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Karthikeyan R, Ganesh V, Berchmans S. Bio-electrocatalysis of Acetobacter aceti through direct electron transfer using a template deposited nickel anode. Catal Sci Technol 2012. [DOI: 10.1039/c2cy20022h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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77
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Ganesh V, Latha Maheswari D, Berchmans S. Electrochemical behaviour of metal hexacyanoferrate converted to metal hydroxide films immobilized on indium tin oxide electrodes—Catalytic ability towards alcohol oxidation in alkaline medium. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2010.11.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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78
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Rahalkar AP, Yeole SD, Ganesh V, Gadre SR. Molecular Tailoring: An Art of the Possible for Ab Initio Treatment of Large Molecules and Molecular Clusters. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2011. [DOI: 10.1007/978-90-481-2853-2_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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79
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Ganesh V, Lakshminarayanan V. Microemulsion phase as a medium for electrodeposition of nickel and electron-transfer study of ferrocyanide–ferricyanide redox system. J Colloid Interface Sci 2010; 349:300-6. [DOI: 10.1016/j.jcis.2010.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 04/30/2010] [Accepted: 05/02/2010] [Indexed: 11/29/2022]
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80
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Hoey ETD, Agrawal SKB, Ganesh V, Gopalan D, Screaton NJ. Dual energy CT pulmonary angiography: findings in a patient with chronic thromboembolic pulmonary hypertension. Thorax 2009; 64:1012. [DOI: 10.1136/thx.2008.112128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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81
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Hoey ETD, Gopalan D, Ganesh V, Agrawal SKB, Screaton NJ. Atrial septal defects: Magnetic resonance and computed tomography appearances. J Med Imaging Radiat Oncol 2009; 53:261-70. [DOI: 10.1111/j.1754-9485.2009.02079.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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82
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Shekar PVR, Nagaraju D, Ganesh V, Rao KK. Microhardness studies on as-grown (111) faces of some alkaline earth nitrates. CRYSTAL RESEARCH AND TECHNOLOGY 2009. [DOI: 10.1002/crat.200800516] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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83
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Kavathekar R, Khire S, Ganesh V, Rahalkar AP, Gadre SR. WebMTA: A web-interface forab initiogeometry optimization of large molecules using molecular tailoring approach. J Comput Chem 2009; 30:1167-73. [DOI: 10.1002/jcc.21132] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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84
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Hoey E, Gopalan D, Ganesh V, Agrawal S, Qureshi N, Tasker A, Clements L, Screaton N. Dual-energy CT pulmonary angiography: a novel technique for assessing acute and chronic pulmonary thromboembolism. Clin Radiol 2009; 64:414-9. [DOI: 10.1016/j.crad.2008.11.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 11/13/2008] [Accepted: 11/23/2008] [Indexed: 10/21/2022]
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Ganesh V, Hoey ETD, Gopalan D. Pulmonary artery sling: an unexpected finding on cardiac multidetector CT. Postgrad Med J 2009; 85:128. [DOI: 10.1136/pgmj.2008.076414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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87
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Ganesh V. MeTA studio: a cross platform, programmable IDE for computational chemist. J Comput Chem 2009; 30:661-72. [PMID: 18711720 DOI: 10.1002/jcc.21088] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The development of a cross-platform, programmable integrated development environment (IDE), MeTA Studio, specifically tailored but not restricted to computational chemists working in the area of quantum chemistry with an emphasis on handling large molecules is presented. The IDE consists of a number of modules which include a visualizer and a programming and collaborative framework. The inbuilt viewer assists in visualizing molecules, their scalar fields, manually fragmenting a molecule, and introduces some innovative but simple techniques for handling large molecules. These include a simple Find language and simultaneous multiple camera views of the molecule. Basic tools needed to handle collaborative computing effectively are also included opening up new vistas for sharing ideas and information among computational chemists working on similar problems. MeTA Studio is an integrated programming environment that provides a rich set of application programming interfaces (APIs) which can be used to easily extend its functionality or build new applications as needed by the users. (http://code.google.com/p/metastudio/).
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Rahalkar AP, Ganesh V, Gadre SR. Enabling ab initio Hessian and frequency calculations of large molecules. J Chem Phys 2009; 129:234101. [PMID: 19102520 DOI: 10.1063/1.2978387] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A linear scaling method, termed as cardinality guided molecular tailoring approach, is applied for the estimation of the Hessian matrix and frequency calculations of spatially extended molecules. The method is put to test on a number of molecular systems largely employing the Hartree-Fock and density functional theory for a variety of basis sets. To demonstrate its ability for correlated methods, we have also performed a few test calculations at the Moller-Plesset second order perturbation theory. A comparison of central processing unit and memory requirements for medium-sized systems with those for the corresponding full ab initio computation reveals substantial gains with negligible loss of accuracy. The technique is further employed for a set of larger molecules, Hessian and frequency calculations of which are not possible on commonly available personal-computer-type hardware.
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Ganesh V, Bodewits K, Bartholdson S, Natale D, Campopiano D, Mareque-Rivas J. Effective Binding and Sensing of Lipopolysaccharide: Combining Complementary Pattern Recognition Receptors. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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90
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Ganesh V, Bodewits K, Bartholdson S, Natale D, Campopiano D, Mareque-Rivas J. Effective Binding and Sensing of Lipopolysaccharide: Combining Complementary Pattern Recognition Receptors. Angew Chem Int Ed Engl 2009; 48:356-60. [DOI: 10.1002/anie.200804168] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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91
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Ganesh V, Pandey RR, Malhotra B, Lakshminarayanan V. Electrochemical characterization of self-assembled monolayers (SAMs) of thiophenol and aminothiophenols on polycrystalline Au: Effects of potential cycling and mixed SAM formation. J Electroanal Chem (Lausanne) 2008. [DOI: 10.1016/j.jelechem.2008.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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92
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Ganesh V, Kavathekar R, Rahalkar A, Gadre SR. WebProp: Web interface for ab initio calculation of molecular one-electron properties. J Comput Chem 2008; 29:488-95. [PMID: 17654647 DOI: 10.1002/jcc.20802] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This note describes the features and implementation issues of WebProp, a web-based interface for evaluating ab initio quality one-electron properties. The interface code is written in HTML and Python, while the backend is handled using Python and our indigenously developed code INDPROP for property evaluation. A novel feature of this setup is that it provides a simple interface for computing first principle one-electron properties of small to medium sized molecules. To facilitate computation of otherwise expensive calculations on large molecular systems, we employ the Molecular Tailoring Approach (MTA) developed in our laboratory to obtain the density matrix (DM). This DM is then employed for computing the one-electron properties of these systems. The backend transparently handles jobs submitted by the user and runs them either on a single machine or over a grid of compute nodes. The results of the calculations, which include the summary and the files necessary for visualization of one-electron properties, are e-mailed to the user. The user can either directly use the data or visualize it using visualization tools such as UNIVIS-2000 or Drishti.
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Ganesh V, Dongare RK, Balanarayan P, Gadre SR. Molecular tailoring approach for geometry optimization of large molecules: energy evaluation and parallelization strategies. J Chem Phys 2007; 125:104109. [PMID: 16999517 DOI: 10.1063/1.2339019] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A linear-scaling scheme for estimating the electronic energy, gradients, and Hessian of a large molecule at ab initio level of theory based on fragment set cardinality is presented. With this proposition, a general, cardinality-guided molecular tailoring approach (CG-MTA) for ab initio geometry optimization of large molecules is implemented. The method employs energy gradients extracted from fragment wave functions, enabling computations otherwise impractical on PC hardware. Further, the method is readily amenable to large scale coarse-grain parallelization with minimal communication among nodes, resulting in a near-linear speedup. CG-MTA is applied for density-functional-theory-based geometry optimization of a variety of molecules including alpha-tocopherol, taxol, gamma-cyclodextrin, and two conformations of polyglycine. In the tests performed, energy and gradient estimates obtained from CG-MTA during optimization runs show an excellent agreement with those obtained from actual computation. Accuracy of the Hessian obtained employing CG-MTA provides good hope for the application of Hessian-based geometry optimization to large molecules.
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Ganesh V, Pal SK, Kumar S, Lakshminarayanan V. Self-assembled monolayers (SAMs) of alkoxycyanobiphenyl thiols on gold surface using a lyotropic liquid crystalline medium. Electrochim Acta 2007. [DOI: 10.1016/j.electacta.2006.09.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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95
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Ganesh V, Calatayud Sanz MP, Mareque-Rivas JC. Effective anion sensing based on the ability of copper to affect electron transport across self-assembled monolayers. Chem Commun (Camb) 2007:5010-2. [DOI: 10.1039/b712857f] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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96
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Ganesh V, Calatayud Sanz MP, Mareque-Rivas JC. Metal-mediated transport of electrons across molecular films. Chem Commun (Camb) 2007:804-6. [PMID: 17308637 DOI: 10.1039/b612676f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron transfer (ET) to a redox probe in solution across the self-assembled monolayers (SAMs) of a tris-(2-pyridylmethyl)amine-based ligand on gold electrodes is greatly enhanced by Cu-binding.
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Ganesh V, Pal SK, Kumar S, Lakshminarayanan V. Self-assembled monolayers (SAMs) of alkoxycyanobiphenyl thiols on gold—A study of electron transfer reaction using cyclic voltammetry and electrochemical impedance spectroscopy. J Colloid Interface Sci 2006; 296:195-203. [PMID: 16209874 DOI: 10.1016/j.jcis.2005.08.051] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Revised: 08/24/2005] [Accepted: 08/24/2005] [Indexed: 10/25/2022]
Abstract
Self-assembled monolayers (SAMs) of liquid crystalline thiol-terminated alkoxycyanobiphenyl molecules with different alkyl chain lengths on Au surface have been studied for the first time using electrochemical techniques such as cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The barrier property of the SAM-modified surfaces was evaluated using two different redox probes, namely potassium ferro/ferri cyanide and hexaammineruthenium(III) chloride. It was found that for short-length alkyl chain thiol (C5) the electron transfer reaction of hexaammineruthenium(III) chloride takes place through tunneling mechanism. In contrast, redox reaction of potassium ferro/ferri cyanide is almost completely blocked by the SAM-modified Au surface. From the impedance data, a surface coverage value of >99.9% was calculated for all the thiol molecules.
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Ganesh V, Lakshminarayanan V. Self-assembled monolayers of alkanethiols on gold prepared in a hexagonal lyotropic liquid crystalline phase of Triton X-100/water system. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:1561-70. [PMID: 16460075 DOI: 10.1021/la0519296] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In this paper, we have reported a new method of preparing self-assembled monolayers (SAMs) of decanethiol and hexadecanethiol on gold surface by using a lyotropic liquid crystalline phase as an adsorbing medium. The stability and blocking ability of these SAMs were characterized using grazing angle Fourier transform infrared (FTIR) spectroscopy and electrochemical techniques such as cyclic voltammetry and electrochemical impedance spectroscopy. The lyotropic liquid crystalline medium possesses a hexagonal structure consisting of a nonionic surfactant Triton X-100, water, and the corresponding thiol, which provides a highly hydrophobic environment to solubilize the alkanethiols and later to facilitate their delivery to the gold surface. We find that the SAMs formed from the hexagonal liquid crystalline phase are highly compact and have excellent electrochemical blocking ability towards the redox probes compared to conventional SAMs prepared from commonly used organic solvents such as ethanol. From the impedance studies, we have determined the capacitance of the monolayer-coated electrodes and the surface coverage of the SAM, which has been found to be >99.98% on gold surface. We have also estimated the extent of ionic permeability through the film and measured the rate constants for the redox reactions on the SAM-modified electrodes. Our results show that the rate constants of [Fe(CN)6](3-/4-) and [Ru(NH3)6](2+/3+) redox couples are very much lower in the case of monolayers prepared in liquid crystalline phase compared to the SAM formed in 1 mM thiol in ethanol solution, suggesting a better blocking ability of the SAMs in the former case. From the grazing angle FTIR spectroscopic studies and capacitance measurements, we have ruled out any coadsorption of surfactant molecules on the Au surface. These results suggest that SAMs of very low defect density and extremely low ionic permeability can be obtained when a hexagonal lyotropic liquid crystalline phase is used as an adsorbing medium.
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Ganesh V, Lakshminarayanan V. Scanning Tunneling Microscopy, Fourier Transform Infrared Spectroscopy, and Electrochemical Characterization of 2-Naphthalenethiol Self-Assembled Monolayers on the Au Surface: A Study of Bridge-Mediated Electron Transfer in Ru(NH3)62+|Ru(NH3)63+ Redox Reactions. J Phys Chem B 2005; 109:16372-81. [PMID: 16853081 DOI: 10.1021/jp052489u] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have studied the structure, adsorption kinetics, and barrier properties of self-assembled monolayers of 2-naphthalenethiol on Au using electrochemical techniques, grazing-angle Fourier transform infrared (FTIR) spectroscopy, and scanning tunneling microscopy (STM). The results of cyclic voltammetric and impedance measurements using redox probes show that 2-naphthalenethiol on Au forms a stable and reproducible, but moderately blocking, monolayer. Annealing of the self-assembled monolayer (SAM)-modified surface at 72 +/- 2 degrees C remarkably improves the blocking property of the monolayer of 2-naphthalenethiol on Au. From the study of kinetics of SAM formation, we find that the self-assembly follows Langmuir adsorption isotherm. Our STM and FTIR results show that the molecules are adsorbed with the naphthalene ring tilted from the surface normal by forming a square root 3 x 3 R30 degrees overlayer structure. From our studies, we conclude that the electron-transfer reaction of ferro/ferricyanide in the freshly formed monolayer occurs predominantly through the pinholes and defects present in the monolayer. However, in the case of thermally annealed specimen, although the ferro/ferricyanide reaction is almost completely blocked, the electron-transfer reaction of hexaammineruthenium(III) chloride is not significantly inhibited. It is proposed that the electron-transfer reaction in the case of the ruthenium redox couple takes place by a tunneling mechanism through the high-electron-density aromatic naphthalene ring acting as a bridge between the monolayer-modified electrode and the ruthenium complex.
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Sheen VL, Jansen A, Chen MH, Parrini E, Morgan T, Ravenscroft R, Ganesh V, Underwood T, Wiley J, Leventer R, Vaid RR, Ruiz DE, Hutchins GM, Menasha J, Willner J, Geng Y, Gripp KW, Nicholson L, Berry-Kravis E, Bodell A, Apse K, Hill RS, Dubeau F, Andermann F, Barkovich J, Andermann E, Shugart YY, Thomas P, Viri M, Veggiotti P, Robertson S, Guerrini R, Walsh CA. Filamin A mutations cause periventricular heterotopia with Ehlers-Danlos syndrome. Neurology 2005; 64:254-62. [PMID: 15668422 DOI: 10.1212/01.wnl.0000149512.79621.df] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To define the clinical, radiologic, and genetic features of periventricular heterotopia (PH) with Ehlers-Danlos syndrome (EDS). METHODS Exonic sequencing and single stranded conformational polymorphism (SSCP) analysis was performed on affected individuals. Linkage analysis using microsatellite markers on the X-chromosome was performed on a single pedigree. Western blotting evaluated for loss of filamin A (FLNA) protein and Southern blotting assessed for any potential chromosome rearrangement in this region. RESULTS The authors report two familial cases and nine additional sporadic cases of the EDS-variant form of PH, which is characterized by nodular brain heterotopia, joint hypermobility, and development of aortic dilatation in early adulthood. MRI typically demonstrated bilateral nodular PH, indistinguishable from PH due to FLNA mutations. Exonic sequencing or SSCP analyses of FLNA revealed a 2762 delG single base pair deletion in one affected female. Another affected female harbored a C116 single point mutation, resulting in an A39G change. A third affected female had a 4147 delG single base pair deletion. One pedigree with no detectable exonic mutation demonstrated positive linkage to the FLNA locus Xq28, an affected individual in this family also had no detectable FLNA protein, but no chromosomal rearrangement was detected. CONCLUSION These results suggest that the Ehlers-Danlos variant of periventricular heterotopia (PH), in part, represents an overlapping syndrome with X-linked dominant PH due to filamin A mutations.
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