Variable-Based Fault Localization via Enhanced Decision Tree

Fault localization, aiming at localizing the root cause of the bug under repair, has been a longstanding research topic. Although many approaches have been proposed in the last decades, most of the existing studies work at coarse-grained statement or method levels with very limited insights about how to repair the bug (granularity problem), but few studies target the finer-grained fault localization. In this paper, we target the granularity problem and propose a novel finer-grained variable-level fault localization technique. Specifically, we design a program-dependency-enhanced decision tree model to boost the identification of fault-relevant variables via discriminating failed and passed test cases based on the variable values. To evaluate the effectiveness of our approach, we have implemented it in a tool called VARDT and conducted an extensive study over the Defects4J benchmark. The results show that VARDT outperforms the state-of-the-art fault localization approaches with at least 247.8% improvements in terms of bugs located at Top-1, and the average improvements are 330.5%. Besides, to investigate whether our finer-grained fault localization result can further improve the effectiveness of downstream APR techniques, we have adapted VARDT to the application of patch filtering, where VARDT outperforms the state-of-the-art PATCH-SIM by filtering 26.0% more incorrect patches. The results demonstrate the effectiveness of our approach and it also provides a new way of thinking for improving automatic program repair techniques

Point-cloud Transformer for Three-dimensional Electrical Impedance Tomography

Electrical impedance tomography (EIT) is an emerging medical imaging modality that offers nonintrusive, label-free, fast, and portable features. However, the three-dimensional (3-D) EIT image reconstruction problem is thwarted by its high dimensionality and nonlinearity, thus suffering from low image quality. This article proposes a novel algorithm named point-cloud transformer for 3-D EIT image reconstruction (ptEIT) to tackle the challenges of 3-D EIT image reconstruction. ptEIT leverages the nonlinear representation ability of deep learning and effectively addresses the computational cost issue by using irregular-grid representation of the 3-D conductivity distribution in point clouds. The permutation invariant property rooted in the self-attention operator makes ptEIT particularly suitable for processing this type of data, and the objectwise chamfer distance (OWCD) effectively solves the mean-shaped behavior problem encountered in reconstructing multiple objects. Our experimental results demonstrate that ptEIT can simultaneously achieve high accuracy, spatial resolution, and visual quality, outperforming the state-of-the-art 3-D EIT image reconstruction approaches. ptEIT also offers the unique feature of variable resolution and demonstrates strong generalization ability toward different noise levels, showing evident superiority over voxel-based 3-D EIT approaches

A numerically strongly stable method for computing the Hamiltonian Schur form

In this paper we solve a long-standing open problem in numerical analysis called 'Van Loan's Curse'. We derive a new numerical method for computing the Hamiltonian Schur form of a Hamiltonian matrix that has no purely imaginary eigenvalues. The proposed method is numerically strongly backward stable, i.e., it computes the exact Hamiltonian Schur form of a nearby Hamiltonian matrix, and it is of complexity O(n^3) and thus Van Loan's curse is lifted. We demonstrate the quality of the new method by showing its performance for the benchmark collection of continuous-time algebraic Riccati equations

Touch and deformation perception of soft manipulators with capacitive e-skins and deep learning

Tactile sensing in soft robots remains particularly challenging because of the coupling between contact and deformation information which the sensor is subject to during actuation and interaction with the environment. This often results in severe interference and makes disentangling tactile sensing and geometric deformation difficult. To address this problem, this paper proposes a soft capacitive e-skin with a sparse electrode distribution and deep learning for information decoupling. Our approach successfully separates tactile sensing from geometric deformation, enabling touch recognition on a soft pneumatic actuator subject to both internal (actuation) and external (manual handling) forces. Using a multi-layer perceptron, the proposed e-skin achieves 99.88\% accuracy in touch recognition across a range of deformations. When complemented with prior knowledge, a transformer-based architecture effectively tracks the deformation of the soft actuator. The average distance error in positional reconstruction of the manipulator is as low as 2.905$\pm$2.207 mm, even under operative conditions with different inflation states and physical contacts which lead to additional signal variations and consequently interfere with deformation tracking. These findings represent a tangible way forward in the development of e-skins that can endow soft robots with proprioception and exteroception

Inhibition of highly pathogenic PRRSV replication in MARC-145 cells by artificial microRNAs

<p>Abstract</p> <p>Background</p> <p>Highly pathogenic porcine reproductive and respiratory syndrome (HP-PRRS) has caused large economic losses in swine industry in recent years. However, current antiviral strategy could not effectively prevent and control this disease. In this research, five artificial microRNAs (amiRNAs) respectively targeted towards ORF5 (amirGP5-243, -370) and ORF6 (amirM-82, -217,-263) were designed and incorporated into a miRNA-based vector that mimics the backbone of murine miR-155 and permits high expression of amiRNAs in a GFP fused form mediated by RNA Pol II promoter CMV.</p> <p>Results</p> <p>It was found that amirGP5-370 could effectively inhibit H-PRRSV replication. The amirM-263-M-263, which was a dual pre-amiRNA expression cassette where two amirM-263s were chained, showed stronger virus inhibitory effects than single amirM-263. H-PRRSV replication was inhibited up to 120 hours in the MARC-145 cells which were stably transduced by recombinant lentiviruses (Lenti-amirGP5-370, -amirM-263-M-263). Additionally, efficacious dose of amirGP5-370 and amirM-263 expression did not trigger the innate interferon response.</p> <p>Conclusions</p> <p>Our study is the first attempt to suppress H-PRRSV replication in MARC-145 cells through vector-based and lentiviral mediated amiRNAs targeting GP5 or M proteins coding sequences of PRRSV, which indicated that artificial microRNAs and recombinant lentiviruses might be applied to be a new potent anti-PRRSV strategy.</p

Origin of mitochondrial DNA diversity of domestic yaks

BACKGROUND: The domestication of plants and animals was extremely important anthropologically. Previous studies have revealed a general tendency for populations of livestock species to include deeply divergent maternal lineages, indicating that they were domesticated in multiple, independent events from genetically discrete wild populations. However, in water buffalo, there are suggestions that a similar deep maternal bifurcation may have originated from a single population. These hypotheses have rarely been rigorously tested because of a lack of sufficient wild samples. To investigate the origin of the domestic yak (Poephagus grunnies), we analyzed 637 bp of maternal inherited mtDNA from 13 wild yaks (including eight wild yaks from a small population in west Qinghai) and 250 domesticated yaks from major herding regions. RESULTS: The domestic yak populations had two deeply divergent phylogenetic groups with a divergence time of > 100,000 yrs BP. We here show that haplotypes clustering with two deeply divergent maternal lineages in domesticated yaks occur in a single, small, wild population. This finding suggests that all domestic yaks are derived from a single wild gene pool. However, there is no clear correlation of the mtDNA phylogenetic clades and the 10 morphological types of sampled yaks indicating that the latter diversified recently. Relatively high diversity was found in Qinghai and Tibet around the current wild distribution, in accordance with previous suggestions that the earliest domestications occurred in this region. Conventional molecular clock estimation led to an unrealistic early dating of the start of the domestication. However, Bayesian estimation of the coalescence time allowing a relaxation of the mutation rate are better in agreement with a domestication during the Holocene as supported by archeological records. CONCLUSION: The information gathered here and the previous studies of other animals show that the demographic histories of domestication of livestock species were highly diverse despite the common general feature of deeply divergent maternal lineages. The results further suggest that domestication of local wild prey ungulate animals was a common occurrence during the development of human civilization following the postglacial colonization in different locations of the world, including the high, arid Qinghai-Tibetan Plateau

Inhibition of HSP90 attenuates porcine reproductive and respiratory syndrome virus production in vitro

BACKGROUND: Porcine reproductive and respiratory syndrome virus (PRRSV) infection leads to substantial economic losses to the swine industry worldwide. However, no effective countermeasures exist to combat this virus infection so far. The most common antiviral strategy relies on directly inhibiting viral proteins. However, this strategy invariably leads to the emergence of drug resistance due to the error-prone nature of viral ploymerase. Targeting cellular proteins required for viral infection for developing new generation of antivirals is gaining concern. Recently, heat shock protein 90 (HSP90) was found to be an important host factor for the replication of multiple viruses and the inhibition of HSP90 showed significant antiviral effects. It is thought that the inhibition of HSP90 could be a promising broad-range antiviral approach. However, the effects of HSP90 inhibition on PRRSV infection have not been evaluated. In the current research, we tried to inhibit HSP90 and test whether the inhibition affect PRRSV infection. METHODS: We inhibit the function of HSP90 with two inhibitors, geldanamycin (GA) and 17- allylamono-demethoxygeldanamycin (17-AAG), and down-regulated the expression of endogenous HSP90 with specific small-interfering RNAs (siRNAs). Cell viability was measured with alamarBlue. The protein level of viral N was determined by western blotting and indirect immunofluorescence (IFA). Besides, IFA was employed to examine the level of viral double-stranded RNA (dsRNA). The viral RNA copy number and the level of IFN-β mRNA were determined by quantitative real-time PCR (qRT-PCR). RESULTS: Our results indicated that both HSP90 inhibitors showed strong anti-PRRSV activity. They could reduce viral production by preventing the viral RNA synthesis. These inhibitory effects were not due to the activation of innate interferon response. In addition, we observed that individual knockdown targeting HSP90α or HSP90β did not show dramatic inhibitory effect. Combined knockdown of these two isoforms was required to reduce viral infection. CONCLUSIONS: Our results shed light on the possibility of developing potential therapeutics targeting HSP90 against PRRSV infection

Tunable and robust room-temperature magnon-magnon entanglement

Although challenging, realizing controllable high-temperature entanglement is of immense importance for practical applications as well as for fundamental research in quantum technologies. Here, we report the existence of entangled steady states in bipartite quantum magnonic systems at high temperatures. We consider dissipative dynamics of two magnons in a bipartite antiferromagnet or ferrimagnet subjected to a vibrational phonon mode and an external rotating magnetic field. To quantify the bipartite magnon-magnon entanglement, we use the entanglement negativity and compute its dependence on the temperature and magnetic field. We show that, for any given phonon frequency and magnon-phonon coupling rates, there are always ranges of the magnetic field amplitudes and frequencies, for which bipartite magnon-magnon entanglement persists up to and above the room temperature. The generality of the result allows for experimental observation in a variety of crystals and synthetic bipartite antiferromagnetic and ferrimagnetic materials.Comment: 6 pages, 5 figure

Quantum analog of Landau-Lifshitz-Gilbert dynamics

The Landau-Lifshitz-Gilbert (LLG) and Landau-Lifshitz (LL) equations play an essential role for describing the dynamics of magnetization in solids. While a quantum analog of the LL dynamics has been proposed in [Phys. Rev. Lett. 110, 147201 (2013)], the corresponding quantum version of LLG remains unknown. Here, we propose such a quantum LLG equation that inherently conserves purity of the quantum state. We examine the quantum LLG dynamics of a dimer consisting of two interacting spin-1/2 particles. Our analysis reveals that, in the case of ferromagnetic coupling, the evolution of initially uncorrelated spins mirrors the classical LLG dynamics. However, in the antiferromagnetic scenario, we observe pronounced deviations from classical behavior, underscoring the unique dynamics of becoming a spinless state, which is non-locally correlated. Moreover, when considering spins that are initially correlated, our study uncovers an unusual form of transient quantum correlation dynamics, which differ significantly from what is typically seen in open quantum systems

Cloning and Comparative Studies of Seaweed Trehalose-6-Phosphate Synthase Genes

The full-length cDNA sequence (3219 base pairs) of the trehalose-6-phosphate synthase gene of Porphyra yezoensis (PyTPS) was isolated by RACE-PCR and deposited in GenBank (NCBI) with the accession number AY729671. PyTPS encodes a protein of 908 amino acids before a stop codon, and has a calculated molecular mass of 101,591 Daltons. The PyTPS protein consists of a TPS domain in the N-terminus and a putative TPP domain at the C-terminus. Homology alignment for PyTPS and the TPS proteins from bacteria, yeast and higher plants indicated that the most closely related sequences to PyTPS were those from higher plants (OsTPS and AtTPS5), whereas the most distant sequence to PyTPS was from bacteria (EcOtsAB). Based on the identified sequence of the PyTPS gene, PCR primers were designed and used to amplify the TPS genes from nine other seaweed species. Sequences of the nine obtained TPS genes were deposited in GenBank (NCBI). All 10 TPS genes encoded peptides of 908 amino acids and the sequences were highly conserved both in nucleotide composition (>94%) and in amino acid composition (>96%). Unlike the TPS genes from some other plants, there was no intron in any of the 10 isolated seaweed TPS genes