Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross-Validation-Based Association Rule Prioritization Metric for Software Defect Characterization

Association rule mining discovers relationships among variables in a data set, representing them as rules. These are expected to often have predictive abilities, that is, to be able to predict future events, but commonly used rule interestingness measures, such as support and confidence, do not directly assess their predictive power. This paper proposes a cross-validation -based metric that quantifies the predictive power of such rules for characterizing software defects. The results of evaluation this metric experimentally using four open-source data sets (Mylyn, NetBeans, Apache Ant and jEdit) show that it can improve rule prioritization performance over conventional metrics (support, confidence and odds ratio) by 72.8% for Mylyn, 15.0% for NetBeans, 10.5% for Apache Ant and 0 for jEdit in terms of SumNormPre(100) precision criterion. This suggests that the proposed metric can provide better rule prioritization performance than conventional metrics and can at least provide similar performance even in the worst case. key words: association rule mining, defect prediction, cross-validation, data mining, software quality
Rotavirus vaccine efficacy: current status and areas for improvement

ABSTRACT The difference noted in Rotavirus vaccine efficiency between high and low income countries correlates with the lack of universal access to clean water and higher standards of hygiene. Overcoming these obstacles will require great investment and also time, therefore more effective vaccines should be developed to meet the needs of those who would benefit the most from them. Increasing our current knowledge of mucosal immunity, response to Rotavirus infection and its modulation by circadian rhythms could point at actionable pathways to improve vaccination efficacy, especially in the case of individuals affected by environmental enteropathy. Also, a better understanding and validation of Rotavirus entry factors as well as the systematic monitoring of dominant strains could assist in tailoring vaccines to individual’s needs. Another aspect that could improve vaccine efficiency is targeting to M cells, for which new ligands could potentially be sought. Finally, alternative mucosal adjuvants and vaccine expression, storage and delivery systems could have a positive impact in the outcome of Rotavirus vaccination.
Omnichannel Service Operations with Online and Offline Self-Order Technologies

Many restaurants have recently implemented self-order technologies across both online and offline channels. Online technology, through websites and mobile apps, allows customers to order and pay before coming to the store; offline technology, such as self-service kiosks, allows store customers to place orders without interacting with a human employee. In this paper, we develop a stylized theoretical model to study the impact of self-order technologies on customer demand, employment levels, and restaurant profits. Our main results follow. First, customers using self-order technologies experience reduced waiting cost and increased demand, and moreover, these benefits may even carry over to customers who do not use these technologies. Second, although public opinion suggests that self-order technologies facilitate job cuts, we find instead that some firms should increase employment levels, and, paradoxically, this recommendation holds for firms with high labor costs. Finally, we find that firms should implement online offline self-order technology when customers have high low wait sensitivity. The supplementary appendix is available at https://doi.org/10.1287/mnsc.2017. 2787 . This paper was accepted by Serguei Netessine, operations management.
Flow Based Video Super-Resolution with Spatio-temporal Patch Similarity

The goal of super-resolution is to fuse several low-resolution images of the same scene into a single one with increased resolution. The classical formulation assumes that the super-resolved image is related to the low-resolution frames by warping, convolution and subsampling. Algorithms divide into those using explicit registration and those avoiding it. The first ones combine for each pixel the information in its estimated trajectory. The second ones exploit both spatial and temporal redundancy. We propose to combine both ideas, making use of optical flow and exploiting spatio-temporal redundancy with patch-based techniques. The proposed non-linear filtering takes into account patch similarities, automatically correcting the flow inaccuracies and avoiding the need of occlusion detection. Total variation and nonlocal regularization are used for the deconvolution stage. The experimental results demonstrate the state-of-the-art performance of the proposed approach.
Bacteroides thetaiotaomicron Ameliorates Colon Inflammation in Preclinical Models of Crohn’s Disease

Abstract Background Alterations in the gut microbiota are strongly associated with the development of inflammatory bowel disease (IBD), particularly with Crohn’s disease, which is characterized by reduced abundance of commensal anaerobic bacteria including members of the Bacteroides genus. Our aim was to investigate the protective effects of Bacteroides thetaiotaomicron, an abundant member of this genus, in different rodent models of IBD. Methods We assessed the effect of B. thetaiotaomicron administration on primary readouts of colitis (weight loss, histopathology, and immune parameters) in dextran sodium sulphate (DSS) and interleukin-10 knockout (IL10KO) models of IBD. Efficacy of a freeze-dried bacterial formulation and a purified recombinant protein of B. thetaiotaomicron was also investigated. Results B. thetaiotaomicron showed protective effects in both DSS and IL10KO rodent models, as demonstrated by significant amelioration of weight loss, colon shortening, histopathological damage and immune activation. This efficacy was not exclusive to actively growing bacterial preparations but was retained by freeze-dried cells of B. thetaiotaomicron. A pirin-like protein (PLP) of B. thetaiotaomicron, identified by microarray analysis during coculture of the bacterial strain with Caco-2 cells, reduced pro-inflammatory NF-κB signalling in these intestinal epithelial cells. Recombinant PLP partially recapitulated the effect of the whole strain in a rat DSS model. Conclusions B. thetaiotaomicron displays strong efficacy in preclinical models of IBD and protects against weight loss, histopathological changes in the colon and inflammatory markers. These data indicate that the live strain or its products may be a novel alternative to current treatment options for Crohn’s disease.
Temporal Trends in Co-trimoxazole Use Among Children on Antiretroviral Therapy and the Impact of Co-trimoxazole on Mortality Rates in Children Without Severe Immunodeficiency.

Background Co-trimoxazole is recommended for all children with human immunodeficiency virus. In this analysis, we evaluate trends in pediatric co-trimoxazole use and survival on co-trimoxazole in children using antiretroviral therapy (ART). Methods We used data collected between January 1, 2006, and March 31, 2016, from the International Epidemiology Databases to Evaluate AIDS. Logistic regression was used to evaluate factors associated with using co-trimoxazole at ART initiation. Competing risk regression was used to assess factors associated with death. Results A total of 54113 children were included in this study. The prevalence of co-trimoxazole use at ART initiation increased from 66.5% in 2006 to a peak of 85.6% in 2010 and then declined to 48.5% in 2015-2016. A similar trend was observed among children who started ART with severe immunodeficiency. After adjusting for year of ART initiation, younger age (odds ratio [OR], 1.18 for <1 vs 1 to <5 years of age [95% confidence interval (CI), 1.09-1.28]), lower height-for-age z score (OR, 1.15 for less than -3 vs greater than -2 [95% CI, 1.08-1.22]), anemia (OR, 1.08 [95% CI, 1.02-1.15]), severe immunodeficiency (OR, 1.25 [95% CI, 1.18-1.32]), and receiving care in East Africa (OR, 8.97 vs Southern Africa [95% CI, 8.17-9.85]) were associated with a high prevalence of co-trimoxazole use. Survival did not differ according to co-trimoxazole use in children without severe immunodeficiency (hazard ratio, 1.01 for nonusers versus users [95% CI, 0.77-1.34]). Conclusions Recent declines in co-trimoxazole use may not be linked to the current shift toward early ART initiation. Randomized trial data might be needed to establish the survival benefit of co-trimoxazole in children without severe immunodeficiency.
Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes

The evolution of signal transduction pathways is constrained by the requirements of signal fidelity, yet flexibility is necessary to allow pathway remodeling in response to environmental challenges. A detailed understanding of how flexibility and constraint shape bacterial two component signaling systems is emerging, but how new signal transduction architectures arise remains unclear. Here, we investigate pathway remodeling using the Firmicute sporulation initiation (Spo0) pathway as a model. The present-day Spo0 pathways in Bacilli and Clostridia share common ancestry, but possess different architectures. In Clostridium acetobutylicum, sensor kinases directly phosphorylate Spo0A, the master regulator of sporulation. In Bacillus subtilis, Spo0A is activated via a four-protein phosphorelay. The current view favors an ancestral direct phosphorylation architecture, with the phosphorelay emerging in the Bacillar lineage. Our results reject this hypothesis. Our analysis of 84 broadly distributed Firmicute genomes predicts phosphorelays in numerous Clostridia, contrary to the expectation that the Spo0 phosphorelay is unique to Bacilli. Our experimental verification of a functional Spo0 phosphorelay encoded by Desulfotomaculum acetoxidans (Class Clostridia) further supports functional phosphorelays in Clostridia, which strongly suggests that the ancestral Spo0 pathway was a phosphorelay. Cross complementation assays between Bacillar and Clostridial phosphorelays demonstrate conservation of interaction specificity since their divergence over 2.7 BYA. Further, the distribution of direct phosphorylation Spo0 pathways is patchy, suggesting multiple, independent instances of remodeling from phosphorelay to direct phosphorylation. We provide evidence that these transitions are likely the result of changes in sporulation kinase specificity or acquisition of a sensor kinase with specificity for Spo0A, which is remarkably conserved in both architectures. We conclude that flexible encoding of interaction specificity, a phenotype that is only intermittently essential, and the recruitment of kinases to recognize novel environmental signals resulted in a consistent and repeated pattern of remodeling of the Spo0 pathway.
A phase III clinical trial to evaluate the safety and immunogenicity of 23-valent pneumococcal polysaccharide vaccine (PPV23) in healthy children, adults, and elderly

ABSTRACT To evaluate the safety and immunogenicity of a newly 23-valent pneumococcal polysaccharide vaccine (PPV23), a phase Ⅲ clinical trial was conducted in population aged ≥ 2 years. We conducted a randomized, double-blinded, active controlled trial, in which 1760 participants were randomly assigned in a 1:1 ratio to receive one dose of either the test vaccine or the control commercial vaccine. The surveillance period was 28 days. The 2-fold increase rate of anti-pneumococcal for 23 serotypes varied from 49.71% to 90.96% in the treatment group and from 44.52% to 88.24% in the control group. According to −10% non-inferiority margin and 95% confidence intervals of rate difference, all the 23 serotypes of the treatment group were non-inferiority to the control group. The 2-fold increase rate of anti-pneumococcal antibody were significantly higher in the treatment group for 11 serotypes including 1, 2, 3, 4, 10A, 11A, 14, 18C, 20, 22F, and 23F. Serious adverse events occurred in 2 in 879 (0.23%) participants in the treatment group and 2 in 880 (0.23%) participants in the control group, and all the adverse events were unrelated to the vaccination. The overall adverse reaction frequency showed no difference between the treatment (51.19%) and control group (47.95%), and most adverse reactions were mild or moderate in intensity. The newly PPV23 is immunologically non-inferior to the control commercial vaccine and well tolerated in healthy Chinese population aged ≥ 2 years. Trial registration: ClinicalTrial.gov identifier: NCT02451969.
Deep compressive autoencoder for action potential compression in large-scale neural recording

Objective. Understanding the coordinated activity underlying brain computations requires large-scale, simultaneous recordings from distributed neuronal structures at a cellular-level resolution. One major hurdle to design high-bandwidth, high-precision, large-scale neural interfaces lies in the formidable data streams (tens to hundreds of Gbps) that are generated by the recorder chip and need to be online transferred to a remote computer. The data rates can require hundreds to thousands of I/O pads on the recorder chip and power consumption on the order of Watts for data streaming alone. One of the solutions is to reduce the bandwidth of neural signals before transmission. Approach. We developed a deep learning-based compression model to reduce the data rate of multichannel action potentials. The proposed compression model is built upon a deep compressive autoencoder (CAE) with discrete latent embeddings. The encoder network of CAE is equipped with residual transformations to extract representative features from spikes, which are mapped into the latent embedding space and updated via vector quantization (VQ). The indexes of VQ codebook are further entropy coded as the compressed signals. The decoder network reconstructs spike waveforms with high quality from the quantized latent embeddings through stacked deconvolution. Main results. Extensive experimental results on both synthetic and in vivo datasets show that the proposed model consistently outperforms conventional methods that utilize hand-crafted features and/or signal-agnostic transformations and compressive sensing by achieving much higher compression ratios (20–500×) and better or comparable reconstruction accuracies. Testing results also indicate that CAE is robust against a diverse range of imperfections, such as waveform variation and spike misalignment, and has minor influence on spike sorting accuracy. Furthermore, we have estimated the hardware cost and real-time performance of CAE and shown that it could support thousands of recording channels simultaneously without excessive power/heat dissipation. Significance. The proposed model can reduce the required data transmission bandwidth in large-scale recording experiments and maintain good signal qualities, which will be helpful to design power-efficient and lightweight wireless neural interfaces. We have open sourced the code implementation of the work at https://github.com/tong-wu-umn/spike-compression-autoencoder.
Geographical inequality in cataract surgery among Iranians between 2006 and 2011.

Background Cataract surgery is a highly cost-effective intervention for sight restoration but inequalities exist in its use which health care systems should aim to reduce. Aims This study aimed to measure the level of inequality in cataract surgery use and the changes in inequality between 2006 and 2011 in the Islamic Republic of Iran. Methods A number of metrics, including ranges and indexes based on Lorenz curves (Gini, concentration and dissimilarity indexes), were used to measure the inequality in cataract surgery use among Iranians in 2006 and 2011. Cataract surgical numbers and socioeconomic data were obtained from a province-based survey and the national census database. Results Significant inter-provincial and inter-regional differences were found in cataract surgical proportions. South Khorasan province had the lowest cataract surgical rate in 2006 and 2011, while Tehran province had the highest rate in both years. Inequality in the distribution of cataract surgery services decreased between 2006 and 2011: the Gini, concentration and dissimilarity indexes decreased by 0.028, 0.03 and 0.037, respectively. However, cataract surgery delivery remained in favour of the better-off provinces. Conclusions To reduce this inequality, policy-makers should improve financial and physical access to cataract surgery, especially in the relatively deprived provinces, and tackle physician-induced demand.
An Edge Detection Method Based on Wavelet Transform at Arbitrary Angles

The quality of edge detection is related to detection angle, scale, and threshold. There have been many algorithms to promote edge detection quality by some rules about detection angles. However these algorithm did not form rules to detect edges at an arbitrary angle, therefore they just used different number of angles and did not indicate optimized number of angles. In this paper, a novel edge detection algorithm is proposed to detect edges at arbitrary angles and optimized number of angles in the algorithm is introduced. The algorithm combines singularity detection with Gaussian wavelet transform and edge detection at arbitrary directions and contain five steps: 1) An image is divided into some pixel lines at certain angle in the range from 45◦ to 90◦ according to decomposition rules of this paper. 2) Singularities of pixel lines are detected and form an edge image at the certain angle. 3) Many edge images at different angles form a final edge images. 4) Detection angles in the range from 45◦ to 90◦ are extended to range from 0◦ to 360◦. 5) Optimized number of angles for the algorithm is proposed. Then the algorithm with optimized number of angles shows better performances. key words: edge detection, arbitrary angles, Gaussian wavelet, optimized number, figure of merit
Impact of mesoscale eddies on chlorophyll variability off the coast of Chile

The mesoscale eddies off the coast of Chile significantly impact the distribution of local chlorophyll and the development of marine ecosystem. Multiple processes, including eddy trapping, pumping, advection, Ekman-pumping, and submesoscale dynamics, exert their impacts simultaneously on transport of water masses at different distances with respect to the eddy center. The cyclonic (anticyclonic) eddies are generally characterized by upwelling (downwelling) within the eddy, which elevates (depresses) chlorophyll inside the eddy. Outside the eddy periphery, multiple processes are involved simultaneously, but their corresponding influences on chlorophyll are not well identified. In this study, the amplitudes of cyclonic and anticyclonic eddies are distinguished as positive and negative values, respectively. A linear regression method is applied to seek the connection between eddy’s amplitude and chlorophyll distribution at different locations w.r. t. the eddy center. The regression slope between eddy amplitude and chlorophyll anomaly is found to be negative in the eddy interior and along the periphery, which gradually changes to positive away from the periphery. The location where the response of chlorophyll to an eddy switches its sign is defined as the transition zone. The location of the transition zone varies with offshore distance and is impacted by topography, such as the presence of islands, which can change the dynamics of eddies. Thus, the distance from eddy center and offshore distance from coast should be taken into consideration when investigating their influences on nutrient transport and chlorophyll distribution.
Fabrication of Dielectric Elastomer Composites by Locking a Pre-Stretched Fibrous TPU Network in EVA

Dielectric elastomer (DE) composites with high electrical breakdown strength and large voltage-induced deformation were developed by retaining pre-stretched thermoplastic polyurethane (TPU) fibers in ethylene vinyl acetate copolymer (EVA). The microstructure of the candidate E-TPU fiber membrane and EVA coated E-TPU (E-TPU/EVA) film were characterized by scanning electron microscopy (SEM). The quasi-static and dynamic mechanical property, and the electromechanical properties, including the dielectric constant, dielectric loss tangent, and electromechanical sensitivity, of the DE composites were evaluated. Initially, tensile tests demonstrated that the DE composites based on E-TPU/EVAs had a higher elongation at break of above 1000% but a low elastic modulus of approximately 1.7 MPa. Furthermore, dielectric spectroscopy showed that the E-TPU/EVA had a dielectric constant of 4.5 at the frequency of 1000 Hz, which was 1.2 times higher than that of pure EVA film. Finally, it was found from electromechanical test that the voltage induced strain of E-TPU/EVA rose to 6%, nearly 3 times higher than that of pure TPU film, indicating an excellent electromechanical property. The DE composites developed have demonstrated the potential to be good candidate materials in the fields of artificial intelligence, biomimicry and renewable energy.
Role of Salivary Immune Parameters in Patients With Primary Sjögren's Syndrome

Background Several factors, including clinical manifestations and laboratory data, have been used to evaluate the disease activity of Sjögren's syndrome (SS). We investigated saliva indicators of disease activity in primary SS patients. Methods We enrolled 138 Taiwanese patients with primary SS and 100 Taiwanese normal controls. Interleukin (IL)-6, IL-17A, tumor necrosis factor-alpha (TNF-α), and rheumatoid factor (RF)-IgA levels in saliva samples were measured using ELISA or fluorescent enzyme-linked immunoassay. Serum IgG, IgA, and IgM levels were measured by nephelometry. Erythrocyte sedimentation rate (ESR) was measured with an automatic ESR analyzer. The t-test and Pearson correlation test were used. Results IL-6 level was higher in primary SS patients than in normal controls (14.23±14.77 vs 9.87±7.32, P=0.012), but there were no significant differences in IL-17A, TNF-α, and RF-IgA levels. In primary SS patients, IL-6 level correlated weakly with ESR and IgG levels (r=0.252, P=0.015, and r=0.248, P=0.017, respectively), and TNF-α level correlated weakly with IgG level (r=0.231, P=0.024). Conclusions IL-6 may play a role in SS pathogenesis. Saliva IL-6 might be an indicator of disease activity in primary SS patients.