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Search Results: 1 - 10 of 4006 matches for " Jacques Zaneveld "
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Dawn of ocular gene therapy: implications for molecular diagnosis in retinal disease
Jacques Zaneveld,Feng Wang,Xia Wang,Rui Chen
Science China Life Sciences , 2013, DOI: 10.1007/s11427-013-4443-y
Abstract: Personalized medicine aims to utilize genomic information about patients to tailor treatment. Gene replacement therapy for rare genetic disorders is perhaps the most extreme form of personalized medicine, in that the patients’ genome wholly determines their treatment regimen. Gene therapy for retinal disorders is poised to become a clinical reality. The eye is an optimal site for gene therapy due to the relative ease of precise vector delivery, immune system isolation, and availability for monitoring of any potential damage or side effects. Due to these advantages, clinical trials for gene therapy of retinal diseases are currently underway. A necessary precursor to such gene therapies is accurate molecular diagnosis of the mutation(s) underlying disease. In this review, we discuss the application of Next Generation Sequencing (NGS) to obtain such a diagnosis and identify disease causing genes, using retinal disorders as a case study. After reviewing ocular gene therapy, we discuss the application of NGS to the identification of novel Mendelian disease genes. We then compare current, array based mutation detection methods against next NGS-based methods in three retinal diseases: Leber’s Congenital Amaurosis, Retinitis Pigmentosa, and Stargardt’s disease. We conclude that next-generation sequencing based diagnosis offers several advantages over array based methods, including a higher rate of successful diagnosis and the ability to more deeply and efficiently assay a broad spectrum of mutations. However, the relative difficulty of interpreting sequence results and the development of standardized, reliable bioinformatic tools remain outstanding concerns. In this review, recent advances NGS based molecular diagnoses are discussed, as well as their implications for the development of personalized medicine.
CGAP-Align: A High Performance DNA Short Read Alignment Tool
Yaoliang Chen, Ji Hong, Wanyun Cui, Jacques Zaneveld, Wei Wang, Richard Gibbs, Yanghua Xiao, Rui Chen
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061033
Abstract: Background Next generation sequencing platforms have greatly reduced sequencing costs, leading to the production of unprecedented amounts of sequence data. BWA is one of the most popular alignment tools due to its relatively high accuracy. However, mapping reads using BWA is still the most time consuming step in sequence analysis. Increasing mapping efficiency would allow the community to better cope with ever expanding volumes of sequence data. Results We designed a new program, CGAP-align, that achieves a performance improvement over BWA without sacrificing recall or precision. This is accomplished through the use of Suffix Tarray, a novel data structure combining elements of Suffix Array and Suffix Tree. We also utilize a tighter lower bound estimation for the number of mismatches in a read, allowing for more effective pruning during inexact mapping. Evaluation of both simulated and real data suggests that CGAP-align consistently outperforms the current version of BWA and can achieve over twice its speed under certain conditions, all while obtaining nearly identical results. Conclusion CGAP-align is a new time efficient read alignment tool that extends and improves BWA. The increase in alignment speed will be of critical assistance to all sequence-based research and medicine. CGAP-align is freely available to the academic community at http://sourceforge.net/p/cgap-align under the GNU General Public License (GPL).
Enige Algemeen voorkomende zeevissen in de Nederlandsche Antillen.
J.S. Zaneveld
Nieuwe West-Indische Gids , 1957,
Asymptotic light field in the presence of a bubble-layer
Piotr J. Flatau,Jacek Piskozub,J. Ronald V. Zaneveld
Physics , 2000, DOI: 10.1364/OE.5.000120
Abstract: We report that the submerged microbubbles are an efficient source of diffuse radiance and may contribute to a rapid transition to the diffuse asymptotic regime. In this asymptotic regime an average cosine is easily predictable and measurable.
Monte Carlo study of the scattering error of a quartz reflective absorption tube
Jacek Piskozub,Piotr J. Flatau,J. V. R. Zaneveld
Physics , 2000, DOI: 10.1175/1520-0426(2001)018<0438:MCSOTS>2.0.CO;2
Abstract: A Monte Carlo model was used to study the scattering error of an absorption meter with a divergent light beam and a limited acceptance angle of the receiver. Reflections at both ends of the tube were taken into account. Calculations of the effect of varying optical properties of water, as well as the receiver geometry, were performed. A weighting function showing the scattering error quantitatively as a function of angle was introduced. Some cases of the practical interests are discussed.
Dark Energy as a Property of Dark Matter  [PDF]
Jacques Leibovitz
Journal of Modern Physics (JMP) , 2011, DOI: 10.4236/jmp.2011.212181
Abstract: A novel model of dark matter (DM), elastically compressible, can contribute to the acceleration of our Universe expansion. While each galaxy compresses its own DM within its gravitation field, the DM bordering neighboring galaxies, far from their centers, is pulled apart. It is shown that, although the DM pressure tends to zero at such locations, the DM compressibility tends to infinity. This allows the DM to expand between galaxies without gravitation hindrance. The model is consistent with the coupled distributions of baryonic and dark matters, with black hole formation at the centers of large galaxies, with galactic flat rotation curves, with a Tully-Fisher relation, and with Milgrom’s MOND relation. Results are discussed.
Mechanism and evolution of multidomain aminoacyl-tRNA synthetases revealed by their inhibition by analogues of a reaction intermediate, and by properties of truncated forms  [PDF]
Jacques Lapointe
Journal of Biomedical Science and Engineering (JBiSE) , 2013, DOI: 10.4236/jbise.2013.610115
Abstract: Many enzymes which catalyze the conversion of large substrates are made of several structural domains belonging to the same polypeptide chain. Transfer RNA (tRNA), one of the substrates of the multidomain aminoacyl-tRNA synthetases (aaRS), is an L-shaped molecule whose size in one dimension is similar to that of its cognate aaRS. Crystallographic structures of aaRS/tRNA complexes show that these enzymes use several of their structural domains to interact with their cognate tRNA. This mini review discusses first some aspects of the evolution and of the flexibility of the pentadomain bacterial glutamyl-tRNA synthetase (GluRS) revealed by kinetic and interaction studies of complementary truncated forms, and then illustrates how stable analogues of aminoacyl-AMP intermediates have been used to probe conformational changes in the active sites of Escherichia coli GluRS and of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) of Pseudomonas aeruginosa.
A Review on Tectonic Record of Strain Buildup and Stress Release across the Andean Forearc along the Gulf of Guayaquil-Tumbes Basin (GGTB) near Ecuador-Peru Border  [PDF]
Jacques Bourgois
International Journal of Geosciences (IJG) , 2013, DOI: 10.4236/ijg.2013.43057

Gravimetric and geologic data show that the reactivation of the Neogene Interandean depression and/or the ~75 - 65 Ma ophiolite suture into the modern dynamic of the Andes controlled the Gulf of Guayaquil Tumbes basin (GGTB) location and evolution during the past 1.8 - 1.6 Myr at least. Depending on whether the remobilization occurred along the interandean depression or the ophiolite suture, the GGTB evolved trough pure or simple shear mechanisms, respectively. Because the GGTB exhibits an along strike tectonic asymmetry associated with a pervasive seismic gap, the simple shear solution is more likely. Tectonic inversion occurred along a mid-crust detachment (the Mid-Crust detachment hereafter) matching the ophiolite suture that accommodates the North Andean Block (NAB) northward drift. The so-called Decoupling Strip located at the shelf slope break accommodated the tensional stress rotation from N-S along the shelf area i.e. NAB-drift induced to E-W along the continental margin i.e. subduction-erosion-induced. The landward dipping Woollard detachment system located at the Upper-Lower slope boundary connects the subduction channel at depth, allowing the Upper slope to evolve independently from the Lower slope wedge. The long-term recurrence interval between earthquakes, the strong interplate coupling, and the aseismic creeping deformation acting along the main low-angle detachments i.e. the Woollard and the Mid-Crust detachments may account for the pervasive seismic gap at the GGTB area. Because the subduction channel exhibits no record of significant seismic activity, no evidence exists to establish a link between the GGTB sustained subsidence and a basin-centered asperity. Because the

New Expansion Dynamics Applied to the Planar Structures of Satellite Galaxies and Space Structuration  [PDF]
Jacques Fleuret
Journal of Modern Physics (JMP) , 2016, DOI: 10.4236/jmp.2016.716204

Recent observations of Dwarf Satellite Galaxies (DSG) show that they have a clear tendency to stay in particular planes. Explanations with standard physics remain controversial. Recently, I proposed a new explanation of the galactic flat rotation curves, introducing a new cosmic acceleration due to expansion. In this paper, I apply this new acceleration to the dynamics of DSG’s (without dark matter). I show that this new acceleration implies planar structures for the DSG trajectories. More generally, it is shown that this acceleration produces a space structuration around any massive center. It remains a candidate to explain several cosmic observations without dark matter.

Studying Differential Invariants in Developmental Variations  [PDF]
Jacques Juhel
Psychology (PSYCH) , 2018, DOI: 10.4236/psych.2018.94041
Abstract: The differential study of intraindividual variability and change is currently reaping the benefits of important methodological advances in longitudinal data modeling. Two major research strategies for detecting invariants in individual differences in developmental change are considered. The most common approach involves operating at a population level to study differences of behavior throughout development. Though rarely used, another approach is the differential study of developmental change based on an individual modeling of the dynamics of intraindividual variability. The potential of these two approaches for improving our understanding of the development of human beings is illustrated.
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