Pixel-Level Domain Adaptation: A New Perspective for Enhancing Weakly Supervised Semantic Segmentation.

Recent attention has been devoted to the pursuit of learning semantic segmentation models exclusively from image tags, a paradigm known as image-level Weakly Supervised Semantic Segmentation (WSSS). Existing attempts adopt the Class Activation Maps (CAMs) as priors to mine object regions yet observe the imbalanced activation issue, where only the most discriminative object parts are located. In this paper, we argue that the distribution discrepancy between the discriminative and the non-discriminative parts of objects prevents the model from producing complete and precise pseudo masks as ground truths. For this purpose, we propose a Pixel-Level Domain Adaptation (PLDA) method to encourage the model in learning pixel-wise domain-invariant features. Specifically, a multi-head domain classifier trained adversarially with the feature extraction is introduced to promote the emergence of pixel features that are invariant with respect to the shift between the source (i.e., the discriminative object parts) and the target (i.e., the non-discriminative object parts) domains. In addition, we come up with a Confident Pseudo-Supervision strategy to guarantee the discriminative ability of each pixel for the segmentation task, which serves as a complement to the intra-image domain adversarial training. Our method is conceptually simple, intuitive and can be easily integrated into existing WSSS methods. Taking several strong baseline models as instances, we experimentally demonstrate the effectiveness of our approach under a wide range of settings.

Targeted lipidomics-based study of radiation-induced metabolite profiles changes in plasma of total body irradiation cases.

PURPOSE: Lipidomics is an important tool for triaging exposed individuals, and helps early adoption of prevention and control strategies. The purpose of this study was to screen significantly perturbed lipids between pre- and post-irradiation of human plasma samples after total body irradiation (TBI) and explore potential radiation biomarkers for early radiation classification. METHODS: Plasma samples were collected before and after irradiation from 22 hospitalized cases of acute myeloid leukemia (AML) prepared for bone marrow transplantation. Acute total-body γ irradiation was performed at doses of 0, 4, 8, and 12 Gy. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) with multiple reaction monitoring (MRM) method was utilized. Self-paired studies before and after irradiation were performed to screen potential lipid categorization markers and markers of dose-response relationships for radiation perturbation in humans. Based on the screened potential markers, a human TBI dose estimation model was developed. RESULTS: In total, 426 individual lipids from 14 major classes were quantified and 152 potential biomarkers with categorical characteristics were screened. A total of 80 lipids (32 TGs, 29 SMs, 9 FAs, 5 CEs, 5 PIs) were upregulated at 4 Gy, and a total of 91 lipids (39 SMs, 18 TGs, 15 HexCers, 7 CEs, 6 Cers, 3 LacCers, 2 LPEs, 1 PI) were upregulated at 12 Gy. Comparison of the ROC curves between the non-exposed and exposed groups at different doses showed AUC values ranging from 0.807 to 0.876. The metabolic pathways of potential lipid markers are mainly sphingolipid and glycerolipid metabolism, unsaturated fatty acid biosynthesis, fatty acid degradation and biosynthesis. Among the 13 dose-dependent radiosensitive lipids, CE (20:5), CE (18:1) and PI (18:2/18:2) were gradually incorporated into the TBI dose estimation model. CONCLUSION: This study suggested that it was feasible to acquire quantitative lipid biomarker panels using targeted lipidomics platforms for rapid, high-throughput triage. Lipidomics strategies for radiation biodosimetry in humans were established with lipid biomarkers with good dose-response relationship.

Prior knowledge-guided multilevel graph neural network for tumor risk prediction and interpretation via multi-omics data integration.

The interrelation and complementary nature of multi-omics data can provide valuable insights into the intricate molecular mechanisms underlying diseases. However, challenges such as limited sample size, high data dimensionality and differences in omics modalities pose significant obstacles to fully harnessing the potential of these data. The prior knowledge such as gene regulatory network and pathway information harbors useful gene-gene interaction and gene functional module information. To effectively integrate multi-omics data and make full use of the prior knowledge, here, we propose a Multilevel-graph neural network (GNN): a hierarchically designed deep learning algorithm that sequentially leverages multi-omics data, gene regulatory networks and pathway information to extract features and enhance accuracy in predicting survival risk. Our method achieved better accuracy compared with existing methods. Furthermore, key factors nonlinearly associated with the tumor pathogenesis are prioritized by employing two interpretation algorithms (i.e. GNN-Explainer and IGscore) for neural networks, at gene and pathway level, respectively. The top genes and pathways exhibit strong associations with disease in survival analyses, many of which such as SEC61G and CYP27B1 are previously reported in the literature.

Multiple exposures to low-dose ionizing radiation induced the initiation and progression of pro-atherosclerotic phenotypes in mice and vascular endothelial cell damage.

OBJECTIVE: This study aimed to investigate the effects of low-dose radiation on the abdominal aorta of mice and vascular endothelial cells. METHODS: Wild-type and tumor-bearing mice were exposed to 15 sessions of low-dose irradiation, resulting in cumulative radiation doses of 187.5, 375, and 750 mGy. The effect on the cardiovascular system was assessed. Immunohistochemistry analyzed protein expressions of PAPP-A, CD62, P65, and COX-2 in the abdominal aorta. Microarray technology, Gene Ontology analysis, and pathway enrichment analysis evaluated gene expression changes in endothelial cells exposed to 375 mGy X-ray. Cell viability was assessed using the Cell Counting Kit 8 assay. Immunofluorescence staining measured γ-H2AX levels, and real-time polymerase chain reaction quantified mRNA levels of interleukin-6 (IL-6), ICAM-1, and Cx43. RESULTS: Hematoxylin and eosin staining revealed thickening of the inner membranes and irregular arrangement of smooth muscle cells in the media membrane at 375 and 750 mGy. Inflammation was observed in the inner membranes at 750 mGy, with a clear inflammatory response in the hearts of tumor-bearing mice. Immunohistochemistry indicated increased levels of PAPP-A, P65, and COX-2 post-irradiation. Microarray analysis showed 425 up-regulated and 235 down-regulated genes, associated with processes like endothelial cell-cell adhesion, IL-6, and NF-κB signaling. Cell Counting Kit 8 assay results indicated inhibited viability at 750 mGy in EA.hy926 cells. Immunofluorescence staining demonstrated a dose-dependent increase in γ-H2AX foci. Reverse transcription quantitative PCR results showed increased expression of IL6, ICAM-1, and Cx43 in EA.hy926 cells post 750 mGy X-ray exposure. CONCLUSION: Repeated low-dose ionizing radiation exposures triggered the development of pro-atherosclerotic phenotypes in mice and damage to vascular endothelial cells.

Screening radiation-differentially expressed circular RNAs and establishing dose classification models in the human lymphoblastoid cell line AHH-1.

PURPOSE: In the event of a large-scale radiological accident, rapid and high-throughput biodosimetry is the most vital basis in medical resource allocation for the prompt treatment of victims. However, the current biodosimeter is yet to be rapid and high-throughput. Studies have shown that ionizing radiation modulates expressions of circular RNAs (circRNAs) in healthy human cell lines and tumor tissue. circRNA expressions can be quantified rapidly and high-throughput. However, whether circRNAs are suitable for early radiation dose classification remains unclear. METHODS: We employed transcriptome sequencing and bioinformatics analysis to screen for radiation-differentially expressed circRNAs in the human lymphoblastoid cell line AHH-1 at 4 h following exposure to 0, 2, and 5 Gy 60Co γ-rays. The dose-response relationships between differentially expressed circRNA expressions and absorbed doses were investigated using real-time polymerase chain reaction and linear regression analysis at 4 h, 24 h, and 48 h post-exposure to 0, 2, 4, 6, and 8 Gy. Six distinct dose classification models of circRNA panels were established and validated by receiver operating characteristic (ROC) curve analysis. RESULTS: A total of 11 radiation-differentially expressed circRNAs were identified and validated. Based on dose-response effects, those circRNAs changed in a dose-responsive or dose-dependent manner were combined into panels A through F at 4 h, 24 h, and 48 h post-irradiation. ROC curve analysis showed that panels A through C had the potential to effectively classify exposed and non-exposed conditions, which area under the curve (AUC) of these three panels were all 1.000, and the associate p values were .009. Panels D through F excellently distinguished between different dose groups (AUC = 0.963-1.000, p < .05). The validation assay showed that panels A through F demonstrated consistent excellence in sensitivity and specificity in dose classification. CONCLUSIONS: Ionizing radiation can indeed modulate the circRNA expression profile in the human lymphoblastoid cell line AHH-1. The differentially expressed circRNAs exhibit the potential for rapid and high-throughput dose classification.

Biodosimetry Based on Gamma-H2AX Quantification in Human Peripheral Blood Lymphocytes after Partial-body Irradiation.

ABSTRACT: Quantification of gamma-H2AX foci can estimate exposure to ionizing radiation. Most nuclear and radiation accidents are partial-body irradiation, and the doses estimated using the total-body irradiation dose estimation formula are often lower than the actual dose. To evaluate the dose-response relation of gamma-H2AX foci in human peripheral blood lymphocytes after partial-body irradiation and establish a simple and high throughput model to estimate partial-body irradiation dose, we collected human peripheral blood and irradiated with 0-, 0.5-, 1-, 2-, 3-, 4-, 5-, 6-, and 8-Gy gamma rays to simulate total-body irradiation in vitro. Gamma-H2AX foci were quantitated by flow cytometry at 1 h after irradiation, and a dose-response curve was established for total-body irradiation dose estimation. Then, a partial-body irradiation dose-response calibration curve was established by adding calibration coefficients based on the Dolphin method. To reflect the data distribution of all doses more realistically, the partial-body irradiation dose-response calibration curve was divided into two sections. In addition, partial-body irradiation was simulated in vitro, and the PBI data were substituted into curves to verify the accuracy of the two partial-body irradiation calibration curves. Results showed that the dose estimation variations were all less than 30% except the 25% partial-body irradiation group at 1 Gy, and the partial-body irradiation calibration dose-response curves were YF 1 = - 3.444 x 2 + 18.532 x + 3.109, R 2 = 0.92 (YF ≤ 27.95); YF 2 = - 2.704 x 2 + 37.97 x - 56.45, R 2 = 0.86 (YF > 27.95). Results also suggested that the partial-body irradiation dose-response calibration curve based on the gamma-H2AX foci quantification in human peripheral blood lymphocytes is a simple and high throughput model to assess partial-body irradiation dose.

Nonreciprocal topological mode conversion by encircling an exceptional point in dynamic waveguides.

The topology of exceptional points (EPs) has been revealed by taking stationary or dynamical encircling around them, which induces eigenstate exchange or chiral mode conversion. However, the conversions are usually reciprocal obeying restricted transmittances. Here we propose the concept of nonreciprocal encircling of EPs in a dynamic waveguide under complex modulation. The waveguide allows direction-dependent EPs in their quasienergy spectra due to different phase-matching conditions for opposite propagation direction. We design a closed loop that will encircle the EP in the backward direction but not in the forward direction. In this way, a nonreciprocal topological conversion is achieved as the forward transmittance from the even to odd mode significantly exceeds the backward transmittance from the odd to even mode. As a result, the forward propagation produces two modes with equal strength while the backward propagation leads to a specific mode regardless of the input. The structure is promising for making robust optical isolators.

Effects of cyclophosphamide and mitomycin C on radiation-induced transcriptional biomarkers in human lymphoblastoid cells.

PURPOSE: Ionizing radiation (IR)-induced transcriptional changes are considered a potential biodosimetry for dose evaluation and health risk monitoring of acute or chronic radiation exposure. It is crucial to understand the impact of confounding factors on the radiation-responsive gene expressions for accurate and reproducible dose assessment. This study aims to explore the potential influence of exposures to chemotherapeutic agents such as cyclophosphamide (CP) and mitomycin C (MMC) on IR-induced transcriptional biomarkers. METHODS: The human B lymphoblastoid cells (AHH-1) were exposed to 0, 20, 50, 100, 200 and 500 µg/ml CP or 0, 0.025, 0.05, 0.1 and 1 µg/ml MMC, respectively. The appropriate concentrations of CP and MMC were added for 1 h before irradiation with 0, 2, 4 and 6 Gy of 60Co γ-rays at a dose rate of 1 Gy/min. Cell viability was evaluated by CCK-8 assay. The gene expression responses of 18 radiation-induced transcriptional biomarkers were examined at 24 h after exposures to CP and MMC, respectively. The expression levels of five crucial DNA interstrand crosslinks (ICLs) repair genes were also evaluated. The biodosimetry models were established based on the specific radiation-responsive gene combinations. RESULTS: The baseline transcriptional levels of the 18 selected genes were slightly affected by CP treatment in the absence of IR, while the transcript responses to IR could be inhibited as the concentration of CP up to 50 µg/ml. MMC treatment up-regulated the background levels in most radiation-responsive gene expressions. Of 18 genes, only the relative mRNA expression levels of CDKN1A and BBC3 were repressed after treatment with IR and MMC in combination. The relative mRNA level of RAD51 was significantly up-regulated after exposure to CP, while the expression of FANCD2, RAD51 and BLM showed an overall increase in response to MMC treatment. After irradiation, the relative mRNA expression levels of FANCD2, BRCA2 and RAD51 exhibited dose-dependent increases in IR alone and MMC treatment groups. In addition, the biodosimetry models were established using 2-4 radiation-responsive genes based on different radiation exposure scenarios. CONCLUSION: Our findings suggested that IR-induced gene expression changes were slightly affected after exposure to a relatively low concentration of CP and MMC. Gene expression combinations might improve the broad applicability of transcriptional biodosimetry across diverse radiation exposures.

Electrospinning Evolution Derived from TRIZ Theory for Directly Writing Patterned Nanofibers.

Nanofibers (NFs) have the advantages of tremendous flexibility, small size and a high surface-to-weight ratio and are widely used in sensors, drug carriers and filters. Patterned NFs have expanded their application fields in tissue engineering and electronics. Electrospinning (ES) is widely used to prepare nonwoven NFs by stretching polymer solution jets with electric forces. However, patterned NFs cannot be easily fabricated using ordinary ES methods: the process gradually deteriorates them as repulsion effects between the deposited NFs and the incoming ones increase while residual charges in the fibers accumulate. Repulsion effects are unavoidable because charges in the polymer solution jets are the fundamental forces that are meant to stretch the jets into NFs. TRIZ theory is an effective innovation method for resolving conflicts and eliminating contradictions. Based on the material-field model and the contradiction matrix of TRIZ theory, we propose a strategy to improve ES devices, neutralizing the charges retained in NFs by alternating the current power of the correct frequency, thus successfully fabricating patterned NFs with clear boundaries and good continuity. This study demonstrates a strategy for resolving conflicts in innovation processes based on TRIZ theory and fabricating patterned NFs for potential applications in flexible electronics and wearable sensors.

Corrigendum: SCTN: event-based object tracking with energy-efficient deep convolutional spiking neural networks.

[This corrects the article DOI: 10.3389/fnins.2023.1123698.].

Low-dose ionizing radiation: Effects on the proliferation and migration of lens epithelial cells via activation of the Wnt/ß-catenin pathway.

Eye lens opacification (cataract) induced by ionizing radiation is an important concern for radiation protection. Human lens epithelial cells (HLE-B3) were irradiated with γ-rays and radiation effects, including cell proliferation, cell migration, cell cycle distribution, and other changes related to the ß-catenin pathway, were determined after 8-72 h and 7 d. In an in vivo model, mice were irradiated; DNA damage (γH2AX foci) in the cell nucleus of the anterior capsule of the lens was detected within 1 h, and radiation effects on the anterior and posterior lens capsules were observed after 3 months. Low-dose ionizing radiation promoted cell proliferation and migration. The expression levels of ß-catenin, cyclin D1, and c-Myc were significantly increased in HLE-B3 cells after irradiation and ß-catenin was translocated into the cell nucleus (activation of the Wnt/ß-catenin pathway). In C57BL/6 J mouse lens, even a very low irradiation dose (0.05 Gy) induced the formation of γH2AX foci, 1 h after irradiation. At 3 months, migratory cells were found in the posterior capsule; expression of ß-catenin was increased and it was clustered at the nucleus in the epithelial cells of the lens anterior capsule. The Wnt/ß-catenin signaling pathway may an important role in promoting abnormal proliferation and migration of lens epithelial cells after low-dose irradiation.

Melatonin inhibits senescence-associated melanin pigmentation through the p53-TYR pathway in human primary melanocytes and the skin of C57BL/6 J mice after UVB irradiation.

UVB exposure accelerates skin aging and pigmentation. Melatonin effectively regulates tyrosinase (TYR) activity and aging. The purpose of this study was to determine the association between premature senescence and pigmentation, and the mechanism of melanin synthesis effected by melatonin. Primary melanocytes were extracted and identified from the male foreskin. To inhibit TYR expression, primary melanocytes were transduced with the lentivirus pLKD-CMV-EGFP-2A-Puro-U6-TYR. The wild-type TYR(+/+) and TYR(-/-) or TYR(+/-) knockout C57BL/6 J mice were used to determine the role of TYR on melanin synthesis in vivo. Results showed that UVB-induced melanin synthesis is dependent on TYR in primary melanocytes and mice. Furthermore, in primary melanocytes pretreated with Nutlin-3 or PFT-α to up or downregulate p53, results showed that premature senescence and melanin synthesis increased in primary melanocytes after UVB irradiation at 80 mJ/cm2, and further increased after being treated with Nutlin-3, while significantly decreased with PFT-α. In addition, melatonin inhibited UVB-induced premature senescence associated with inactivation of p53 and phosphorylation of p53 on Ser15 (ser-15), a decrease of melanin synthesis accompanied by reduced TYR expression. Moreover, skin erythema and pigmentation induced by UVB were reduced in the dorsal and ear skin of mice topically pretreated with 2.5% melatonin. These indicate that melatonin inhibits UVB-induced senescence-associated pigmentation via the p53-TYR pathway in primary melanocytes and prevents pigmentation obviously in the dorsal and ear skin of C57BL/6 J mice after UVB irradiation. KEY MESSAGES: P53 links UVB irradiation-induced senescence and senescence-associated pigmentation and regulates TYR in primary melanocytes after UVB irradiation. Melatonin inhibits senescence-associated pigmentation through the p53-TYR pathway in primary melanocytes. Melatonin prevents skin erythema and melanin pigmentation induced by UVB irradiation in the dorsal and ear skin of C57BL/6J mice.

SCTN: Event-based object tracking with energy-efficient deep convolutional spiking neural networks.

Event cameras are asynchronous and neuromorphically inspired visual sensors, which have shown great potential in object tracking because they can easily detect moving objects. Since event cameras output discrete events, they are inherently suitable to coordinate with Spiking Neural Network (SNN), which has a unique event-driven computation characteristic and energy-efficient computing. In this paper, we tackle the problem of event-based object tracking by a novel architecture with a discriminatively trained SNN, called the Spiking Convolutional Tracking Network (SCTN). Taking a segment of events as input, SCTN not only better exploits implicit associations among events rather than event-wise processing, but also fully utilizes precise temporal information and maintains the sparse representation in segments instead of frames. To make SCTN more suitable for object tracking, we propose a new loss function that introduces an exponential Intersection over Union (IoU) in the voltage domain. To the best of our knowledge, this is the first tracking network directly trained with SNN. Besides, we present a new event-based tracking dataset, dubbed DVSOT21. In contrast to other competing trackers, experimental results on DVSOT21 demonstrate that our method achieves competitive performance with very low energy consumption compared to ANN based trackers with very low energy consumption compared to ANN based trackers. With lower energy consumption, tracking on neuromorphic hardware will reveal its advantage.

Pyroelectric Janus nanomotors for synergistic electrodynamic-photothermal-antibiotic therapies of bacterial infections.

Antibacterial electrotherapy is currently activated by external electric field or self-powered generators, but usually needs complicated power management circuits. Herein, near-infrared illumination (NIR) of pyroelectric nanoparticles (NPs) produces a built-in electric field to address the effectiveness and safety concerns in the antibacterial treatment. Janus tBT@PDA NPs were obtained by capping polydopamine (PDA) on tetragonal BaTiO3 (tBT) NPs through defining the polymerization time, followed by ciprofloxacin (CIP) loading on the PDA caps to fabricate Janus tBT@PDA-Cip NPs. NIR illumination of PDA caps creates temperature variations on tBT NPs to generate photothermal and pyroelectric effects. Finite element simulation reveals a pyroelectric potential of over 1 V and sufficient reactive oxygen species (ROS) are produced to exhibit pyroelectric dynamic therapy (PEDT). The elevated temperature on one side of the Janus NPs produces thermophoretic force to drive NP motion, which enhances interactions with bacteria and overcomes limitations in the short action distance and lifespan of ROS. The pyroelectric field accelerates CIP release through weakening the π-π stacking and electrostatic interaction with PDA and also interrupts membrane potentials of bacteria to enhance CIP invasion into bacteria. The synergistic antibacterial effect of pyroelectric tBT@PDA-Cip NPs causes the fully recovery of S. aureus-infected skin wounds and regeneration of intact epidermis, blood vessels and hair follicles, while no obvious pathological change or inflammatory lesion is detected in the major organs. Thus, the pyroelectric Janus nanomotors demonstrate synergistic PEDT/photothermal/antibiotic effects to enhance antibacterial efficacy while avoiding the necessity of excessive heat, ROS and antibiotic doses. STATEMENT OF SIGNIFICANCE: Antibacterial treatment is challenged by antibiotics-derived side effects and the evolution of resistant strains. Phototherapy is commonly associated with excessive heat and oxidative stress, and their combinations with other agents are especially encouraged to strengthen antibacterial efficacy while alleviating the associated side effects. Electric field is another activator to generate antibacterial abilities, but usually requires complicated power management and bulk electrodes, making it inconvenient in a biological setup. To address these challenges, we propose a strategy to generate microelectric field on nanoparticles themselves and achieve synergistic electrodynamic-photothermal-antibiotic therapies. The pyroelectric effect weakens interactions between nanoparticles and antibiotics to accelerate drug release, and the built-in pyroelectric field increases membrane fluidity to enhance bacterial uptake of antibiotics.

Plastic Deformation Mechanism of High Strength and Toughness ZK61 Magnesium Alloy Plate by Multipass Horizontal Continuous Rolling.

ZK61 magnesium-alloy plate with high tensile strength and elongation is obtained by combined multipass symmetric hot rolling and asymmetric warm rolling. Deformation history considering varying strain rate obtained from the macro-finite element analysis of the selected passes are introduced into the viscoplastic self-consistent model (VPSC) as initial boundary conditions for macro- multiscale and micro-multiscale coupling analysis. VPSC simulation results show that in the initial stage of rolling deformation, the basal slip is the dominated deformation mode, supplemented by prismatic slip and pyramidal slip. With increased rolling strain, the pyramidal slip presents competitive relationship with basal slip, and the activation amount of {101-1} compression twins is limited. During asymmetric rolling, the basal slip is dominant, followed by the pyramidal slip. Experimental results show that the basal texture is gradually strengthened after symmetric rolling, and grain size is refined due to the activation and recrystallization of twins. Asymmetric rolling makes the basal texture deflect 10° to the rolling direction and further refine the grain size. With the ongoing of symmetric rolling, the mechanical anisotropy of the plate weakens, and the yield strength, tensile strength, and plasticity of the material improves. In particular, after asymmetric rolling, the tensile strength in the RD and TD directions of the plate reaches 391.2 MPa and 398.9 MPa, whereas the elongation reaches 19.8% and 25.5%.

Solution Evolution Knowledge Service Based on Design Iteration in Strain Sensor Design.

Product design is a process of repeated iteration and gradual improvement, and knowledge push is one of the bottlenecks that needs to be solved to improve the product design level. With the increase in design complexity and iteration rounds, the existing knowledge application methods can hardly meet the needs of product design solution iteration and evolution. In order to better assist designers in acquiring and applying knowledge in the process of product design solution evolution, a knowledge service method for product design solution evolution based on the problem-strategy-solution (PSS) interaction iteration is proposed. The mapping and feedback process between design problems, design strategies, and design solutions are analyzed, a model of the solution evolution process based on design iteration is proposed, and a PSS-based product design solution evolution mechanism is established. On this basis, the product design solution evolution knowledge service dimension is built, and the solution evolution knowledge service model based on design iteration is established. The corresponding solution evolution function module is developed based on the pre-developed computer-aided product innovation design platform. The validity of the iterated-based design was proved in the technical innovation of nanofiber preparation and further application of strain sensors.

Genome-Wide Identification and Evolutionary Analyses of SrfA Operon Genes in Bacillus.

A variety of secondary metabolites contributing to plant growth are synthesized by bacterial nonribosomal peptide synthases (NRPSs). Among them, the NRPS biosynthesis of surfactin is regulated by the SrfA operon. To explore the molecular mechanism for the diversity of surfactins produced by bacteria within the genus Bacillus, we performed a genome-wide identification study focused on three critical genes of the SrfA operon-SrfAA, SrfAB and SrfAC-from 999 Bacillus genomes (belonging to 47 species). Gene family clustering indicated the three genes can be divided into 66 orthologous groups (gene families), of which a majority comprised members of multiple genes (e.g., OG0000009 had members of all three SrfAA, SrfAB and SrfAC genes), indicating high sequence similarity among the three genes. Phylogenetic analyses also found that none of the three genes formed monophyletic groups, but were usually arranged in a mixed manner, suggesting the close evolutionary relationship among the three genes. Considering the module structure of the three genes, we propose that self-duplication, especially tandem duplications, might have contributed to the initial establishment of the entire SrfA operon, and further gene fusion and recombination as well as accumulated mutations might have continuously shaped the different functional roles of SrfAA, SrfAB and SrfAC. Overall, this study provides novel insight into metabolic gene clusters and operon evolution in bacteria.

pH and Nitrate Drive Bacterial Diversity in Oil Reservoirs at a Localized Geographic Scale.

Oil reservoirs are one of the most important deep subsurface biospheres. They are inhabited by diverse microorganisms including bacteria and archaea with diverse metabolic activities. Although recent studies have investigated the microbial communities in oil reservoirs at large geographic scales, it is still not clear how the microbial communities assemble, as the variation in the environment may be confounded with geographic distance. In this work, the microbial communities in oil reservoirs from the same oil field were identified at a localized geographic scale. We found that although the injected water contained diverse exogenous microorganisms, this had little effect on the microbial composition of the produced water. The Neutral Community Model analysis showed that both bacterial and archaeal communities are dispersal limited even at a localized scale. Further analysis showed that both pH and nitrate concentrations drive the assembly of bacterial communities, of which nitrate negatively correlated with bacterial alpha diversity and pH differences positively correlated with the dissimilarity of bacterial communities. In contrast, the physiochemical parameters had little effect on archaeal communities at the localized scale. Our results suggest that the assembly of microbial communities in oil reservoirs is scale- and taxonomy-dependent. Our work provides a comprehensive analysis of microbial communities in oil reservoirs at a localized geographic scale, which improves the understanding of the assembly of the microbial communities in oil reservoirs.

Soil copper concentration map in mining area generated from AHSI remote sensing imagery.

Hyperspectral remote sensing has the advantages to predict and map soil heavy metal concentration over conventional monitoring methods and multispectral remote sensing. In quantitative applications of hyperspectral remote sensing imagery, the contribution of hyperspectral bands is different, and abnormal prediction values resulted from incorrectly classified bare soil images are a major problem. In this study, a variable weighting method was proposed to weight the hyperspectral bands, and a probability threshold was used to improve the classification to mitigate the problem of abnormal prediction values. The variable weighting was conducted by using the absorption depths obtained by continuum removal. Soil samples were collected from a mining area in southwestern China. Hyperspectral remote sensing imagery was acquired by the Advanced Hyperspectral Imager (AHSI) abroad on Geofen-5 (GF-5) satellite. Genetic algorithm and partial least squares regression (PLSR) were adopted to calibrate prediction models. In prediction of soil copper (Cu) concentration, root mean square error (RMSE) and coefficient of determination (R2) were 21.59 mg kg-1 and 0.60 for the prediction using raw reflectance spectra, and the values were improved to 18.33 mg kg-1 and 0.71 by using the weighted reflectance spectra. The developed prediction model was applied to the AHSI imagery to predict Cu concentration in bare soil areas. In prediction of Cu concentration using the AHSI imagery, negative prediction values were eliminated by using the bare soil image extracted by the improved classification. Based on the prediction, soil Cu concentration map was generated by kriging spatial interpolation. The result indicates that the proposed variable weighting method is effective and the problem of abnormal prediction values could be mitigated by using improved bare soil images. Further analysis indicates that some indices with proper thresholds also could be used to get improved bare soil images.

Epidemiological Characteristics and Clinical Manifestations of Brucellosis and Q Fever Among Humans from Northeastern Inner Mongolia.

Objective: To investigate the distribution, epidemiology, and clinical symptoms of brucellosis and Q fever in northeastern Inner Mongolia. Methods: In this study, 64 townships of Bairin left flag and Alukerqin flag, Jarud flag and Horqin right front flag in four counties with frequent brucellosis and Q fever were selected. Epidemiological characteristics, clinical features, and exposure to risk factors were identified and descriptively analyzed in patients from these areas. Results: There were 367 brucellosis cases in the four regions and 78 positive cases of Q-fever infection. In addition, 24 cases of brucellosis and Q-fever co-infection were identified, with a co-infection rate of 1.13%. Brucellosis and Q fever were mainly concentrated in the 30-65 and 40-55 age groups. For brucellosis, the difference between age groups was statistically significant (χ2 = 29.121, P < 0.05). The sex distribution for brucellosis was 225 men (61.31%) and 142 women (38.69%), and 45 men (57.69%) and 33 women (42.31%) had Q fever. Those with brucellosis and Q fever were mainly farmers, accounting for 79.19% and 78.38% of the total number, respectively. Of the 367 cases of brucellosis infection, the main symptoms were joint pain (52.59%), fatigue (47.14%), lower back pain (38.96%), fever (33.24%), hyperhidrosis (28.88%), and muscle pain (20.44%). Of the 78 cases of Q-fever infection, the main symptoms were joint pain (35.90%), fatigue (30.77%), lower back pain (26.92%), fever (21.79%), and hyperhidrosis (17.95%). Muscle pain also accounted for 12.82%. Conclusion: Occupational distribution suggests that we should strengthen the protection measures against diseases infected through animal husbandry. Among the clinical symptoms, fever, hyperhidrosis and fatigue were associated with brucellosis, while fever, headache, and fatigue were significantly associated with Q fever.