Search Results (16)

Numerical Association Rule Mining (NARM), which simultaneously handles both numerical and categorical attributes, is a powerful approach for uncovering meaningful associations in heterogeneous datasets. However, designing effective NARM solutions is a complex task involving multiple sequential steps, such as data preprocessing, algorithm selection, hyper-parameter tuning, and the definition of rule quality metrics, which together form a complete processing pipeline. In this paper, we introduce NiaAutoARM, a novel Automated Machine Learning (AutoML) framework that leverages stochastic population-based metaheuristics to automatically construct full association rule mining pipelines. Extensive experimental evaluation on ten benchmark datasets demonstrated that NiaAutoARM consistently identifies high-quality pipelines, improving both rule accuracy and interpretability compared to baseline configurations. Furthermore, NiaAutoARM achieves superior or comparable performance to the state-of-the-art VARDE algorithm while offering greater flexibility and automation. These results highlight the framework’s practical value for automating NARM tasks, reducing the need for manual tuning, and enabling broader adoption of association rule mining in real-world applications. Full article

The nucleocapsid (N) protein is one of the four structural proteins in SARS-CoV-2, playing key roles in viral assembly, immune evasion, and stability. One of its primary functions is to protect viral RNA by forming the nucleocapsid. However, the precise mechanisms by which the N protein interacts with viral RNA and assembles into a nucleocapsid remain unclear. Compared to other SARS-CoV-2 components, targeting the N protein has several advantages: it exhibits higher sequence conservation, lower mutation rates, and stronger immunogenicity, making it an attractive target for antiviral drug development and diagnostics. Therefore, a detailed understanding of the N protein’s structure is essential for deciphering its role in viral assembly and developing effective therapeutics. In this study, we report the expression and purification of a soluble recombinant N protein, along with a 1.55 Å resolution crystal structure of its nucleic acid-binding domain (N-NTD) in complex with ssDNA. Our structure revealed new insights into the conformation and interaction of the flexible N-arm, which could aid in understanding nucleocapsid assembly. Additionally, we identified residues that are critical for ssDNA interaction. Full article

A design methodology for a resistorless low-power two-in-one voltage and current reference source working in subthreshold and moderate regions is described. The presented novel universal reference voltage–current source was implemented in ten different designs for seven different CMOS technologies. Six versions of these designs were silicon-proven using four different CMOS technologies. The example of implementation in 130 nm technology provides a reference current of 5 µA and reference voltage of 800 mV at supply voltages ranging from 0.9 V to 2.0 V with a total current consumption of 15 µA. The proposed circuit occupies a 1200 µm² chip area and achieves 280 and 118 ppm/°C for all process corners and temperature variation from −40 °C to 125 °C. The power supply rejection ratio of output I_REF without any filtering capacitor at 100 Hz and 10 MHz is 128 dB and 100 dB, respectively. The equivalent output current noise in the bandwidth from 1 Hz to 10 MHz reaches 9.1 nA_RMS. Full article

This study examined the impact of the 2017 Veterinary Feed Directive (VFD) rule changes on the prevalence of tetracycline-resistant and erythromycin-resistant bacteria (Salmonella spp., Campylobacter spp., and Escherichia coli) in cecal samples of food animals (cattle, swine, chicken, and turkey) at US slaughterhouses. Multivariable logistic regression was used to analyze 2013–2019 cecal samples of food-producing animals surveillance data from the National Antimicrobial Resistance Monitoring System (NARMS) in the U.S. The variables included year (used to evaluate VFD rule changes), host, and quarter of year. The analysis of surveillance data showed that the VFD rule changes have varying effects on tetracycline-resistant and erythromycin-resistant bacteria in food animals. For example, the odds of detecting tetracycline-resistant Salmonella spp. decreased in cattle but increased in chickens following the implementation of the VFD rule changes. Similarly, the odds of detecting tetracycline-resistant Escherichia coli decreased in chickens but increased in swine after the VFD rule changes. The odds of detecting erythromycin-resistant Campylobacter spp. increased in cattle but decreased in chickens after the VFD rule changes. In conclusion, the implementation of VFD rule changes has been beneficial in reducing the odds of detecting tetracycline-resistant Escherichia coli and erythromycin-resistant Campylobacter spp. in chickens, as well as tetracycline-resistant Salmonella spp. in cattle at US slaughterhouses. Full article

The outcome of bacterial infection management relies on prompt diagnosis and effective treatment, but conventional antimicrobial susceptibility testing can be slow and labor-intensive. Therefore, this study aims to predict phenotypic antimicrobial susceptibility of selected beta-lactam antimicrobials in the bacteria of the family Enterobacteriaceae from different beta-lactamase resistance genotypes. Using human datasets extracted from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program conducted by Pfizer and retail meat datasets from the National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS), we used a robust or weighted least square multivariable linear regression modeling framework to explore the relationship between antimicrobial susceptibility data of beta-lactam antimicrobials and different types of beta-lactamase resistance genes. In humans, in the presence of the bla_CTX-M-1, bla_CTX-M-2, bla_CTX-M-8/25, and bla_CTX-M-9 groups, MICs of cephalosporins significantly increased by values between 0.34–3.07 μg/mL, however, the MICs of carbapenem significantly decreased by values between 0.81–0.87 μg/mL. In the presence of carbapenemase genes (bla_KPC, bla_NDM, bla_IMP, and bla_VIM), the MICs of cephalosporin antimicrobials significantly increased by values between 1.06–5.77 μg/mL, while the MICs of carbapenem antimicrobials significantly increased by values between 5.39–67.38 μg/mL. In retail meat, MIC of ceftriaxone increased significantly in the presence of bla_CMY-2, bla_CTX-M-1, bla_CTX-M-55, bla_CTX-M-65, and bla_SHV-2 by 55.16 μg/mL, 222.70 μg/mL, 250.81 μg/mL, 204.89 μg/mL, and 31.51 μg/mL respectively. MIC of cefoxitin increased significantly in the presence of bla_CTX-M-65 and bla_TEM-1 by 1.57 μg/mL and 1.04 μg/mL respectively. In the presence of bla_CMY-2, MIC of cefoxitin increased by an average of 8.66 μg/mL over 17 years. Compared to E. coli isolates, MIC of cefoxitin in Salmonella enterica isolates decreased significantly by 0.67 μg/mL. On the other hand, MIC of ceftiofur increased in the presence of bla_CTX-M-1, bla_CTX-M-65, bla_SHV-2, and bla_TEM-1 by 8.82 μg/mL, 9.11 μg/mL, 8.18 μg/mL, and 1.04 μg/mL respectively. In the presence of bla_CMY-2, MIC of ceftiofur increased by an average of 10.20 μg/mL over 14 years. The ability to predict antimicrobial susceptibility of beta-lactam antimicrobials directly from beta-lactamase resistance genes may help reduce the reliance on routine phenotypic testing with higher turnaround times in diagnostic, therapeutic, and surveillance of antimicrobial-resistant bacteria of the family Enterobacteriaceae. Full article

Salmonella spp., a leading cause of foodborne illness, is a formidable global menace due to escalating antimicrobial resistance (AMR). The evaluation of minimum inhibitory concentration (MIC) for antimicrobials is critical for characterizing AMR. The current whole genome sequencing (WGS)-based approaches for predicting MIC are hindered by both computational and feature identification constraints. We propose an innovative methodology called the “Genome Feature Extractor Pipeline” that integrates traditional machine learning (random forest, RF) with deep learning models (multilayer perceptron (MLP) and DeepLift) for WGS-based MIC prediction. We used a dataset from the National Antimicrobial Resistance Monitoring System (NARMS), comprising 4500 assembled genomes of nontyphoidal Salmonella, each annotated with MIC metadata for 15 antibiotics. Our pipeline involves the batch downloading of annotated genomes, the determination of feature importance using RF, Gini-index-based selection of crucial 10-mers, and their expansion to 20-mers. This is followed by an MLP network, with four hidden layers of 1024 neurons each, to predict MIC values. Using DeepLift, key 20-mers and associated genes influencing MIC are identified. The 10 most significant 20-mers for each antibiotic are listed, showcasing our ability to discern genomic features affecting Salmonella MIC prediction with enhanced precision. The methodology replaces binary indicators with k-mer counts, offering a more nuanced analysis. The combination of RF and MLP addresses the limitations of the existing WGS approach, providing a robust and efficient method for predicting MIC values in Salmonella that could potentially be applied to other pathogens. Full article

SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 𝜒² tests and t tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations’ associations with clinical outcomes. Full article

The emergence of antimicrobial resistance (AMR) in commensal and pathogenic enteric bacteria of swine is a public health threat. This study evaluated publicly available AMR surveillance data collected by the National Antimicrobial Resistance Monitoring System (NARMS) by assessing AMR patterns and temporal trends in commensal E. coli isolated from cecal samples of swine at slaughter across the United States. We applied the Mann-Kendall test (MKT) and a linear regression trend line to detect significant trends in the proportion of resistant isolates to individual antimicrobials over the study period. A Poisson regression model assessed differences among years in the number of antimicrobials to which an E. coli isolate was resistant. Among the 3237 E. coli isolates, a very high prevalence of resistance for tetracycline (67.62%), and high resistance for streptomycin (24.13%), and ampicillin (21.10%) were identified. The MKT and the linear trend line showed a significantly increasing temporal trend for amoxicillin-clavulanic acid, ampicillin, azithromycin, cefoxitin, ceftriaxone, and trimethoprim-sulfamethoxazole. Compared to 2013 the number of antimicrobials to which an E. coli isolate was resistant was significantly higher in the years 2017, 2018, and 2019. The increasing temporal trend of resistance to important antimicrobials for human medicine (e.g., third-generation cephalosporins) and the increase in multidrug resistance in the later years of the study are concerning and should be followed up by studies to identify sources and risk factors for the selection of AMR. Full article

Chicken is the most popular meat in the United States, and consumers may be exposed to multidrug resistant Salmonella and Campylobacter through consumption of retail chicken breasts. This study aimed to (i) determine the percentage of raw, packaged, retail chicken breasts from 27 metro areas that tested positive for Salmonella and Campylobacter; (ii) investigate the antibiotic susceptibility profiles of a subset of the isolates; and (iii) compare the Salmonella prevalence data to establishment level Salmonella categorization data published by the U.S. Department of Agriculture (USDA). USDA Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook (MLG) methodology was used to isolate and identify Salmonella (n = 672), Campylobacter (n = 499) from 400 g samples. National Antimicrobial Resistance Monitoring System (NARMS) methodology was followed for antimicrobial susceptibility testing of Salmonella (n = 52) and Campylobacter (n = 16) isolates. Salmonella was found in 8.6% of samples and Campylobacter in 4.2%. Having a 3 rating in USDA’s Salmonella Categorization of Individual Establishments for chicken parts was predictive of having a higher Salmonella percent positive in our data set (p ≤ 0.05). A total of 73.1% of Salmonella isolates, and 62.5% of Campylobacter isolates were resistant to ≥one class of antibiotics, with 48.1% of Salmonella isolates resistant to ≥three classes. Current results support interventions that take a ‘farm-to-fork’ approach with distinction by poultry types and parts as well as serovars, to lower antibiotic resistant Salmonella infections in humans due to poultry. Highlights: Salmonella was found in 8.6% and Campylobacter in 4.2% of chicken breasts tested; A 3 rating by USDA was predictive of a higher Salmonella percent positive; 48.1% of Salmonella isolates were resistant to 3 or more classes of antibiotics. Full article

Infrared point-target detection is one of the key technologies in infrared guidance systems. Due to the long observation distance, the point target is often submerged in the background clutter and large noise in the process of atmospheric transmission and scattering, and the signal-to-noise ratio is low. On the other hand, the target in the image appears in the form of fuzzy points, so that the target has no obvious features and texture information. Therefore, scholars have proposed many object detection methods for dimming infrared images, which has become a hot research topic on account of the flow-rank model based on the image patch. However, the result has a high false alarm rate because the most low-rank models based on the image patch do not consider the spatial-temporal characteristics of the infrared sequences. Therefore, we introduce 3D total variation (3D-TV) to regularize the foreground on account of the non-convex rank approximation minimization method, so as to consider the spatial-temporal continuity of the target and effectively suppress the interference caused by dynamic background and target movement on the foreground extraction. Finally, this paper proposes the minimization of the non-convex spatial-temporal tensor low-rank approximation algorithm (MNSTLA) by studying the related algorithms of the point infrared target detection, and the experimental results show strong robustness and a low false alarm rate for the proposed method compared with other advanced algorithms, such as NARM, RIPT, and WSNMSTIPT. Full article

Salmonella enterica subsp. enterica serovar Dublin (S.Dublin) is a cattle-adapted pathogen that has emerged as one of the most commonly isolated and multidrug resistant (MDR) serovars in cattle. S.Dublin may be shed in feces, milk, and colostrum and persist in asymptomatic cattle, leading to spread and outbreaks in herds. Though infections with S.Dublin in humans are rare, they are frequently severe, with extraintestinal spread that requires hospitalization and antimicrobial therapy. To determine minimum inhibitory concentration (MIC) and antimicrobial resistance (AMR) patterns and trends in cattle in California, broth microdilution testing was performed on 247 clinical S. Dublin isolates recovered from cattle at the California Animal Health and Food Safety Laboratory System (CAHFS) over the last three decades (1993–2019). Mean MICs and classification of resistance to antimicrobial drugs using a clinical livestock panel and the National Antimicrobial Resistance Monitoring System (NARMS) Gram-negative drug panels were utilized to assess prevalence and trends in AMR. Findings indicate an increase in AMR for the years 1993 to 2015. Notably, compared to the baseline year interval (1993–1999), there was an increase in resistance among quinolone and cephalosporin drugs, as well as an increased number of isolates with an MDR profile. Full article

This paper presents innovative reinforcement learning methods for automatically tuning the parameters of a proportional integral derivative controller. Conventionally, the high dimension of the Q-table is a primary drawback when implementing a reinforcement learning algorithm. To overcome the obstacle, the idea underlying the n-armed bandit problem is used in this paper. Moreover, gain-scheduled actions are presented to tune the algorithms to improve the overall system behavior; therefore, the proposed controllers fulfill the multiple performance requirements. An experiment was conducted for the piezo-actuated stage to illustrate the effectiveness of the proposed control designs relative to competing algorithms. Full article

Salmonella Infantis carrying extended spectrum β-lactamase bla_CTX-M-65 on a pESI-like megaplasmid has recently emerged in United States poultry. In order to determine the carriage rate and gene content variability of this plasmid in U.S. Salmonella Infantis, whole genome sequences of Salmonella isolates from humans and animals in the U.S. and internationally containing the pESI-like plasmid were analyzed. The U.S. Department of Agriculture Food Safety and Inspection Service (FSIS) identified 654 product sampling isolates containing pESI-like plasmids through hazard analysis and critical control point (HACCP) verification testing in 2017 and 2018. The Centers for Disease Control and Prevention identified 55 isolates with pESI-like plasmids in 2016–2018 through the National Antimicrobial Resistance Monitoring System. Approximately 49% of pESI-like plasmids from FSIS verification isolates and 71% from CDC NARMS contained bla_CTX-M-65. Pan-plasmid genome analysis was also performed. All plasmids contained traN and more than 95% contained 172 other conserved genes; 61% contained bla_CTX-M-65. In a hierarchical clustering analysis, some plasmids from U.S. animal sources clustered together and some plasmids from South America clustered together, possibly indicating multiple plasmid lineages. However, most plasmids contained similar genes regardless of origin. Carriage of the pESI-like plasmid in U.S. appears to be limited to Salmonella Infantis and carriage rates increased from 2017 to 2018. Full article

The role animal food plays in the introduction of antimicrobial-resistant bacteria into the human food chain is not well understood. We conducted an analysis of 1025 samples (647 pet food and 378 animal feed) collected across the United States during 2005–2011 for two indicator organisms (Escherichia coli and Enterococcus spp.). The overall prevalence ranged from 12.5% for E. coli to 45.2% for Enterococcus spp., and 11.2% of samples harbored both organisms. Regardless of bacterial genus, animal feed had significantly higher prevalence than pet food (p < 0.001). A general downward trend in prevalence was observed from 2005 to 2009 followed by an upward trend thereafter. Among E. coli isolates (n = 241), resistance was highest to tetracycline (11.2%) and below 5% for fourteen other antimicrobials. Among Enterococcus spp. isolates (n = 1074), Enterococcus faecium (95.1%) was the predominant species. Resistance was most common to tetracycline (30.1%) and ciprofloxacin (10.7%), but below 10% for thirteen other antimicrobials. Multidrug-resistant organisms were observed among both E. coli and Enterococcus spp. isolates at 3.3%. Compared to National Antimicrobial Resistance Monitoring System (NARMS) 2011 retail meat and animal data, the overall resistance for both organisms was much lower in animal food. These findings help establish a historic baseline for the prevalence and antimicrobial resistance among U.S. animal food products and future efforts may be needed to monitor changes over time. Full article

Intracortical neural interfaces (INI) have made impressive progress in recent years but still display questionable long-term reliability. Here, we report on the development and characterization of highly resilient monolithic silicon carbide (SiC) neural devices. SiC is a physically robust, biocompatible, and chemically inert semiconductor. The device support was micromachined from p-type SiC with conductors created from n-type SiC, simultaneously providing electrical isolation through the resulting p-n junction. Electrodes possessed geometric surface area (GSA) varying from 496 to 500 K μm². Electrical characterization showed high-performance p-n diode behavior, with typical turn-on voltages of ~2.3 V and reverse bias leakage below 1 nArms. Current leakage between adjacent electrodes was ~7.5 nArms over a voltage range of −50 V to 50 V. The devices interacted electrochemically with a purely capacitive relationship at frequencies less than 10 kHz. Electrode impedance ranged from 675 ± 130 kΩ (GSA = 496 µm²) to 46.5 ± 4.80 kΩ (GSA = 500 K µm²). Since the all-SiC devices rely on the integration of only robust and highly compatible SiC material, they offer a promising solution to probe delamination and biological rejection associated with the use of multiple materials used in many current INI devices. Full article