Learning Raw Image Denoising with Bayer Pattern Unification and Bayer Preserving Augmentation

In this paper, we present new data pre-processing and augmentation techniques for DNN-based raw image denoising. Compared with traditional RGB image denoising, performing this task on direct camera sensor readings presents new challenges such as how to effectively handle various Bayer patterns from different data sources, and subsequently how to perform valid data augmentation with raw images. To address the first problem, we propose a Bayer pattern unification (BayerUnify) method to unify different Bayer patterns. This allows us to fully utilize a heterogeneous dataset to train a single denoising model instead of training one model for each pattern. Furthermore, while it is essential to augment the dataset to improve model generalization and performance, we discovered that it is error-prone to modify raw images by adapting augmentation methods designed for RGB images. Towards this end, we present a Bayer preserving augmentation (BayerAug) method as an effective approach for raw image augmentation. Combining these data processing technqiues with a modified U-Net, our method achieves a PSNR of 52.11 and a SSIM of 0.9969 in NTIRE 2019 Real Image Denoising Challenge, demonstrating the state-of-the-art performance. Our code is available at https://github.com/Jiaming-Liu/BayerUnifyAug.Comment: Accepted by CVPRW 201

Using a conceptual Bayesian network to investigate environmental management of vegetable production in the Lake Taihu region of China

AbstractVegetable farms are one of many nitrogen (N) sources adversely affecting Lake Taihu in eastern China. Given the lack of quantitative “cause and effect” relationships and data relating to these systems, we developed a conceptual Bayesian network to investigate and demonstrate causal relationships and the effects of different mitigation strategies on N exports from vegetable farms in the Lake Taihu region. Structurally, the network comprised one primary transport factor, one primary source factor and three post-mobilisation strategies, and three output factors.In general the network suggests that N exports are more sensitive to transport factors (i.e. runoff volumes) than source factors (i.e. fertiliser application rates) although the cumulative effects of excessive fertiliser were not considered. Post-mobilisation mitigations such as wetlands and ecoditches appear to be particularly effective in decreasing N exports however their implementation on a regional scale may be limited by land availability. While optimising N inputs would be prudent, the network suggests that better irrigation practice, including improved irrigation scheduling, using less imported water and optimising rainfall utilisation would be more effective in achieving environmental goals than simply limiting N supply

Transcriptome profiling of genes regulated by phosphate-solubilizing bacteria Bacillus megaterium P68 in potato (Solanum tuberosum L.)

The insoluble phosphorus in the soil is extremely difficult to be absorbed and used directly through the potato root system. Although many studies have reported that phosphorus-solubilizing bacteria (PSB) can promote plant growth and uptake of phosphorus, the molecular mechanism of phosphorus uptake and growth by PSB has not been investigated yet. In the present study, PSB were isolated from rhizosphere soil in soybean. The data of potato yield and quality revealed that the strain P68 was the most effective In the present study, PSB identification, potato field experiment, pot experiment and transcriptome profiling to explored the role of PSB on potato growth and related molecular mechanisms. The results showed that the P68 strain (P68) was identified as Bacillus megaterium by sequencing, with a P-solubilizing ability of 461.86 mg·L−1 after 7-day incubation in National Botanical Research Institute’s Phosphate (NBRIP) medium. Compared with the control group (CK), P68 significantly increased the yield of potato commercial tubers by 17.02% and P accumulation by 27.31% in the field. Similarly, pot trials showed that the application of P68 significantly increased the biomass, total phosphorus content of the potato plants, and available phosphorus of the soil up by 32.33, 37.50, and 29.15%, respectively. Furthermore, the transcriptome profiling results of the pot potato roots revealed that the total number of bases was about 6G, and Q30 (%) was 92.35–94.8%. Compared with the CK, there were a total of 784 differential genes (DEGs) regulated when treated with P68, which 439 genes were upregulated and 345 genes were downregulated. Interestingly, most of the DEGs were mainly related to cellular carbohydrate metabolic process, photosynthesis, and cellular carbohydrate biosynthesis process. According to the KEGG pathway analysis, a total of 46 categorical metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were annotated to 101 DEGs found in potato roots. Compared with the CK, most of the DEGs were mainly enriched in glyoxylate and dicarboxylate metabolism (sot00630), nitrogen metabolism (sot00910), tryptophan metabolism (sot00380), and plant hormone signal transduction (sot04075), and these DEGs might be involved in the interactions between Bacillus megaterium P68 and potato growth. The qRT-PCR analysis of differentially expressed genes showed that inoculated treatments P68 significantly upregulated expression of the phosphate transport, nitrate transport, glutamine synthesis, and abscisic acid regulatory pathways, respectively, and the data from qRT-PCR were consistent with that obtained from RNA-seq. In summary, PSB may be involved in the regulation of nitrogen and phosphorus nutrition, glutaminase synthesis, and abscisic acid-related metabolic pathways. This research would provide a new perspective for studying the molecular mechanism of potato growth promotion by PSB in the level of gene expression and related metabolic pathways in potato roots under the application of Bacillus megaterium P68

Biological control of potato common scab and growth promotion of potato by Bacillus velezensis Y6

Potato common scab, caused mainly by Streptomyces scabies, causes surface necrosis and reduces the economic value of potato tubers, but effective chemical control is still lacking. In this study, an attempt was made to control potato common scab by inoculating potatoes with Bacillus velezensis (B. velezensis) and to further investigate the mechanism of biological control. The results showed that B. velezensis Y6 could reduce the disease severity of potato common scab from 49.92 ± 25.74% [inoculated with Streptomyces scabies (S. scabies) only] to 5.56 ± 1.89% (inoculated with S. scabies and Y6 on the same day) and increase the potato yield by 37.32% compared with the control under pot experiment in this study. Moreover, in the field trial, it was found that Y6 could also significantly reduce disease severity from 13.20 ± 1.00% to 4.00 ± 0.70% and increase the potato yield from 2.07 ± 0.10 ton/mu to 2.87 ± 0.28 ton/mu (p < 0.01; Tukey’s test). Furthermore, RNA-seq analysis indicated that 256 potato genes were upregulated and 183 potato genes were downregulated in response to B. velezensis Y6 inoculation. In addition, strain Y6 was found to induce the expression of plant growth-related genes in potato, including cell wall organization, biogenesis, brassinosteroid biosynthesis, and plant hormone transduction genes, by 1.01–4.29 times. As well as up-regulate hydroquinone metabolism-related genes and several transcription factors (bHLH, MYB, and NAC) by 1.13–4.21 times. In summary, our study will help to understand the molecular mechanism of biological control of potato common scab and improve potato yield

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Distinct Effects of Stimulus Repetition on Various Temporal Stages of Subject’s Own Name Processing

The self is one of the most important concepts in psychology, which is of great significance for human survival and development. As an important self-related stimulus, the subject’s own name (SON) shows great advantages in cognitive and social processing and is widely used as an oddball stimulus in previous studies. However, it remained unknown whether the multiple repetition of stimulus would have similar influence on the neural response to SON and the other names under equal probability. In this study, adopting EEG and an equal–probability paradigm, we first detected the SON-related ERP components which could differentiate SON from other names, and then investigated how these components are influenced by repeated exposure of the stimulus. Our results showed that SON evoked an earlier SON-related negativity (SRN) at the fronto-central region and a late positive potential (LPP) at the centro-parietal region. More intriguingly, the earlier SRN demonstrated reduction after multiple repetitions, whereas LPP did not exhibit significant changes. In conclusion, these findings revealed that multiple repetitions of the stimulus might influence the various temporal stages in SON-related processing and highlighted the robustness of the late stage in this processing

Improvement to Calculation Method of Flood Force on T-Girder Considering Entrapped Air in Chambers

Entrapped air in the chambers of a T-girder bridge generates a considerably large vertical force which is harmful to the safety of the bridge superstructure. The contribution of the entrapped air is not considered when calculating flood force in the related specifications, and also it has not been taken into account by researchers. Two-dimensional, scaled-down models at a 1:40 scale are selected as the research object. Analytical and numerical methods are employed to investigate the contribution of entrapped air in T-girder chambers to flood forces. Results show that the entrapped air in the rear chambers could escape easier than that in the front chambers and the compressibility of entrapped air has a small influence on drag force and vertical force (generated by dynamic pressure) coefficients, but it reduces the buoyancy of the T-girder. Considering the entrapped air compressibility and entrapped air escape, the calculation method of the buoyancy of entrapped air is proposed to improve the precision of the existing flood force calculation method

Correction: Gong et al. Neuroprotective and Cytotoxic Phthalides from <i>Angelicae Sinensis</i> Radix. <i>Molecules</i> 2016, <i>21</i>, 549

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