Archaea oxidizing alkanes through alkyl-coenzyme M reductases.

This review synthesizes recent discoveries of novel archaea clades capable of oxidizing higher alkanes, from volatile ones like ethane to longer-chain alkanes like hexadecane. These archaea, termed anaerobic multicarbon alkane-oxidizing archaea (ANKA), initiate alkane oxidation using alkyl-coenzyme M reductases, enzymes similar to the methyl-coenzyme M reductases of methanogenic and anaerobic methanotrophic archaea (ANME). The polyphyletic alkane-oxidizing archaea group (ALOX), encompassing ANME and ANKA, harbors increasingly complex alkane degradation pathways, correlated with the alkane chain length. We discuss the evolutionary trajectory of these pathways emphasizing metabolic innovations and the acquisition of metabolic modules via lateral gene transfer. Additionally, we explore the mechanisms by which archaea couple alkane oxidation with the reduction of electron acceptors, including electron transfer to partner sulfate-reducing bacteria (SRB). The phylogenetic and functional constraints that shape ALOX-SRB associations are also discussed. We conclude by highlighting the research needs in this emerging research field and its potential applications in biotechnology.

Contrastive Prototype-Guided Generation for Generalized Zero-Shot Learning.

Generalized zero-shot learning (GZSL) aims to recognize both seen and unseen classes, while only samples from seen classes are available for training. The mainstream methods mitigate the lack of unseen training data by simulating the visual unseen samples. However, the sample generator is actually learned with just seen-class samples, and semantic descriptions of unseen classes are just provided to the pre-trained sample generator for unseen data generation, therefore, the generator would have bias towards seen categories, and the unseen generation quality, including both precision and diversity, is still the main learning challenge. To this end, we propose a Prototype-Guided Generation for Generalized Zero-Shot Learning (PGZSL), in order to guide the sample generation with unseen knowledge. First, unseen data generation is guided and rectified in PGZSL by contrastive prototypical anchors with both class semantic consistency and feature discriminability. Second, PGZSL introduces Certainty-Driven Mixup for generator to enrich the diversity of generated unseen samples, while suppress the generation of uncertain boundary samples as well. Empirical results over five benchmark datasets show that PGZSL significantly outperforms the SOTA methods in both ZSL and GZSL tasks.

Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities.

The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.

Artificial light at night causes community instability of bacterial community in urban soils.

Urban soils host diverse bacteria crucial for ecosystem functions and urban health. As urbanization rises, artificial light at night (ALAN) imposes disturbances on soil ecosystems, yet how ALAN affects the structure and stability of soil bacterial community remains unclear. Here we coupled a short-term incubation experiment, community profiling, network analysis, and in situ field survey to assess the ecological impacts of ALAN. We showed that ALAN influenced bacterial compositions and shifted the bacterial network to a less stable phase, altering denitrification potential. Such transition in community stability probably resulted from an ALAN-induced decrease in competition and/or an increase in facilitation, in line with the Stress Gradient Hypothesis. Similar destabilizing effects were also detected in bacterial networks in multiple urban soils subjected to different levels of ALAN stress, supporting the action of ALAN on naturally-occurring soil bacterial communities. Overall, our findings highlight ALAN as a new form of anthropogenic stress that jeopardizes the stability of soil bacterial community, which would facilitate ecological projection of expanding ALAN exposure.

Dual-Correction-Adaptation Network for Noisy Knowledge Transfer.

Unsupervised domain adaptation (UDA) promotes target learning via a single-directional transfer from label-rich source domain to unlabeled target, while its reverse adaption from target to source has not been jointly considered yet. In real teaching practice, a teacher helps students learn and also gets promotion from students, and such a virtuous cycle inspires us to explore dual-directional transfer between domains. In fact, target pseudo-labels predicted by source commonly involve noise due to model bias; moreover, source domain usually contains innate noise, which inevitably aggravates target noise, leading to noise amplification. Transfer from target to source exploits target knowledge to rectify the adaptation, consequently enables better source transfer, and exploits a virtuous transfer circle. To this end, we propose a dual-correction-adaptation network (DualCAN), in which adaptation and correction cycle between domains, such that learning in both domains can be boosted gradually. To the best of our knowledge, this is the first naive attempt of dual-directional adaptation. Empirical results validate DualCAN with remarkable performance gains, particularly for extreme noisy tasks (e.g., approximately + 10 % on D → A of Office-31 with 40 % label corruption).

Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.

Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.

Universum-Inspired Supervised Contrastive Learning.

As an effective data augmentation method, Mixup synthesizes an extra amount of samples through linear interpolations. Despite its theoretical dependency on data properties, Mixup reportedly performs well as a regularizer and calibrator contributing reliable robustness and generalization to deep model training. In this paper, inspired by Universum Learning which uses out-of-class samples to assist the target tasks, we investigate Mixup from a largely under-explored perspective - the potential to generate in-domain samples that belong to none of the target classes, that is, universum. We find that in the framework of supervised contrastive learning, Mixup-induced universum can serve as surprisingly high-quality hard negatives, greatly relieving the need for large batch sizes in contrastive learning. With these findings, we propose Universum-inspired supervised Contrastive learning (UniCon), which incorporates Mixup strategy to generate Mixup-induced universum as universum negatives and pushes them apart from anchor samples of the target classes. We extend our method to the unsupervised setting, proposing Unsupervised Universum-inspired contrastive model (Un-Uni). Our approach not only improves Mixup with hard labels, but also innovates a novel measure to generate universum data. With a linear classifier on the learned representations, UniCon shows state-of-the-art performance on various datasets. Specially, UniCon achieves 81.7% top-1 accuracy on CIFAR-100, surpassing the state of art by a significant margin of 5.2% with a much smaller batch size, typically, 256 in UniCon vs. 1024 in SupCon (Khosla et al., 2020) using ResNet-50. Un-Uni also outperforms SOTA methods on CIFAR-100. The code of this paper is released on https://github.com/hannaiiyanggit/UniCon.

TIToK: A solution for bi-imbalanced unsupervised domain adaptation.

Unsupervised domain adaptation (UDA) aims to transfer knowledge via domain alignment, and typically assumes balanced data distribution. When deployed in real tasks, however, (i) each domain usually suffers from class imbalance, and (ii) different domains may have different class imbalance ratios. In such bi-imbalanced cases with both within-domain and across-domain imbalance, source knowledge transfer may degenerate the target performance. Some recent efforts have adopted source re-weighting to this issue, in order to align label distributions across domains. However, since target label distribution is unknown, the alignment might be incorrect or even risky. In this paper, we propose an alternative solution named TIToK for bi-imbalanced UDA, by directly Transferring Imbalance-Tolerant Knowledge across domains. In TIToK, a class contrastive loss is presented for classification, in order to alleviate the sensitivity to imbalance in knowledge transfer. Meanwhile, knowledge of class correlation is transferred as a supplementary, which is commonly invariant to imbalance. Finally, discriminative feature alignment is developed for a more robust classifier boundary. Experiments over benchmark datasets show that TIToK achieves competitive performance with the state-of-the-arts, and its performance is less sensitive to imbalance.

Partial Domain Adaptation Without Domain Alignment.

Unsupervised domain adaptation (UDA) aims to transfer knowledge from a well-labeled source domain to a related and unlabeled target domain with identical label space. The main workhorse in UDA is domain alignment and has proven successful. However, it is practically difficult to find an appropriate source domain with identical label space. A more practical scenario is partial domain adaptation (PDA) where the source label space subsumes the target one. Unfortunately, due to the non-identity between label spaces, it is extremely hard to obtain an ideal alignment, conversely, easier resulting in mode collapse and negative transfer. These motivate us to find a relatively simpler alternative to solve PDA. To achieve this, we first explore a theoretical analysis, which says that the target risk is bounded by both model smoothness and between-domain discrepancy. Then, we instantiate the model smoothness as an intra-domain structure preserving (IDSP) while giving up possibly riskier domain alignment. To our best knowledge, this is the first naive attempt for PDA without alignment. Finally, our empirical results on benchmarks demonstrate that IDSP is not only superior to the PDA SOTAs (e.g.,  âˆ¼ +10% on Cl → Rw and  âˆ¼ +8% on Ar → Rw), but also complementary to domain alignment in the standard UDA.

Multiplane Convex Proximal Support Vector Machine.

As an effective method for XOR problems, generalized eigenvalue proximal support vector machine (GEPSVM) recently has gained widespread attention accompanied with many variants proposed. Although these variants strengthen the classification performance to different extents, the number of fitting hyperplanes, similar to GEPSVM, for each class is still limited to just one. Intuitively, using single hyperplane seems not enough, especially for the datasets with complex feature structures. Therefore, this article mainly focuses on extending the fitting hyperplanes for each class from single one to multiple ones. However, such an extension from the original GEPSVM is not trivial even though, if possible, the elegant solution via generalized eigenvalues will also not be guaranteed. To address this issue, we first make a simple yet crucial transformation for the optimization problem of GEPSVM and then propose a novel multiplane convex proximal support vector machine (MCPSVM), where a set of hyperplanes determined by the features of the data are learned for each class. We adopt a strictly (geodesically) convex objective to characterize this optimization problem; thus, a more elegant closed-form solution is obtained, which only needs a few lines of MATLAB codes. Besides, MCPSVM is more flexible in form and can be naturally and seamlessly extended to the feature weighting learning, whereas GEPSVM and its variants can hardly straightforwardly work like this. Extensive experiments on benchmark and large-scale image datasets indicate the advantages of our MCPSVM.

Convex Subspace Clustering by Adaptive Block Diagonal Representation.

Subspace clustering is a class of extensively studied clustering methods where the spectral-type approaches are its important subclass. Its key first step is to desire learning a representation coefficient matrix with block diagonal structure. To realize this step, many methods were successively proposed by imposing different structure priors on the coefficient matrix. These impositions can be roughly divided into two categories, i.e., indirect and direct. The former introduces the priors such as sparsity and low rankness to indirectly or implicitly learn the block diagonal structure. However, the desired block diagonalty cannot necessarily be guaranteed for noisy data. While the latter directly or explicitly imposes the block diagonal structure prior such as block diagonal representation (BDR) to ensure so-desired block diagonalty even if the data is noisy but at the expense of losing the convexity that the former's objective possesses. For compensating their respective shortcomings, in this article, we follow the direct line to propose adaptive BDR (ABDR) which explicitly pursues block diagonalty without sacrificing the convexity of the indirect one. Specifically, inspired by Convex BiClustering, ABDR coercively fuses both columns and rows of the coefficient matrix via a specially designed convex regularizer, thus naturally enjoying their merits and adaptively obtaining the number of blocks. Finally, experimental results on synthetic and real benchmarks demonstrate the superiority of ABDR to the state-of-the-arts (SOTAs).

Human Collective Intelligence Inspired Multi-View Representation Learning - Enabling View Communication by Simulating Human Communication Mechanism.

In real-world applications, we often encounter multi-view learning tasks where we need to learn from multiple sources of data or use multiple sources of data to make decisions. Multi-view representation learning, which can learn a unified representation from multiple data sources, is a key pre-task of multi-view learning and plays a significant role in real-world applications. Accordingly, how to improve the performance of multi-view representation learning is an important issue. In this work, inspired by human collective intelligence shown in group decision making, we introduce the concept of view communication into multi-view representation learning. Furthermore, by simulating human communication mechanism, we propose a novel multi-view representation learning approach that can fulfill multi-round view communication. Thus, each view of our approach can exploit the complementary information from other views to help with modeling its own representation, and mutual help between views is achieved. Extensive experiment results on six datasets from three significant fields indicate that our approach substantially improves the average classification accuracy by 4.536% in medicine and bioinformatics fields as well as 4.115% in machine learning field.

Unsupervised Multitarget Domain Adaptation With Dictionary-Bridged Knowledge Exploitation.

Unsupervised domain adaptation (UDA) is an emerging learning paradigm that models on unlabeled datasets by leveraging model knowledge built on other labeled datasets, in which the statistical distributions of these datasets are usually not identical. Formally, UDA is to leverage knowledge from a labeled source domain to promote an unlabeled target domain. Although there have been a variety of methods proposed to address the UDA problem, most of them are dedicated to single-source-to-single-target domain, while the works on single-source-to-multitarget domain are relatively rare. Compared to the single-source domain with single-target domain scenario, the UDA from single-source domain to multitarget domain is more challenging since it needs to consider not only the relationships between the source and the target domains but also those among the target domains. To this end, this article proposes a kind of dictionary learning-based unsupervised multitarget domain adaptation method (DL-UMTDA). In DL-UMTDA, a common dictionary is constructed to correlate the single-source and multitarget domains, while individual dictionaries are designed to exploit the private knowledge for the target domains. Through learning the corresponding dictionary representation coefficients in the UDA process, the correlations from the source to the target domains as well as these potential relationships between the target domains can be effectively exploited. In addition, we design an alternating algorithm to solve the DL-UMTDA model with theoretical convergence guarantee. Finally, extensive experiments on benchmark (Office + Caltech) and real datasets (AgeDB, Morph, and CACD) validate the superiority of the proposed method.

Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist.

The metabolic potential of the sulfate-reducing bacterium Desulfosarcina sp. strain BuS5, currently the only pure culture able to oxidize the volatile alkanes propane and butane without oxygen, was investigated via genomics, proteomics and physiology assays. Complete genome sequencing revealed that strain BuS5 encodes a single alkyl-succinate synthase, an enzyme which apparently initiates oxidation of both propane and butane. The formed alkyl-succinates are oxidized to CO2 via beta oxidation and the oxidative Wood-Ljungdahl pathways as shown by proteogenomics analyses. Strain BuS5 conserves energy via the canonical sulfate reduction pathway and electron bifurcation. An ability to utilize long-chain fatty acids, mannose and oligopeptides, suggested by automated annotation pipelines, was not supported by physiology assays and in-depth analyses of the corresponding genetic systems. Consistently, comparative genomics revealed a streamlined BuS5 genome with a remarkable paucity of catabolic modules. These results establish strain BuS5 as an exceptional metabolic specialist, able to grow only with propane and butane, for which we propose the name Desulfosarcina aeriophaga BuS5. This highly restrictive lifestyle, most likely the result of habitat-driven evolutionary gene loss, may provide D. aeriophaga BuS5 a competitive edge in sediments impacted by natural gas seeps. Etymology: Desulfosarcina aeriophaga, aério (Greek): gas; phágos (Greek): eater; D. aeriophaga: a gas eating or gas feeding Desulfosarcina.

A Concise Yet Effective Model for Non-Aligned Incomplete Multi-View and Missing Multi-Label Learning.

In reality, learning from multi-view multi-label data inevitably confronts three challenges: missing labels, incomplete views, and non-aligned views. Existing methods mainly concern the first two and commonly need multiple assumptions to attack them, making even state-of-the-arts involve at least two explicit hyper-parameters such that model selection is quite difficult. More toughly, they will fail in handling the third challenge, let alone addressing the three jointly. In this paper, we aim at meeting these under the least assumption by building a concise yet effective model with just one hyper-parameter. To ease insufficiency of available labels, we exploit not only the consensus of multiple views but also the global and local structures hidden among multiple labels. Specifically, we introduce an indicator matrix to tackle the first two challenges in a regression form while aligning the same individual labels and all labels of different views in a common label space to battle the third challenge. In aligning, we characterize the global and local structures of multiple labels to be high-rank and low-rank, respectively. Subsequently, an efficient algorithm with linear time complexity in the number of samples is established. Finally, even without view-alignment, our method substantially outperforms state-of-the-arts with view-alignment on five real datasets.

A Convex Discriminant Semantic Correlation Analysis for Cross-View Recognition.

Canonical correlation analysis (CCA) is a typical statistical model used to analyze the correlation components between different view representations of the same objects. When the label information is available with the data representations, CCA can be extended to its discriminative counterparts by incorporating supervision in the analysis. Although most discriminative variants of CCA have achieved improved results, nearly all of their objective functions are nonconvex, implying that optimal solutions are difficult to obtain. More important, that cross-view representations from the same sample should be consistent, that is, the cross-view semantic consistency has however not been modeled. To overcome these drawbacks, in this article, we propose a discriminant semantic correlation analysis (DSCA) model by modeling the cross-view semantic consistency for each object in the sample space rather than in the commonly used feature space. To boost the nonlinear discriminating capability of DSCA, we extend it from the Euclidean to the geodesic space by transforming the metric and incorporating both the cross-view semantic and representation correlation information and consequently obtain our final model with convex objective, namely, convex DSCA (C-DSCA). Finally, with extensive experiments and comparisons, we validate the effectiveness and superiority of the proposed method.

Heterogeneous Domain Adaptation With Structure and Classification Space Alignment.

Domain adaptation (DA) aims at facilitating the target model training by leveraging knowledge from related but distribution-inconsistent source domain. Most of the previous DA works concentrate on homogeneous scenarios, where the source and target domains are assumed to share the same feature space. Nevertheless, frequently, in reality, the domains are not consistent in not only data distribution but also the representation space and feature dimensions. That is, these domains are heterogeneous. Although many works have attempted to handle such heterogeneous DA (HDA) by transforming HDA to homogeneous counterparts or performing DA jointly with domain transformation, nearly all of them just concentrate on the feature and distribution alignment across domains, neglecting the structure and classification space preservation for domains themselves. In this work, we propose a novel HDA model, namely, heterogeneous classification space alignment (HCSA), which leverages knowledge from both the source samples and model parameters to the target. In HCSA, structure preservation, distribution, and classification space alignment are implemented, jointly with feature representation by transferring both the source-domain representation and model knowledge. Moreover, we design an alternating algorithm to optimize the HCSA model with guaranteed convergence and complexity analysis. In addition, the HCSA model is further extended with deep network architecture. Finally, we experimentally evaluate the effectiveness of the proposed method by showing its superiority to the compared approaches.

High Arsenic Levels Increase Activity Rather than Diversity or Abundance of Arsenic Metabolism Genes in Paddy Soils.

Arsenic (As) metabolism genes are generally present in soils, but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes (ars) including arsR, acr3, arsB, arsC, arsM, arsI, arsP, and arsH as well as energy-generating As respiratory oxidation (aioA) and reduction (arrA) genes. Somewhat unexpectedly, the relative DNA abundances and diversities of ars, aioA, and arrA genes were not significantly different between low and high (∼10 versus ∼100 mg kg-1) As soils. Compared to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars gene abundance only when its concentration was higher than 410 mg kg-1. In contrast, metatranscriptomics revealed that relative to low-As soils, high-As soils showed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community wide as opposed to taxon specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil or other environments should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level; thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.

Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses.

Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used 13C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active cells using single-cell analyses and protein-stable isotope probing. The detection of 13C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. The quantitative role of these microorganisms in pollutant degradation was resolved using single-cell-based uptake measurements. Our strategy advances our understanding of microbially mediated biodegradation processes and has general application potential for elucidating the ecological roles of uncultured microorganisms in their natural habitats.

Recent Advances in Open Set Recognition: A Survey.

In real-world recognition/classification tasks, limited by various objective factors, it is usually difficult to collect training samples to exhaust all classes when training a recognizer or classifier. A more realistic scenario is open set recognition (OSR), where incomplete knowledge of the world exists at training time, and unknown classes can be submitted to an algorithm during testing, requiring the classifiers to not only accurately classify the seen classes, but also effectively deal with unseen ones. This paper provides a comprehensive survey of existing open set recognition techniques covering various aspects ranging from related definitions, representations of models, datasets, evaluation criteria, and algorithm comparisons. Furthermore, we briefly analyze the relationships between OSR and its related tasks including zero-shot, one-shot (few-shot) recognition/learning techniques, classification with reject option, and so forth. Additionally, we also review the open world recognition which can be seen as a natural extension of OSR. Importantly, we highlight the limitations of existing approaches and point out some promising subsequent research directions in this field.