Miracle-dz/UniFAR-FTUs huggingface dataset:
A Systematic Survey of Just-in-Time Software Defect Prediction

Recent years have experienced sustained focus in research on software defect prediction that aims to predict the likelihood of software defects. Moreover, with the increased interest in continuous deployment, a variant of software defect prediction called Just-in-Time Software Defect Prediction (JIT-SDP) focuses on predicting whether each incremental software change is defective. JIT-SDP is unique in that it consists of two interconnected data streams, one consisting of the arrivals of software changes stemming from design and implementation, and the other the (defective or clean) labels of software changes resulting from quality assurance processes. We present a systematic survey of 67 JIT-SDP studies with the objective to help researchers advance the state of the art in JIT-SDP and to help practitioners become familiar with recent progress. We summarize best practices in each phase of the JIT-SDP workflow, carry out a meta-analysis of prior studies, and suggest future research directions. Our meta-analysis of JIT-SDP studies indicates, among other findings, that the predictive performance correlates with change defect ratio, suggesting that JIT-SDP is most performant in projects that experience relatively high defect ratios. Future research directions for JIT-SDP include situating each technique into its application domain, reliability-aware JIT-SDP, and user-centered JIT-SDP.
A Novel Deep Learning Based Attention Mechanism for Android Malware Detection and Explanation

With the popularity of Android mobile devices and the increase of related applications, hackers regard it as the primary attack target. Therefore, malware detection is essential nowadays, and many of these studies employ deep learning techniques. In recent years, the attention mechanism provides corresponding attention weights for different hidden states, and it is widely used in many fields, such as machine translation and image markup. However, no research has applied the attention mechanism to Android malware analysis. Hence, this paper completes the goal of malware family classification based on the static features of Android applications. We compare the difference between the original convolutional neural network (CNN) and the addition of the attention mechanism. The final experimental results show that the attention mechanism improves the accuracy of the existing CNN model by 1.99% in static opcode images. In addition, we further adopt the occlusion sensitivity method to try to explain the classification model proposed in this paper. Finally, the experimental results of model interpretation show that the classification model can effectively identify the threat behavior of malware.
A Study on Improving the Value of Ubiquitous Data on the Internet: Evaluation of a recipe recommendation system for food loss reduction as an example

Abstract: In the IoT era where all "things" are connected to the Internet, a lot of information is overflowing on the Internet. Each piece of data on the Internet is extremely valuable, but its effectiveness is limited by itself. In order to increase the value of information, it is necessary to coordinate the information and extract useful information. However, most of the obtained data is unformatted data that can be freely posted and has no type, and it is difficult to recognize and process it by a computer as it is. Therefore, when using data on a computer, it is necessary to unify data formats and values. In this paper, we report specific examples and results of collecting data on the Internet using cooking recipes in Japan as a theme, automatically unifying the structure and values, and increasing the information value.
4.1: Simulation and Analysis of Edge Ghosting for Microcapsule E‐Paper Based on Particles Dynamics

A model of particles dynamics of electrophoretic display was established to simulate the distribution of charged particles, edge ghosting effect with different thicknesses, dielectric constants of back binder layer. Reflectivities corresponding to particles distributions were simulated, which evaluated the extent of edge ghosting. The model can suggest the best values of the above parameters.
X-rays from the oxygen-type Wolf-Rayet binary WR 30a

We present an analysis of XMM-Newton X-ray data of WR30a (WO+O), a close massive binary that harbours an oxygen-rich Wolf-Rayet star. Its spectrum is characterized by the presence of two well-separated broad peaks, or `bumps', one peaking at energies between 1 and 2 keV and the other between 5 and 7 keV. A two-component model is required to match the observed spectrum. The higher energy spectral peak is considerably more absorbed and dominates the X-ray luminosity. For the currently accepted distance of 7.77 kpc, the X-ray luminosity of WR30a is L_X > 10^{34} erg s^{-1}, making it one of the most X-ray luminous WR+O binary amongst those in the Galaxy with orbital periods less than ~20 d. The X-ray spectrum can be acceptably fitted using either thermal or nonthermal models, so the X-ray production mechanism is yet unclear.
19.4: Simulation and Analysis of Edge Ghosting for Microcapsule E‐Paper Based on Particles Dynamics

A model of particles dynamics of electrophoretic display was established to simulate the distribution of charged particles, edge ghosting effect with different thicknesses, dielectric constants of back binder layer. Reflectivities corresponding to particles distributions were simulated, which evaluated the extent of edge ghosting. The model can suggest the best values of the above parameters.
P‐15.3: An EIT Based Large Area Touch Interface

Nowadays, electronic devices are taking over the market and touch panel is a necessary part, among which capacitive touch panel has greater development potential and development space because of its high transparency, multitouch support and low cost. Electrical impedance tomography (EIT) is a technology with the goal of reconstructing tissue image with impedance distribution, which can realize the goal of accurate measurement and maintaining the original characteristics of the medium to the greatest extent at the same time. In this paper, we use EIT‐based approach to achieve a large area touch perception imaging system with high light transmittance, which is to obtain the distribution of the permittivity of the touch penal by just detecting the impedance of the electrode scattered around the panel. We use Sensitivity theory to solve the mapping problem between the permittivity distribution and the signal collected by the electrode in the EIT problem. Besides, we innovatively combine LBP with Landweber algorithm to achieve high precision and fast imaging of touch area, which greatly reduces the discomfort caused by inverse problem in EIT method.
P‐5.7: Selective Laser Lift‐off of GaN Micro‐LED from a Sapphire Substrate Using 266‐nm Solid‐state Laser

In this paper, we realize the process of 8*8μm micro‐LED arrays laser lift‐off to remove the sapphire substrate and get integrated GaN epitaxial films by 266nm SPSS solid‐state laser. Several blue light flip‐chip micro‐LED arrays with a resolution of 1280x720 are designed and fabricated based on the known silicon‐substrate‐based drive circuit panel. The LED side is welded to the silicon substrate by metallic bonding process. Epoxy resin structured adhesive is filled between the interface between the silicon carrier and Micro‐LED array to supply a strong mechanical support and an avoidance of de‐bonding.
33.2: A Tunable Filter with Single Layer Twist Structure Liquid Crystals

A bandwidth tunable filter and a multi‐pitch filter based on twist structure liquid crystals (LCs) were proposed. The LC filters can be fabricated by multiple templating and refilling process, which shows large bandwidth and good extensibility. The bandwidth of the twist structure LC filter can be tuned from 111 nm to 244 nm with central wavelength shift of 16 nm. Furthermore, the bandwidth can be broadened to a great extent theoretically by the simple fabrication process. Three‐pitch twist structure LC filter was obtained, and the pitch number can be increased by utilizing multiple templating technique. The fabricated tunable twist structure LC filters show a potential application in optical communication device and spectral systems.
Contact Sensitization Dendritic Cell TLR4 Activation and Allergic Cathelicidin Antimicrobial Peptides Block

Cathelicidins are antimicrobial peptides of the innate immune system that establish an antimicrobial barrier at epithelial inter-faces and have been proposed to have a proinﬂammatory function. We studied the role of cathelicidin in allergic contact dermatitis, a model requiring dendritic cells of the innate immune response and T cells of the adaptive immune response. Deletion of the murine cathelicidin gene Cnlp enhanced an allergic contact response, whereas local administration of cathelicidin before sensitization inhibited the allergic response. Cathelicidins inhibited TLR4 but not TLR2 mediated induction of dendritic cell maturation and cytokine release, and this inhibition was associated with an alteration of cell membrane function and structure. Further analysis in vivo connected these observations because inhibition of sensitization by exogenous cathelicidin was dependent on the presence of functional TLR4. These observations provide evidence that cathelicidin antimicrobial peptides mediate an anti-inﬂammatory response in part by their activity at the membrane. The Journal of Immunology, 2007, 178: 1829–1834.
30.1: Invited Paper: Device Physics and Compact Modeling of Metal Oxide Thin‐Film Transistors

In this paper, we have proposed a direct current model and noise model, which are physically based on the metal oxide thin‐film transistors (TFTs) operation mechanisms. Based on the calculated surface potential and the Pao‐Sah double integral formula, the direct current characteristics of metal oxide TFTs are predicted. According to low‐frequency noise (LFN) models, the mechanism affecting the noise properties of metal oxide TFTs is analyzed, and the density of trap states near the device interface is extracted by the LFN method. Through comparisons between model results and numerical iteration or experimental data, the validity of the proposed models is strongly supported. Due to the simplicity of algorithm and clear physical conception, it is easy to implement these models into circuit simulators.
54.2: Invited Paper: Flat Liquid Crystal Microlens Based on Spatially‐variant Photoalignment

Microlenses have attracted increasing attention in recent years due to the emergent demand in the booming stereoscopic imaging industry and highly integrated optical systems. In this study, we propose a customized approach to design liquid crystal microlens (LCM) for subwavelength focusing, based on the vectorial Rayleigh‐Sommerfeld (VRS) method and the trust region algorithm. It is demonstrated that the computation time and computing resources can be greatly reduced by using our proposal when compared to the commercial software. Both the polarization of the incidence and diffraction field is taken into account in the design, which makes it more reliable. We fabricated the LCM by using photoalignment technology based on the digital micromirror device (DMD), and experimentally characterized the focusing performance of the sample. A Frank‐Oseen model is also established to simulate the mechanical properties of the liquid crystal (LC) layer and analyze the effect of the transition region on the LC directors.
Modelling clumpy photon-dominated regions in 3D. Understanding the Orion Bar stratification

Context. Models of photon-dominated regions (PDRs) still fail to fully reproduce some of the observed properties. In particular they do not reproduce the combination of the intensities of different PDR cooling lines together with the chemical stratification, as observed for example for the Orion Bar PDR. Aims. We aim to construct a numerical PDR model, KOSMA- τ 3D, to simulate full spectral cubes of line emission from arbitrary PDRs in three dimensions (3D). The model will reproduce the intensity of the main cooling lines from the Orion Bar PDR and the observed layered structure of the different transitions. Methods. We built up a 3D compound, made of voxels (3D pixels) that contain a discrete mass distribution of spherical “clumpy” structures, approximating the fractal ISM. To analyse each individual clump the new code was combined with the KOSMA- τ PDR model. Probabilistic algorithms were used to calculate the local FUV flux for each voxel as well as the voxel-averaged line emissivities and optical depths, based on the properties of the individual clumps. Finally, the computation of the radiative transfer through the compound provided full spectral cubes. To test the new model we tried to simulate the structure of the Orion Bar PDR and compared the results to observations from HIFI/ Herschel and from the Caltech Submillimetre Observatory (CSO). In this context new Herschel data from the HEXOS guaranteed-time key program is presented. Results. Our model is able to reproduce the line-integrated intensities within a factor of 2.5 and the observed stratification pattern within 0.016 pc for the [Cii] 158 μ m and different 12/13 CO and HCO + transitions, based on the representation of the Orion Bar PDR by a clumpy edge-on cavity wall. In the cavity wall, a large fraction of the total mass needs to be contained in clumps. The mass of the interclump medium is constrained by the FUV penetration. Furthermore, the stratification profile cannot be reproduced by a model that has the same amount of clump and interclump mass in each voxel; dense clumps need to be removed from the PDR surface.
Equilibration in phi**4 theory in 3+1 dimensions

The process of equilibration in ${\ensuremath{\varphi}}^{4}$ theory is investigated for a homogeneous system in $3+1$ dimensions and a variety of out-of-equilibrium initial conditions, both in the symmetric and broken phase, by means of the 2PI effective action. Two $\ensuremath{\Phi}$-derivable approximations including scattering effects are used: the two-loop and the basketball, the latter corresponding to the truncation of the 2PI effective action at $\mathcal{O}({\ensuremath{\lambda}}^{2})$. The approach to equilibrium, as well as the kinetic and chemical equilibration is investigated.
Competing risk regression models in cohort studies with the R package CohortMethod

Background In survival analysis, competing risks are outcomes that preclude the main study outcome of interest, or alter the probability of experiencing the main outcome(s) [1]. The Fine and Gray model is an extension of the Cox proportional hazards model with subdistribution hazard function (Eq. 1), defined through the instantaneous rate λ k ( t ) of experiencing the event of interest D = k for subjects given they have survival already to time t without any competing events K ̸ = k having occurred for observed failure time T [2]:
Pole-zero identification based on simultaneous realization of normalized covariances and Markov parameters

Given the pole-zero configuration of a stable and rational transfer function it is trivial to determine the normalized covariances and Markov parameters. It is nontrivial and was recently shown that for finite windows of these parameters there corresponds a unique minimal and stable rational transfer function. Furthermore, small changes in the parameters corresponds to small changes of the transfer function, which makes the method robust. However, the proof was non-constructive and no algorithm for determining the inverse map was known. An efficient algorithm for determining the pole-zero configuration of the interpolating transfer function is the main contribution of this paper. As a corollary a novel and simplified approach to the minimal stochastic realization problem is obtained. Using an example from speech processing it is shown how this realization theory result can be used for identification of time series.
Structural centrality of networks can improve the diffusion-based recommendation algorithm

The recommendation system has become an indispensable information technology in the real world. The recommendation system based on the diffusion model has been widely used because of its simplicity, scalability, interpretability, and many other advantages. However, the traditional diffusion-based recommendation model only uses the nearest neighbor information, which limits its efficiency and performance. Therefore, in this article, we introduce the centralities of complex networks into the diffusion-based recommendation system and test its performance. The results show that the overall performance of heat conduction algorithm can be improved by 184%–280%, using the centrality of complex networks, reaching almost the same accuracy level as the mass diffusion algorithm. Therefore, the recommendation system combining the high-order network structure information is a potentially promising research direction in the future.
miRNA-150_R-1 mediates the HIF-1/ErbB signaling pathway to regulate the adhesion of endometrial epithelial cells in cows experiencing retained placenta

Retained placenta (RP) refers to reproductive disorders caused by the failure of fetal membranes to be expelled 12 h after delivery in dairy cows. Postpartum adhesion of the fetal membranes to the uterus causes diseases such as mastitis or endometritis, which threatening the profitability of the dairy industry. Emerging evidence suggests that micro RNAs (miRNAs) play crucial roles in various processes, such as the occurrence and progression of fetal membranes discharge. However, the molecular mechanisms of miRNAs in RP remain unknown. In this study, we performed RNA-sequencing to characterize the expression profiles of mRNAs and miRNAs in caudal vein blood samples of postpartum Holstein cows whose fetal membranes were discharged normally or retained to identify RP-related genes and evaluate their molecular mechanisms. We identified 44 differentially expressed miRNAs (19 upregulated and 25 downregulated) and 706 differentially expressed mRNAs (325 upregulated and 381 downregulated) in the RP group compared to the normal fetal membranes discharge group. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis revealed that differentially expressed mRNAs were mainly enriched in the extracellular matrix, cell adhesion, and autoimmunity-related biological processes or pathways. Further analyses using RNA-sequencing, a dual luciferase reporter system, quantitative reverse transcription-PCR, immunofluorescence, and western blotting verified that endothelial PAS domain protein 1 (EPAS1) is regulated by miR-150_R-1 in endometrial epithelial cells. We demonstrated the relationship between EPAS1 and RP and confirmed that EPAS1 is upregulated in the blood and placenta of cows that experience RP. Further, we proposed a model of the miRNA-mRNA negative regulatory network mediated by the HIF-1/ErbB signaling pathway to show its regulatory role in RP.
Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola

Angola, located in Central Africa, has around 320,000 (270,000–380,000) people living with human immunodeficiency virus (HIV)/AIDS, equivalent to 1% of the country’s population at the end of 2021. A previous study conducted in 2012, using Angolan samples collected between 2008 and 2010 revealed a high prevalence of HIV-1 recombinants, around 42% of sequences, with 21% showing the same UH profile in partial pol region which were grouped into a monophyletic cluster with high bootstrap support. Thus, the objective of the present work was to obtain complete genomes of those sequences and characterize them, aiming at a description of a new circulating recombinant form (CRF). Whole blood from nine HIV-1 UH pol-infected individuals had their genomic DNA extracted, and nested PCR was used to amplify seven overlapping fragments targeting the full-length HIV-1 genome. The final classification was based on maximum likelihood trees, and recombination analyses were performed using a bootscan from the Simplot program. BLAST and Los Alamos Database inspections were used to search other similar H-like pol sequences. Complete genome amplification was possible for three samples, partial genomes were obtained for the other three, and only pol was available for the remaining three sequences. Bootscan analysis of the two whole-genome and three partial genome sequences retrieved from people living with HIV/AIDS (PLHIVA) without epidemiological linkage showed the same complex recombination profile involving HIV-1 subtypes A/G/H/CRF27_cpx, with a total of six recombinant breakpoints, aiming to classify a new HIV-1 CRF124_cpx. We found no other full-length HIV-1 genomes with the same mosaic profile; however, we identified 33 partial pol sequences, mainly sampled from Angola between 2001 to 2019, with the same H-like profile. Bayesian analysis of H and H-like pol sequences indicates that CRF124_cpx probably originated in Angola at mid-1970s, indicating that this CRF has been circulating in the country for a long time. In summary, our study describes a new CRF circulating principally in Angola and highlights the importance of continuing molecular surveillance studies, especially in countries with high molecular diversity of HIV.
Machine learning-based characterization of cuprotosis-related biomarkers and immune infiltration in Parkinson’s disease

Background: Parkinson’s disease (PD) is a neurodegenerative disease commonly seen in the elderly. On the other hand, cuprotosis is a new copper-dependent type of cell death that can be observed in various diseases. Methods: This study aimed to identify potential novel biomarkers of Parkinson’s disease by biomarker analysis and to explore immune cell infiltration during the onset of cuprotosis. Gene expression profiles were retrieved from the GEO database for the GSE8397, GSE7621, GSE20163, and GSE20186 datasets. Three machine learning algorithms: the least absolute shrinkage and selection operator (LASSO), random forest, and support vector machine-recursive feature elimination (SVM-RFE) were used to screen for signature genes for Parkinson’s disease onset and cuprotosis-related genes (CRG). Immune cell infiltration was estimated by ssGSEA, and cuprotosis-related genes associated with immune cells and immune function were examined using spearman correlation analysis. Nomogram was created to validate the accuracy of these cuprotosis-related genes in predicting PD disease progression. Classification of Parkinson’s specimens using consensus clustering methods. Result: Three PD datasets from the Gene Expression Omnibus (GEO) database were combined after eliminating batch effects. By ssGSEA, we identified three cuprotosis-related genes ATP7A, SLC31A1, and DBT associated with immune cells or immune function in PD and more accurate for the diagnosis of Parkinson’s disease course. Patients could benefit clinically from a characteristic line graph based on these genes. Consistent clustering analysis identified two subtypes, with the C2 subtype exhibiting higher immune cell infiltration and immune function. Conclusion: In conclusion, our study reveals that several newly identified cuprotosis-related genes intervene in the progression of Parkinson’s disease through immune cell infiltration.