Barry Merriman | University of California, Los Angeles (original) (raw)
Papers by Barry Merriman
Journal of Computational Physics, 1996
The point at which they meet (the triple junction) has prescribed angles which can be shown [12] ... more The point at which they meet (the triple junction) has prescribed angles which can be shown [12] to be defined by A coupled level set method for the motion of multiple junctions (of, e.g., solid, liquid, and grain boundaries), which follows the gradient flow for an energy functional consisting of surface tension (proportional to length) and bulk energies (proportional to area), is sin 1 f 23 ϭ sin 2 f 31 ϭ sin 3 f 12 , (1.2) developed. The approach combines the level set method of S. Osher and J. A. Sethian with a theoretical variational formulation of the motion by F. Reitich and H. M. Soner. The resulting method uses as many level set functions as there are regions and the energy where i is the angle between the two curves ⌫ ij and ⌫ ijЈ , functional is evaluated entirely in terms of level set functions. The j ϶ jЈ; see Fig. 1. gradient projection method leads to a coupled system of perturbed This problem was defined and analyzed clearly in a paper (by curvature terms) Hamilton-Jacobi equations. The coupling is by Reitich and Soner [12], and we base our approach in enforced using a single Lagrange multiplier associated with a conpart on their theoretical framework. Their method does straint which essentially prevents (a) regions from overlapping and (b) the development of a vacuum. The numerical implementation not lend itself to a direct numerical treatment. is relatively simple and the results agree with (and go beyond) Our objective here is to develop and implement numerithe theory as given in [12]. Other applications of this methocal algorithms which ''capture'' rather than ''track'' the dology, including the decomposition of a domain into subregions interfaces, based on the level set method of Osher and with minimal interface length, are discussed. Finally, some new Sethian [9]. The usual advantages of the level set method techniques and results in level set methodology are presented. ᮊ 1996 Academic Press, Inc. hold (see, e.g., [2, 8, 9, 16]). In the case of a single interface separating two phases the central idea is to follow the evolution of a function , whose zero-level set corresponds * Research supported by ARPA/ONR-N00014-92-J-1890, NSF DMS94-04942, and ARO DAAH04-95-1-0155. face, thus vacuum and overlapping regions generally de-179
Journal of Computational Physics, 1999
Computer Vision and Image Understanding, 2000
... marching algorithm introduced in [Se] applies to a much more restricted class of equations ..... more ... marching algorithm introduced in [Se] applies to a much more restricted class of equations ... This leads to slightly coupled system of geometrically driven motion perturbed by the constraints ... Together, they provide a promising new framework for doing analysis and control of thin ...
PLoS genetics, May 1, 2018
This Research Article [1] reports the sequencing of "U87MG" cells, which were acquired from ATCC.... more This Research Article [1] reports the sequencing of "U87MG" cells, which were acquired from ATCC. It has come to the authors' attention that recent work from Allen et al. reveals that the U87 cell line used in this study is distinct from the original U87MG cell line [2]. Additional analyses by Allen et al. indicate that the cell line presented in the work is of (or likely of) glioblastoma cell origin. The conclusions in the manuscript remain unaltered. "U87MG" is incorrect in the title, and in all other instances in the text. In all of these cases, the cell line referred to as "U87MG" should be called "U87(ATCC)".
Journal of Clinical Laboratory Analysis, 2016
Despite recent advances in the investigation of myeloproliferative neoplasms (MPN), the impact of... more Despite recent advances in the investigation of myeloproliferative neoplasms (MPN), the impact of genetic heterogeneity on its molecular pathogenesis has not been fully elucidated. Thus, in this study, we aim to characterize the genetic complexity in Korean patients with polycythemia vera (PV) and essential thrombocythemia (ET). We conducted association studies using 84 single-nucleotide polymorphisms (SNPs) in 229 patients (96 with PV and 133 with ET) and 170 controls. Further, whole-genome sequencing was performed in six patients (two with JAK2 V617F and four with wild-type JAK2), and putative somatic mutations were validated in a further 69 ET patients. Clinical and laboratory characteristics were also analyzed. Several germline SNPs and the 46 haplotype were significantly associated with PV and ET. Three somatic mutations in MPDZ, IQCH, and CALR genes were selected and validated. The frequency of the CALR mutation was 58.0% (40/69) in ET patients, who did not carry JAK2/MPL mutations. Moreover, compared with JAK2 V617F-positive patients, those with CALR mutations showed lower hemoglobin and hematocrit levels (P = 0.004 and P = 0.002, respectively), higher platelet counts (P =0.008), and a lower frequency of cytoreductive therapy (P = 0.014). This study was the first comprehensive investigation of the genetic characteristics of Korean patients with PV and ET. We found that somatic mutations and the 46 haplotype contribute to PV and ET pathogenesis in Korean patients.
Computer Vision and Image Understanding, 2000
ABSTRACT Moving interfaces that self-intersect arise naturally in the geometric optics model of w... more ABSTRACT Moving interfaces that self-intersect arise naturally in the geometric optics model of wavefront motion. Ray tracing techniques can be used to compute these motions, but they lose resolution as rays diverge. In this paper we develop a new numerical method that maintains uniform spatial resolution of the front at all times. Our approach is a fixed grid, interface capturing formulation based on the Dynamic Surface Extension method of Steinhoff and Fan [10]. The new methods can treat arbitrarily complicated self intersecting fronts, as well as refraction, reflection and focusing. We also further extend this approach to curvature dependent front motions, and the motion of filaments. We validate the new methods with numerical experiments. Department of Mathematics, University of California at Los Angeles. (ruuth@math.ucla.edu). The work of this author was partially supported by AFOSR STTR FQ8671-9801346. y Department of Mathematics, University of California at Los Angeles. (barry@math.u...
Siam Journal on Scientific Computing, 1993
Journal of Computational Physics, 1996
The point at which they meet (the triple junction) has prescribed angles which can be shown [12] ... more The point at which they meet (the triple junction) has prescribed angles which can be shown [12] to be defined by A coupled level set method for the motion of multiple junctions (of, e.g., solid, liquid, and grain boundaries), which follows the gradient flow for an energy functional consisting of surface tension (proportional to length) and bulk energies (proportional to area), is sin 1 f 23 ϭ sin 2 f 31 ϭ sin 3 f 12 , (1.2) developed. The approach combines the level set method of S. Osher and J. A. Sethian with a theoretical variational formulation of the motion by F. Reitich and H. M. Soner. The resulting method uses as many level set functions as there are regions and the energy where i is the angle between the two curves ⌫ ij and ⌫ ijЈ , functional is evaluated entirely in terms of level set functions. The j ϶ jЈ; see Fig. 1. gradient projection method leads to a coupled system of perturbed This problem was defined and analyzed clearly in a paper (by curvature terms) Hamilton-Jacobi equations. The coupling is by Reitich and Soner [12], and we base our approach in enforced using a single Lagrange multiplier associated with a conpart on their theoretical framework. Their method does straint which essentially prevents (a) regions from overlapping and (b) the development of a vacuum. The numerical implementation not lend itself to a direct numerical treatment. is relatively simple and the results agree with (and go beyond) Our objective here is to develop and implement numerithe theory as given in [12]. Other applications of this methocal algorithms which ''capture'' rather than ''track'' the dology, including the decomposition of a domain into subregions interfaces, based on the level set method of Osher and with minimal interface length, are discussed. Finally, some new Sethian [9]. The usual advantages of the level set method techniques and results in level set methodology are presented. ᮊ 1996 Academic Press, Inc. hold (see, e.g., [2, 8, 9, 16]). In the case of a single interface separating two phases the central idea is to follow the evolution of a function , whose zero-level set corresponds * Research supported by ARPA/ONR-N00014-92-J-1890, NSF DMS94-04942, and ARO DAAH04-95-1-0155. face, thus vacuum and overlapping regions generally de-179
Journal of Computational Physics, 1999
Computer Vision and Image Understanding, 2000
... marching algorithm introduced in [Se] applies to a much more restricted class of equations ..... more ... marching algorithm introduced in [Se] applies to a much more restricted class of equations ... This leads to slightly coupled system of geometrically driven motion perturbed by the constraints ... Together, they provide a promising new framework for doing analysis and control of thin ...
PLoS genetics, May 1, 2018
This Research Article [1] reports the sequencing of "U87MG" cells, which were acquired from ATCC.... more This Research Article [1] reports the sequencing of "U87MG" cells, which were acquired from ATCC. It has come to the authors' attention that recent work from Allen et al. reveals that the U87 cell line used in this study is distinct from the original U87MG cell line [2]. Additional analyses by Allen et al. indicate that the cell line presented in the work is of (or likely of) glioblastoma cell origin. The conclusions in the manuscript remain unaltered. "U87MG" is incorrect in the title, and in all other instances in the text. In all of these cases, the cell line referred to as "U87MG" should be called "U87(ATCC)".
Journal of Clinical Laboratory Analysis, 2016
Despite recent advances in the investigation of myeloproliferative neoplasms (MPN), the impact of... more Despite recent advances in the investigation of myeloproliferative neoplasms (MPN), the impact of genetic heterogeneity on its molecular pathogenesis has not been fully elucidated. Thus, in this study, we aim to characterize the genetic complexity in Korean patients with polycythemia vera (PV) and essential thrombocythemia (ET). We conducted association studies using 84 single-nucleotide polymorphisms (SNPs) in 229 patients (96 with PV and 133 with ET) and 170 controls. Further, whole-genome sequencing was performed in six patients (two with JAK2 V617F and four with wild-type JAK2), and putative somatic mutations were validated in a further 69 ET patients. Clinical and laboratory characteristics were also analyzed. Several germline SNPs and the 46 haplotype were significantly associated with PV and ET. Three somatic mutations in MPDZ, IQCH, and CALR genes were selected and validated. The frequency of the CALR mutation was 58.0% (40/69) in ET patients, who did not carry JAK2/MPL mutations. Moreover, compared with JAK2 V617F-positive patients, those with CALR mutations showed lower hemoglobin and hematocrit levels (P = 0.004 and P = 0.002, respectively), higher platelet counts (P =0.008), and a lower frequency of cytoreductive therapy (P = 0.014). This study was the first comprehensive investigation of the genetic characteristics of Korean patients with PV and ET. We found that somatic mutations and the 46 haplotype contribute to PV and ET pathogenesis in Korean patients.
Computer Vision and Image Understanding, 2000
ABSTRACT Moving interfaces that self-intersect arise naturally in the geometric optics model of w... more ABSTRACT Moving interfaces that self-intersect arise naturally in the geometric optics model of wavefront motion. Ray tracing techniques can be used to compute these motions, but they lose resolution as rays diverge. In this paper we develop a new numerical method that maintains uniform spatial resolution of the front at all times. Our approach is a fixed grid, interface capturing formulation based on the Dynamic Surface Extension method of Steinhoff and Fan [10]. The new methods can treat arbitrarily complicated self intersecting fronts, as well as refraction, reflection and focusing. We also further extend this approach to curvature dependent front motions, and the motion of filaments. We validate the new methods with numerical experiments. Department of Mathematics, University of California at Los Angeles. (ruuth@math.ucla.edu). The work of this author was partially supported by AFOSR STTR FQ8671-9801346. y Department of Mathematics, University of California at Los Angeles. (barry@math.u...
Siam Journal on Scientific Computing, 1993