Sleep state classification using power spectral density and residual neural network with multichannel EEG signals.

This paper proposes a classification framework for automatic sleep stage detection in both male and female human subjects by analyzing the electroencephalogram (EEG) data of polysomnography (PSG) recorded for three regions of the human brain, i.e., the pre-frontal, central, and occipital lobes. Without considering any artifact removal approach, the residual neural network (ResNet) architecture is used to automatically learn the distinctive features of different sleep stages from the power spectral density (PSD) of the raw EEG data. The residual block of the ResNet learns the intrinsic features of different sleep stages from the EEG data while avoiding the vanishing gradient problem. The proposed approach is validated using the sleep dataset of the Dreams database, which comprises of EEG signals for 20 healthy human subjects, 16 female and 4 male. Our experimental results demonstrate the effectiveness of the ResNet based approach in identifying different sleep stages in both female and male subjects compared to state-of-the-art methods with classification accuracies of 87.8% and 83.7%, respectively

Adaptively evolved Escherichia coli for improved ability of formate utilization as a carbon source in sugar???free conditions

Background: Formate converted from CO2 reduction has great potential as a sustainable feedstock for biological production of biofuels and biochemicals. Nevertheless, utilization of formate for growth and chemical production by microbial species is limited due to its toxicity or the lack of a metabolic pathway. Here, we constructed a formate assimilation pathway in Escherichia coli and applied adaptive laboratory evolution to improve formate utilization as a carbon source in sugar-free conditions. Results: The genes related to the tetrahydrofolate and serine cycles from Methylobacterium extorquens AM1 were overexpressed for formate assimilation, which was proved by the 13C-labeling experiments. The amino acids detected by GC/MS showed significant carbon labeling due to biomass production from formate. Then, 150 serial subcultures were performed to screen for evolved strains with improved ability to utilize formate. The genomes of evolved mutants were sequenced and the mutations were associated with formate dehydrogenation, folate metabolism, and biofilm formation. Last, 90 mg/L of ethanol production from formate was achieved using fed-batch cultivation without addition of sugars. Conclusion: This work demonstrates the effectiveness of the introduction of a formate assimilation pathway, combined with adaptive laboratory evolution, to achieve the utilization of formate as a carbon source. This study suggests that the constructed E. coli could serve as a strain to exploit formate and captured CO2

The Arabidopsis thaliana Homeobox Gene ATHB12 Is Involved in Symptom Development Caused by Geminivirus Infection

BACKGROUND: Geminiviruses are single-stranded DNA viruses that infect a number of monocotyledonous and dicotyledonous plants. Arabidopsis is susceptible to infection with the Curtovirus, Beet severe curly top virus (BSCTV). Infection of Arabidopsis with BSCTV causes severe symptoms characterized by stunting, leaf curling, and the development of abnormal inflorescence and root structures. BSCTV-induced symptom development requires the virus-encoded C4 protein which is thought to interact with specific plant-host proteins and disrupt signaling pathways important for controlling cell division and development. Very little is known about the specific plant regulatory factors that participate in BSCTV-induced symptom development. This study was conducted to identify specific transcription factors that are induced by BSCTV infection. METHODOLOGY/PRINCIPAL FINDINGS: Arabidopsis plants were inoculated with BSCTV and the induction of specific transcription factors was monitored using quantitative real-time polymerase chain reaction assays. We found that the ATHB12 and ATHB7 genes, members of the homeodomain-leucine zipper family of transcription factors previously shown to be induced by abscisic acid and water stress, are induced in symptomatic tissues of Arabidopsis inoculated with BSCTV. ATHB12 expression is correlated with an array of morphological abnormalities including leaf curling, stunting, and callus-like structures in infected Arabidopsis. Inoculation of plants with a BSCTV mutant with a defective c4 gene failed to induce ATHB12. Transgenic plants expressing the BSCTV C4 gene exhibited increased ATHB12 expression whereas BSCTV-infected ATHB12 knock-down plants developed milder symptoms and had lower ATHB12 expression compared to the wild-type plants. Reporter gene studies demonstrated that the ATHB12 promoter was responsive to BSCTV infection and the highest expression levels were observed in symptomatic tissues where cell cycle genes also were induced. CONCLUSIONS/SIGNIFICANCE: These results suggest that ATHB7 and ATHB12 may play an important role in the activation of the abnormal cell division associated with symptom development during geminivirus infection

Enhancing the tyosine production from acetate in Escherichia coli by optimization of glyoxylate cycle

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Biosensor Engineering for Efficient Caprolactam Production in Bacterial Strain

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Development of a Caprolactam Biosensor Based on RNA for Rapid Selection of Caprolactam Producer Cell

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Development of Caprolactam-specific Riboswitch that Regulates Translation Initiation

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Artificial lactam riboswitch for high-throughput screening and selection

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Development of Caprolactam-Specific RNA-Based Biosensor

Caprolactam is a monomer that is used in synthesis of value-added chemical, Nylon-6. Production of caprolactam in recombinant microbial strain entails unwanted byproduct, valerolactam with five carbons. To engineer the strain as an efficient caprolactam producer, development of biosensor that reports the intracellular concentration of caprolactam is required. Here, we selected caprolactam-specific aptamer from random RNA library and engineered it into a riboswitch that regulates translation initiation. Iterative selections in controlled conditions in vitro and in vivo allowed enrichment of aptamers with target-specific binding affinity and riboswitches with target-dependent conformation-changing ability from randomized oligonucleotide pool. Screened riboswitch successfully discriminated caprolactam from valerolactam, which reported a proportional fluorescence signal only to intracellular caprolactam concentration and high fold-activation ratio. The modular design of riboswitch circuit could drive diverse cellular responses by swapping reporter genes, which broadens its scope of application. We expect that novel synthetic biology toolkit sparks the evolutionary engineering of value-added producer strains.2