A Novel Self-Intersection Penalty Term for Statistical Body Shape Models and Its Applications in 3D Pose Estimation

Statistical body shape models are widely used in 3D pose estimation due to their low-dimensional parameters representation. However, it is difficult to avoid self-intersection between body parts accurately. Motivated by this fact, we proposed a novel self-intersection penalty term for statistical body shape models applied in 3D pose estimation. To avoid the trouble of computing self-intersection for complex surfaces like the body meshes, the gradient of our proposed self-intersection penalty term is manually derived from the perspective of geometry. First, the self-intersection penalty term is defined as the volume of the self-intersection region. To calculate the partial derivatives with respect to the coordinates of the vertices, we employed detection rays to divide vertices of statistical body shape models into different groups depending on whether the vertex is in the region of self-intersection. Second, the partial derivatives could be easily derived by the normal vectors of neighboring triangles of the vertices. Finally, this penalty term could be applied in gradient-based optimization algorithms to remove the self-intersection of triangular meshes without using any approximation. Qualitative and quantitative evaluations were conducted to demonstrate the effectiveness and generality of our proposed method compared with previous approaches. The experimental results show that our proposed penalty term can avoid self-intersection to exclude unreasonable predictions and improves the accuracy of 3D pose estimation indirectly. Further more, the proposed method could be employed universally in triangular mesh based 3D reconstruction

A topological approach for protein classification

Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity be- tween proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics. Persistent homology is a new branch of algebraic topology that has found its success in the topological data analysis in a variety of disciplines, including molecular biology. The present work explores the potential of using persistent homology as an indepen- dent tool for protein classification. To this end, we propose a molecular topological fingerprint based support vector machine (MTF-SVM) classifier. Specifically, we construct machine learning feature vectors solely from protein topological fingerprints, which are topological invariants generated during the filtration process. To validate the present MTF-SVM approach, we consider four types of problems. First, we study protein-drug binding by using the M2 channel protein of influenza A virus. We achieve 96% accuracy in discriminating drug bound and unbound M2 channels. Additionally, we examine the use of MTF-SVM for the classification of hemoglobin molecules in their relaxed and taut forms and obtain about 80% accuracy. The identification of all alpha, all beta, and alpha-beta protein domains is carried out in our next study using 900 proteins. We have found a 85% success in this identifica- tion. Finally, we apply the present technique to 55 classification tasks of protein superfamilies over 1357 samples. An average accuracy of 82% is attained. The present study establishes computational topology as an independent and effective alternative for protein classification

The Emergent Landscape of Detecting EGFR Mutations Using Circulating Tumor DNA in Lung Cancer.

The advances in targeted therapies for lung cancer are based on the evaluation of specific gene mutations especially the epidermal growth factor receptor (EGFR). The assays largely depend on the acquisition of tumor tissue via biopsy before the initiation of therapy or after the onset of acquired resistance. However, the limitations of tissue biopsy including tumor heterogeneity and insufficient tissues for molecular testing are impotent clinical obstacles for mutation analysis and lung cancer treatment. Due to the invasive procedure of tissue biopsy and the progressive development of drug-resistant EGFR mutations, the effective initial detection and continuous monitoring of EGFR mutations are still unmet requirements. Circulating tumor DNA (ctDNA) detection is a promising biomarker for noninvasive assessment of cancer burden. Recent advancement of sensitive techniques in detecting EGFR mutations using ctDNA enables a broad range of clinical applications, including early detection of disease, prediction of treatment responses, and disease progression. This review not only introduces the biology and clinical implementations of ctDNA but also includes the updating information of recent advancement of techniques for detecting EGFR mutation using ctDNA in lung cancer

Controlling the Intrinsic Josephson Junction Number in a Bi2Sr2CaCu2O8+δ\mathbf{Bi_2Sr_2CaCu_2O_{8+\delta}} Mesa

In fabricating $\mathrm{Bi_2Sr_2CaCu_2O_{8+\delta}}$ intrinsic Josephson junctions in 4-terminal mesa structures, we modify the conventional fabrication process by markedly reducing the etching rates of argon ion milling. As a result, the junction number in a stack can be controlled quite satisfactorily as long as we carefully adjust those factors such as the etching time and the thickness of the evaporated layers. The error in the junction number is within $\pm 1$. By additional ion etching if necessary, we can controllably decrease the junction number to a rather small value, and even a single intrinsic Josephson junction can be produced.Comment: to bu published in Jpn. J. Appl. Phys., 43(7A) 200