Fast Mesh-Based Medical Image Registration

In this paper a fast triangular mesh based registration method is proposed. Having Template and Reference images as inputs, the template image is triangulated using a content adaptive mesh generation algorithm. Considering the pixel values at mesh nodes, interpolated using spline interpolation method for both of the images, the energy functional needed for image registration is minimized. The minimization process was achieved using a mesh based discretization of the distance measure and regularization term which resulted in a sparse system of linear equations, which due to the smaller size in comparison to the pixel-wise registration method, can be solved directly. Mean Squared Difference (MSD) is used as a metric for evaluating the results. Using the mesh based technique, higher speed was achieved compared to pixel-based curvature registration technique with fast DCT solver. The implementation was done in MATLAB without any specific optimization. Higher speeds can be achieved using C/C++ implementations.Comment: Accepted manuscript for ISVC'201

Magnetism and spin-orbit coupling in Ir-based double perovskites La(2−x_(2-xSrx_xCoIrO6_6

We have studied Ir spin and orbital magnetic moments in the double perovskites La$_{2-x}$Sr$_x$CoIrO$_6$ by x-ray magnetic circular dichroism. In La$_2$CoIrO$_6$, Ir$^{4+}$ couples antiferromagnetically to the weak ferromagnetic moment of the canted Co$^{2+}$ sublattice and shows an unusually large negative total magnetic moment (-0.38\,$\mu_{\text B}$/f.u.) combined with strong spin-orbit interaction. In contrast, in Sr$_2$CoIrO$_6$, Ir$^{5+}$ has a paramagnetic moment with almost no orbital contribution. A simple kinetic-energy-driven mechanism including spin-orbit coupling explains why Ir is susceptible to the induction of substantial magnetic moments in the double perovskite structure.Comment: 6 pages, 8 figure

Application of Photogrammetry in Biomedical Science

Peer reviewedPostprin

Grouped Multilevel Space-Time Trellis Codes

Space-time trellis codes (STTCs) generally provide coding and diversity gains, but only transmit one data symbol per time slot. Using higher order modulations incurs high decoding complexity and lengthy code searches. Multi-layer schemes using multiple STTCs over subgroups of antennas provide higher throughput, but require as many receive as transmit antennas and have reduced diversity gains. Here, we develop grouped multilevel STTCs that can provide the high throughput of multi-layered schemes while realizing larger diversity gains. Any number of receive antennas can be used. An example is shown that achieves 6 bits/sec/Hz using 16-QAM and 4 transmit antennas

Detection of Mutations in Exons 5 and 8 of Tumor Suppressor Tp53 Gene in Patients with Squamous Cell Carcinoma of Lung Hospitalized in Afzalipour Hospital, Kerman, Iran

Abstract: Introduction: Despite improvements in the diagnosis and treatment of lung cancer in the past two decades, it has remained the most common cause of death from cancer worldwide. Among all genes that are mutated in lung cancer, TP53 located on chromosome 17P13/1 has a significant diagnostic and prognostic value. TP53 mutations have been extensively studied in lung cancer and TP53 mutational spectra have been used for finding the origin(s) and mechanisms of these mutations in lung cancer development. The present study was conducted to investigate the TP53 mutations in patients with Non- small cell lung cancer hospitalized during 1997-2005 in Afzalipour Hospital, Kerman, Iran. Method: Formalin- fixed, Paraffin- embedded tissues from lung cancer patients undergone surgery between 1997 to 2005 were evaluated. The mutational status of the TP53 gene (exons 5 & 8) was screened by polymerase chain reaction (PCR) analysis followed by sequencing. Results: Of all cases of squamous cell carcinoma, 73 mutations were found in Exon 5 (in 18 cases) and 47 mutations in Exon 8 of TP53 gene (in 15 cases). we identified mutation hot spot at codons 6, 14, 25 of exon 5 and codons 2, 27, 35 of exon 8 of TP53 gene. Tansversions (G to T, A to T and G to C) and deletion mutations were the most in both exons 5 and 8. The incidence of G to T transversion mutations did not significantly differ between Exons 5 and 8. Conclusion: Higher prevalence of mutations in TP53 gene in the present study comparing to previous studies may be due to genetic, environmental and some epidemiological factors such as diet and life style of studied subjects. Keywords: TP53Gene, Squamous cell carcinoma, Mutatio

Detection of Mutations in Exons 5 and 8 of Tumor Suppressor Tp53 Gene in Patients with Squamous Cell Carcinoma of Lung Hospitalized in Afzalipour Hospital, Kerman, Iran

Abstract: Introduction: Despite improvements in the diagnosis and treatment of lung cancer in the past two decades, it has remained the most common cause of death from cancer worldwide. Among all genes that are mutated in lung cancer, TP53 located on chromosome 17P13/1 has a significant diagnostic and prognostic value. TP53 mutations have been extensively studied in lung cancer and TP53 mutational spectra have been used for finding the origin(s) and mechanisms of these mutations in lung cancer development. The present study was conducted to investigate the TP53 mutations in patients with Non- small cell lung cancer hospitalized during 1997-2005 in Afzalipour Hospital, Kerman, Iran. Method: Formalin- fixed, Paraffin- embedded tissues from lung cancer patients undergone surgery between 1997 to 2005 were evaluated. The mutational status of the TP53 gene (exons 5 & 8) was screened by polymerase chain reaction (PCR) analysis followed by sequencing. Results: Of all cases of squamous cell carcinoma, 73 mutations were found in Exon 5 (in 18 cases) and 47 mutations in Exon 8 of TP53 gene (in 15 cases). we identified mutation hot spot at codons 6, 14, 25 of exon 5 and codons 2, 27, 35 of exon 8 of TP53 gene. Tansversions (G to T, A to T and G to C) and deletion mutations were the most in both exons 5 and 8. The incidence of G to T transversion mutations did not significantly differ between Exons 5 and 8. Conclusion: Higher prevalence of mutations in TP53 gene in the present study comparing to previous studies may be due to genetic, environmental and some epidemiological factors such as diet and life style of studied subjects. Keywords: TP53Gene, Squamous cell carcinoma, Mutatio

Stereo Scanning Electron Microscopy Dataset

This is the dataset for the paper titled "Slanted Support Window-Based Stereo Matching for Surface Reconstruction of Microscopic Samples" published in Micron. (https://doi.org/10.1016/j.micron.2017.09.003) For each microscopic sample, a pair of Scanning Electron Microscopy (SEM) micrographs is provided which acquired by a Hitachi S-4800 field emission scanning electron microscope (FE-SEM). This device is equipped with a computer controlled 5 axes motorized specimen stage, enabling movements in X, Y and Z directions as well as tilt (-5 to 70 degrees) and rotation (0 to 360 degrees). Specimen manipulations, such as tilt, Z-positioning, and rotation of the specimen stage are done through the Hitachi PC-SEM software. The working distance was determined at the maximum tilt for every sample at the chosen magnification factor. The SEM image was centered manually while the specimen was tilted in successive 1-degree increments until reaching the final value. Here, the tilt angle between the micrographs in each pair is 7 degrees. It should be noted that the micrograph pairs are not true stereo images as the acquisition is done by tilting the specimen stage. Therefore, an initial step of stereo rectification is necessary, as described in the paper. The dataset is available free of charge for any academic and research purposes. Please cite the following publications if you used the dataset in your research: 1- Baghaie, Ahmadreza, et al. "Slanted Support Window-Based Stereo Matching for Surface Reconstruction of Microscopic Samples." Micron, (2017): https://doi.org/10.1016/j.micron.2017.09.003 2- Baghaie, Ahmadreza; Owen, Heather A, “Stereo Scanning Electron Microscopy Dataset”, Mendeley Data, v1, (2017), http://dx.doi.org/10.17632/nztd83gxdc.1 3- Baghaie, Ahmadreza. Study of Computational Image Matching Techniques: Improving Our View of Biomedical Image Data. Diss. Ph. D. Thesis, University of Wisconsin-Milwaukee (UWM), Milwaukee, WI, USA, 2016. http://dc.uwm.edu/etd/1346 4- Baghaie, Ahmadreza, et al. "Three-dimensional reconstruction of highly complex microscopic samples using scanning electron microscopy and optical flow estimation." PloS one 12.4 (2017), https://doi.org/10.1371/journal.pone.017507