In this paper, we present a mathematical and computational framework for comparing and matching distributions in reproducing kernel Hilbert spaces (RKHS). This framework, called optimal transport in ...RKHS, is a generalization of the optimal transport problem in input spaces to (potentially) infinite-dimensional feature spaces. We provide a computable formulation of Kantorovich's optimal transport in RKHS. In particular, we explore the case in which data distributions in RKHS are Gaussian, obtaining closed-form expressions of both the estimated Wasserstein distance and optimal transport map via kernel matrices. Based on these expressions, we generalize the Bures metric on covariance matrices to infinite-dimensional settings, providing a new metric between covariance operators. Moreover, we extend the correlation alignment problem to Hilbert spaces, giving a new strategy for matching distributions in RKHS. Empirically, we apply the derived formulas under the Gaussianity assumption to image classification and domain adaptation. In both tasks, our algorithms yield state-of-the-art performances, demonstrating the effectiveness and potential of our framework.
Environmental antibiotic resistance has drawn increasing attention due to its great threat to human health. In this study, we investigated concentrations of antibiotics (tetracyclines, sulfonamides ...and (fluoro)quinolones) and abundances of antibiotic resistance genes (ARGs), including tetracycline resistance genes, sulfonamide resistance genes, and plasmid-mediated quinolone resistance genes, and analyzed bacterial community composition in aquaculture environment in Guangdong, China. The concentrations of sulfametoxydiazine, sulfamethazine, sulfamethoxazole, oxytetracycline, chlorotetracycline, doxycycline, ciprofloxacin, norfloxacin, and enrofloxacin were as high as 446 μg kg⁻¹ and 98.6 ng L⁻¹ in sediment and water samples, respectively. The relative abundances (ARG copies/16S ribosomal RNA (rRNA) gene copies) of ARGs (sul1, sul2, sul3, tetM, tetO, tetW, tetS, tetQ, tetX, tetB/P, qepA, oqxA, oqxB, aac(6′)-Ib, and qnrS) were as high as 2.8 × 10⁻². The dominant phyla were Proteobacteria, Bacteroidetes, and Firmicutes in sediment samples and Proteobacteria, Actinobacteria and Bacteroidetes in water samples. The genera associated with pathogens were also observed, such as Acinetobacter, Arcobacter, and Clostridium. This study comprehensively investigated antibiotics, ARGs, and bacterial community composition in aquaculture environment in China. The results indicated that fish ponds are reservoirs of ARGs and the presence of potential resistant and pathogen-associated taxonomic groups in fish ponds might imply the potential risk to human health.
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BFBNIB, EMUNI, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UL, UM, UPUK, VKSCE, ZAGLJ
Sparse linear arrays, such as nested and co-prime arrays, are capable of resolving O(M2) sources using only O(M) sensors by exploiting their so-called difference coarray model. One popular approach ...to exploit the difference coarray model is to construct an augmented covariance matrix from the sample covariance matrix. By applying common direction-of-arrival (DOA) estimation algorithms to this augmented covariance matrix, more sources than the number of sensors can be identified. In this letter, inspired by the optimal transport theory, we develop a new approach to construct this augmented covariance matrix. We formulate a structured covariance estimation problem that minimizes the Bures-Wasserstein distance between the sample covariance matrix and the subsampled augmented covariance matrix, which can be either casted to a semi-definite programming problem, or directly solved using gradient-based methods. Our approach contributes to a new grid-less DOA estimation algorithm for sparse linear arrays. Numerical examples show that our approach achieves state-of-art estimation performance.
Sparse linear arrays, such as co-prime and nested arrays, can resolve more uncorrelated sources than the number of sensors by applying the MUtiple SIgnal Classification (MUSIC) algorithm to their ...difference coarray model. We aim at statistically analyzing the performance of the MUSIC algorithm applied to the difference coarray model, namely, the coarray-based MUSIC, in the presence of sensor location errors. We first introduce a signal model for sparse linear arrays in the presence of deterministic unknown location errors. Based on this signal model, we derive a closed-form expression of the asymptotic mean-squared error of a commonly used coarray-based MUSIC algorithm, SS-MUSIC, in the presence of small sensor location errors. We show that the sensor location errors introduce a constant bias that depends on both the physical array geometry and the coarray geometry, which cannot be mitigated by only increasing the signal-to-noise ratio. We next give a short extension of our analysis to cases when the sensor location errors are stochastic and investigate the Gaussian case. Finally, we derive the Cramér-Rao bound for joint estimation of direction-of-arrivals and sensor location errors for sparse linear arrays, which can be applicable even if the number of sources exceeds the number of sensors. Numerical simulations show good agreement between empirical results and our theoretical results.
Huge number of antibiotic resistance genes (ARGs) have been widely detected in phage genomes from anthropogenic environment or animal farms, whereas little is known about the dynamic changes of phage ...contribution to resistance under a feedlot wastewater treatment facility (WTF) pressure. Here, a metagenomics method was used to characterize the sewage phageome and identifies the antibiotic resistome. The results showed that the phage families of Siphoviridae, Myoviridae, and Podoviridae were always the most dominant. Analysis of ARGs carried by bacterial and phages showed that MLS and tetracycline resistance genes always had the highest abundances and the other ARG types also have a fixed hierarchy, showing that there is no significant change in overall ARGs abundance distribution. However, an extensively cored antibiotic resistome were specifically identified in aerobic environment. ARGs encoding ribosomal protection proteins, especially for the ARG subtypes lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2, were more inclined to be selected by phages, suggesting that a more refined mechanism, such as specialized transduction and lateral transduction, was probably involved. In all, these results suggest that monitoring of dynamic changes of phage contribution to resistance should be given more attention and ARGs-carrying phage management should focus on using technologies for controlling cored ARGs rather than only the overall distribution of ARGs in phages.
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•Siphoviridae, Myoviridae and Podoviridae were the most dominant phages.•ARGs encoding ribosomal protection proteins were specifically identified.•These ARGs subtypes are lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2.•ARGs-carrying phage management should mainly focus on these cored ARGs.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The aim of this study was to investigate the fate of nine potential indicator antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, intI1) and the diversity of ...bacterial communities in response to poultry manure applications to arable soil over a 90 day period. Quantitative real time PCR and Illumina high-throughput sequencing of 16S rDNA gene were used to quantify and trace ARG fate. The levels of all genes dramatically decreased over time and intI1, sul1, sul2 and tetM always had the greatest abundance and lowest dissipation rates. This indicated that more effort should be focused on the ARG elimination from manure rather than waiting for subsequent attenuation in the environment. Our sequencing results documented dramatic changes in the microbial community structure and diversity during these experiments. In poultry manure groups, Bacteroidetes and Actinobacteria were the two dominant phyla while Acidobacteria dominated the control groups. Moreover, the relative abundance of genera Corynebacterium, Pseudomonas, Ochrobactrum, Actinomadura and Bacillus, which contained potential opportunistic pathogens, changed over time suggesting that poultry manure not only strongly influenced bacterial community composition, but also selected specific bacterial communities. This study provides a glimpse of ARG fates and bacterial community diversity in soil after the application of poultry manure.
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•Nine potential proxy ARGs were used to overall assess the behavior of ARGs.•Low dissipation rate of tetM was firstly reported in poultry manure-soil microcosms.•Soil microbial community diversities were disturbed by the pure manure application.•Bacterial diversity in poultry manure-soil hardly back to the background levels within 90 days.•Phyla of Bacteroidetes and Actinobacteria were selected by poultry manure application.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
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Enterotoxigenic Escherichia coli (ETEC) cause acute secretory diarrhoea in pigs, posing a great economic loss to the swine industry. This study analysed the prevalence and genetic ...characteristics of prophages from 132 ETEC isolates from symptomatic pigs to determine their potential for spreading antibiotic resistance. A total of 1105 potential prophages were identified, and the distribution of the genome size showed three ‘overlapping’ trends. Similarity matrix comparison showed that prophages correlated with the ETEC lineage distribution, and further identification of these prophages corroborated the lineage specificity. In total, 1206 antibiotic resistance genes (ARGs) of 52 different categories were identified in 132 ETEC strains; among these, 2.65% (32/1206) of ARGs were found to be carried by prophages. Analysis of flanking sequences showed that almost all the ARGs could be grouped into two types: ‘blaTEM‐1B’ and ‘classic class 1 integron (IntI1)’. They co‐occurred with a strictly conserved recombinase and transposon Tn3 family but with a difference: the ‘blaTEM‐1B type’ prophages exhibited a classic Tn2 transposon structure with 100% sequence identity, whereas the ‘IntI1 type’ co‐occurred with the TnAs2 transposon with only 84% sequence identity. These results imply that ARGs might be pervasive in natural bacterial populations through transmission by transposable bacteriophages.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
In this study, we examined the types of antibiotic resistance genes (ARGs) possessed by bacteria and bacteriophages in swine feedlot wastewater before and after treatment using a metagenomics ...approach. We found that the relative abundance of ARGs in bacterial DNA in all water samples was significantly higher than that in phages DNA (>10.6-fold), and wastewater treatment did not significantly change the relative abundance of bacterial- or phage-associated ARGs. We further detected the distribution and diversity of the different types of ARGs according to the class of antibiotics to which they confer resistance, the tetracycline resistance genes were the most abundant resistance genes and phages were more likely to harbor ATP-binding cassette transporter family and ribosomal protection genes. Moreover, the colistin resistance gene
was also detected in the phage population. When assessing the contribution of phages in spreading different groups of ARGs, β-lactamase resistance genes had a relatively high spreading ability even though the abundance was low. These findings possibly indicated that phages not only could serve as important reservoir of ARG but also carry particular ARGs in swine feedlot wastewater, and this phenomenon is independent of the environment.
Domain shift, which occurs when there is a mismatch between the distributions of training (source) and testing (target) datasets, usually results in poor performance of the trained model on the ...target domain. Existing algorithms typically solve this issue by reducing the distribution discrepancy in the input spaces. However, for kernel-based learning machines, performance highly depends on the statistical properties of data in reproducing kernel Hilbert spaces (RKHS). Motivated by these considerations, we propose a novel strategy for matching distributions in RKHS, which is done by aligning the RKHS covariance matrices (descriptors) across domains. This strategy is a generalization of the correlation alignment problem in Euclidean spaces to (potentially) infinite-dimensional feature spaces. In this paper, we provide two alignment approaches, for both of which we obtain closed-form expressions via kernel matrices. Furthermore, our approaches are scalable to large datasets since they can naturally handle out-of-sample instances. We conduct extensive experiments (248 domain adaptation tasks) to evaluate our approaches. Experiment results show that our approaches outperform other state-of-the-art methods in both accuracy and computationally efficiency.
Due to ethical issues and the nature of the ear, it is difficult to directly perform experimental measurements on living body elements of the human ear. Therefore, a numerical model has been ...developed to effectively assess the effect of the replacement of artificial ossicles on hearing in the inner ear. A healthy volunteer's right ear was scanned to obtain CT data, which were digitalized through the use of a self-compiling program and coalescent Patran-Nastran software to establish a 3D numerical model of the whole ear, and a frequency response of a healthy human ear was analyzed. The vibration characteristics of the basilar membrane (BM) after total ossicular replacement prosthesis (TORP) implantation were then analyzed. The results show that although the sound conduction function of the middle ear was restored after replacement of the TORP, the sensory sound function of the inner ear was affected. In the low frequency and medium frequency range, hearing loss was 5.2~10.7%. Meanwhile, in the middle-high frequency range, the replacement of a middle ear TORP in response to high sound pressure produced a high acoustic stimulation effect in the inner ear, making the inner ear structures susceptible to fatigue and more prone to fatigue damage compared to the structures in healthy individuals. This developed model is able to assess the effects of surgical operation on the entire hearing system.
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