis of haptoglobin.hemoglobin complexes. The extracellular region consisting of nine scavenger receptor cysteine rich (SRCR) domains also circulates in plasma as a soluble protein. By ligand binding analysis of a broad spectrum of soluble CD163...... truncation variants, the amino-terminal third of the SRCR region was shown to be crucial for the binding of haptoglobin.hemoglobin complexes. By Western blotting of the CD163 variants, a panel of ten monoclonal antibodies was mapped to SRCR domains 1, 3, 4, 6, 7, and 9, respectively. Only the two antibodies...... to CD163 demonstrated that optimal ligand binding requires physiological plasma calcium concentrations, and an immediate ligand release occurs at the low calcium concentrations measured in acidifying endosomes. In conclusion, SRCR domain 3 of CD163 is an exposed domain and a critical determinant...

  13. Measuring coherence with entanglement concurrence

    Science.gov (United States)

    Qi, Xianfei; Gao, Ting; Yan, Fengli

    2017-07-01

    Quantum coherence is a fundamental manifestation of the quantum superposition principle. Recently, Baumgratz et al (2014 Phys. Rev. Lett. 113 140401) presented a rigorous framework to quantify coherence from the view of theory of physical resource. Here we propose a new valid quantum coherence measure which is a convex roof measure, for a quantum system of arbitrary dimension, essentially using the generalized Gell-Mann matrices. Rigorous proof shows that the proposed coherence measure, coherence concurrence, fulfills all the requirements dictated by the resource theory of quantum coherence measures. Moreover, strong links between the resource frameworks of coherence concurrence and entanglement concurrence is derived, which shows that any degree of coherence with respect to some reference basis can be converted to entanglement via incoherent operations. Our work provides a clear quantitative and operational connection between coherence and entanglement based on two kinds of concurrence. This new coherence measure, coherence concurrence, may also be beneficial to the study of quantum coherence.

  14. Energy and Information Transfer Via Coherent Exciton Wave Packets

    Science.gov (United States)

    Zang, Xiaoning

    associated excitations were dubbed twisted excitons. Twisted exciton packets can be manipulated as they travel down molecular chains, and this has applications in quantum information science as well. In each setting considered, exciton dynamics were initially studied using a simple tight-binding formalism. This misses the actual many-body interactions and multiple energy levels associated real systems. To remedy this, I adapted an existing time-domain Density Functional Theory code and applied it to study the dynamics of exciton wave packets on quasi-one-dimensional systems. This required the use of high-performance computing and the construction of a number of key auxiliary codes. Establishing the requisite methodology constituted a substantial part of the entire thesis. Surprisingly, this effort uncovered a computational issue associated with Rabi oscillations that had been incorrectly characterized in the literature. My research elucidated the actual problem and a solution was found. This new methodology was an integral part of the overall computational analysis. The thesis then takes up the a detailed consideration of the prospect for creating systems that support a strong measure of transport coherence. While physical implementations include molecular assemblies, solid-state superlattices, and even optical lattices, I decided to focus on assemblies of nanometer-sized silicon quantum dots. First principles computational analysis was used to quantify reorganization within individual dots and excitonic coupling between dots. Quantum dot functionalizations were identified that make it plausible to maintain a measure of excitonic coherence even at room temperatures. Attention was then turned to the use of covalently bonded bridge material to join quantum dots in a way that facilitates efficient exciton transfer. Both carbon and silicon structures were considered by considering the way in which subunits might be best brought together. This resulted in a set of design criteria

  15. Molecular determinants of interactions between the N-terminal domain and the transmembrane core that modulate hERG K+ channel gating.

    Directory of Open Access Journals (Sweden)

    Jorge Fernández-Trillo

    Full Text Available A conserved eag domain in the cytoplasmic amino terminus of the human ether-a-go-go-related gene (hERG potassium channel is critical for its slow deactivation gating. Introduction of gene fragments encoding the eag domain are able to restore normal deactivation properties of channels from which most of the amino terminus has been deleted, and also those lacking exclusively the eag domain or carrying a single point mutation in the initial residues of the N-terminus. Deactivation slowing in the presence of the recombinant domain is not observed with channels carrying a specific Y542C point mutation in the S4-S5 linker. On the other hand, mutations in some initial positions of the recombinant fragment also impair its ability to restore normal deactivation. Fluorescence resonance energy transfer (FRET analysis of fluorophore-tagged proteins under total internal reflection fluorescence (TIRF conditions revealed a substantial level of FRET between the introduced N-terminal eag fragments and the eag domain-deleted channels expressed at the membrane, but not between the recombinant eag domain and full-length channels with an intact amino terminus. The FRET signals were also minimized when the recombinant eag fragments carried single point mutations in the initial portion of their amino end, and when Y542C mutated channels were used. These data suggest that the restoration of normal deactivation gating by the N-terminal recombinant eag fragment is an intrinsic effect of this domain directed by the interaction of its N-terminal segment with the gating machinery, likely at the level of the S4-S5 linker.

  16. Coherent Bichromatic Force Deflection of Molecules

    Science.gov (United States)

    Kozyryev, Ivan; Baum, Louis; Aldridge, Leland; Yu, Phelan; Eyler, Edward E.; Doyle, John M.

    2018-02-01

    We demonstrate the effect of the coherent optical bichromatic force on a molecule, the polar free radical strontium monohydroxide (SrOH). A dual-frequency retroreflected laser beam addressing the X˜2Σ+↔A˜2Π1 /2 electronic transition coherently imparts momentum onto a cryogenic beam of SrOH. This directional photon exchange creates a bichromatic force that transversely deflects the molecules. By adjusting the relative phase between the forward and counterpropagating laser beams we reverse the direction of the applied force. A momentum transfer of 70 ℏk is achieved with minimal loss of molecules to dark states. Modeling of the bichromatic force is performed via direct numerical solution of the time-dependent density matrix and is compared with experimental observations. Our results open the door to further coherent manipulation of molecular motion, including the efficient optical deceleration of diatomic and polyatomic molecules with complex level structures.

  17. Intracoronary optical coherence tomography

    DEFF Research Database (Denmark)

    Tenekecioglu, Erhan; Albuquerque, Felipe N; Sotomi, Yohei

    2017-01-01

    By providing valuable information about the coronary artery wall and lumen, intravascular imaging may aid in optimizing interventional procedure results and thereby could improve clinical outcomes following percutaneous coronary intervention (PCI). Intravascular optical coherence tomography (OCT...

  18. Coherence in Industrial Transformation

    DEFF Research Database (Denmark)

    Jørgensen, Ulrik; Lauridsen, Erik Hagelskjær

    2003-01-01

    The notion of coherence is used to illustrate the general finding, that the impact of environmental management systems and environmental policy is highly dependent of the context and interrelatedness of the systems, procedures and regimes established in society....

  19. Optical Coherence Tomography

    DEFF Research Database (Denmark)

    Fercher, A.F.; Andersen, Peter E.

    2017-01-01

    Optical coherence tomography (OCT) is a technique that is used to peer inside a body noninvasively. Tissue structure defined by tissue absorption and scattering coefficients, and the speed of blood flow, are derived from the characteristics of light remitted by the body. Singly backscattered light...... detected by partial coherence interferometry (PCI) is used to synthesize the tomographic image coded in false colors. A prerequisite of this technique is a low time-coherent but high space-coherent light source, for example, a superluminescent diode or a supercontinuum source. Alternatively, the imaging...... technique can be realized by using ultrafast wavelength scanning light sources. For tissue imaging, the light source wavelengths are restricted to the red and near-infrared (NIR) region from about 600 to 1300 nm, the so-called therapeutic window, where absorption (μa ≈ 0.01 mm−1) is small enough. Transverse...

  20. Coherent imaging at FLASH

    International Nuclear Information System (INIS)

    Chapman, H N; Bajt, S; Duesterer, S; Treusch, R; Barty, A; Benner, W H; Bogan, M J; Frank, M; Hau-Riege, S P; Woods, B W; Boutet, S; Cavalleri, A; Hajdu, J; Iwan, B; Seibert, M M; Timneanu, N; Marchesini, S; Sakdinawat, A; Sokolowski-Tinten, K

    2009-01-01

    We have carried out high-resolution single-pulse coherent diffractive imaging at the FLASH free-electron laser. The intense focused FEL pulse gives a high-resolution low-noise coherent diffraction pattern of an object before that object turns into a plasma and explodes. In particular we are developing imaging of biological specimens beyond conventional radiation damage resolution limits, developing imaging of ultrafast processes, and testing methods to characterize and perform single-particle imaging.