Prediction of amyloid fibril-forming segments based on a support vector machine

<p>Abstract</p> <p>Background</p> <p>Amyloid fibrillar aggregates of proteins or polypeptides are known to be associated with many human diseases. Recent studies suggest that short protein regions trigger this aggregation. Thus, identifying these short peptides is critical for understanding diseases and finding potential therapeutic targets.</p> <p>Results</p> <p>We propose a method, named Pafig (Prediction of amyloid fibril-forming segments) based on support vector machines, to identify the hexpeptides associated with amyloid fibrillar aggregates. The features of Pafig were obtained by a two-round selection from AAindex. Using a 10-fold cross validation test on Hexpepset dataset, Pafig performed well with regards to overall accuracy of 81% and Matthews correlation coefficient of 0.63. Pafig was used to predict the potential fibril-forming hexpeptides in all of the 64,000,000 hexpeptides. As a result, approximately 5.08% of hexpeptides showed a high aggregation propensity. In the predicted fibril-forming hexpeptides, the amino acids – alanine, phenylalanine, isoleucine, leucine and valine occurred at the higher frequencies and the amino acids – aspartic acid, glutamic acid, histidine, lysine, arginine and praline, appeared with lower frequencies.</p> <p>Conclusion</p> <p>The performance of Pafig indicates that it is a powerful tool for identifying the hexpeptides associated with fibrillar aggregates and will be useful for large-scale analysis of proteomic data.</p

Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines

<p>Abstract</p> <p>Background</p> <p>Human genetic variations primarily result from single nucleotide polymorphisms (SNPs) that occur approximately every 1000 bases in the overall human population. The non-synonymous SNPs (nsSNPs) that lead to amino acid changes in the protein product may account for nearly half of the known genetic variations linked to inherited human diseases. One of the key problems of medical genetics today is to identify nsSNPs that underlie disease-related phenotypes in humans. As such, the development of computational tools that can identify such nsSNPs would enhance our understanding of genetic diseases and help predict the disease.</p> <p>Results</p> <p>We propose a method, named Parepro (Predicting the amino acid replacement probability), to identify nsSNPs having either deleterious or neutral effects on the resulting protein function. Two independent datasets, HumVar and NewHumVar, taken from the PhD-SNP server, were applied to train the model and test the robustness of Parepro. Using a 20-fold cross validation test on the HumVar dataset, Parepro achieved a Matthews correlation coefficient (MCC) of 50% and an overall accuracy (Q2) of 76%, both of which were higher than those predicted by the methods, such as PolyPhen, SIFT, and HydridMeth. Further analysis on an additional dataset (NewHumVar) using Parepro yielded similar results.</p> <p>Conclusion</p> <p>The performance of Parepro indicates that it is a powerful tool for predicting the effect of nsSNPs on protein function and would be useful for large-scale analysis of genomic nsSNP data.</p

Device modeling of superconductor transition edge sensors based on the two-fluid theory

In order to support the design and study of sophisticated large scale transition edge sensor (TES) circuits, we use basic SPICE elements to develop device models for TESs based on the superfluid-normal fluid theory. In contrast to previous studies, our device model is not limited to small signal simulation, and it relies only on device parameters that have clear physical meaning and can be easily measured. We integrate the device models in design kits based on powerful EDA tools such as CADENCE and OrCAD, and use them for versatile simulations of TES circuits. Comparing our simulation results with published experimental data, we find good agreement which suggests that device models based on the two-fluid theory can be used to predict the behavior of TES circuits reliably and hence they are valuable for assisting the design of sophisticated TES circuits.Comment: 10pages,11figures. Accepted to IEEE Trans. Appl. Supercon

AltNeRF: Learning Robust Neural Radiance Field via Alternating Depth-Pose Optimization

Neural Radiance Fields (NeRF) have shown promise in generating realistic novel views from sparse scene images. However, existing NeRF approaches often encounter challenges due to the lack of explicit 3D supervision and imprecise camera poses, resulting in suboptimal outcomes. To tackle these issues, we propose AltNeRF -- a novel framework designed to create resilient NeRF representations using self-supervised monocular depth estimation (SMDE) from monocular videos, without relying on known camera poses. SMDE in AltNeRF masterfully learns depth and pose priors to regulate NeRF training. The depth prior enriches NeRF's capacity for precise scene geometry depiction, while the pose prior provides a robust starting point for subsequent pose refinement. Moreover, we introduce an alternating algorithm that harmoniously melds NeRF outputs into SMDE through a consistence-driven mechanism, thus enhancing the integrity of depth priors. This alternation empowers AltNeRF to progressively refine NeRF representations, yielding the synthesis of realistic novel views. Additionally, we curate a distinctive dataset comprising indoor videos captured via mobile devices. Extensive experiments showcase the compelling capabilities of AltNeRF in generating high-fidelity and robust novel views that closely resemble reality

A Theoretically Guaranteed Quaternion Weighted Schatten p-norm Minimization Method for Color Image Restoration

Inspired by the fact that the matrix formulated by nonlocal similar patches in a natural image is of low rank, the rank approximation issue have been extensively investigated over the past decades, among which weighted nuclear norm minimization (WNNM) and weighted Schatten $p$-norm minimization (WSNM) are two prevailing methods have shown great superiority in various image restoration (IR) problems. Due to the physical characteristic of color images, color image restoration (CIR) is often a much more difficult task than its grayscale image counterpart. However, when applied to CIR, the traditional WNNM/WSNM method only processes three color channels individually and fails to consider their cross-channel correlations. Very recently, a quaternion-based WNNM approach (QWNNM) has been developed to mitigate this issue, which is capable of representing the color image as a whole in the quaternion domain and preserving the inherent correlation among the three color channels. Despite its empirical success, unfortunately, the convergence behavior of QWNNM has not been strictly studied yet. In this paper, on the one side, we extend the WSNM into quaternion domain and correspondingly propose a novel quaternion-based WSNM model (QWSNM) for tackling the CIR problems. Extensive experiments on two representative CIR tasks, including color image denoising and deblurring, demonstrate that the proposed QWSNM method performs favorably against many state-of-the-art alternatives, in both quantitative and qualitative evaluations. On the other side, more importantly, we preliminarily provide a theoretical convergence analysis, that is, by modifying the quaternion alternating direction method of multipliers (QADMM) through a simple continuation strategy, we theoretically prove that both the solution sequences generated by the QWNNM and QWSNM have fixed-point convergence guarantees.Comment: 46 pages, 10 figures; references adde

An Improved Timing Attack with Error Detection on RSA-CRT

Several types of timing attacks have been published, but they are either in theory or hard to be taken into practice. In order to improve the feasibility of attack, this paper proposes an advance timing attack scheme on RSA-CRT with T-test statistical tool. Similar timing attacks have been presented, such as BB-Attack and Shindler’s attack, however none of them applied statistical tool in their methods with such efficiency, and showed the complete recovery in practice by attacking on RSA-CRT. With T-test, we enlarge the 0-1 gap, reduce the neighborhood size and improve the precision of decision. However, the most contribution of this paper is that our algorithm has an error detection property which can detect the erroneous decision of guessing qk and correct it. We could make the success rate of recovering q to be 100% indeed for interprocess timing attack, recovery 1024bits RSA key completely in practice