The promoter is a key DNA sequence whose primary function is to control the initiation time and the degree of expression of gene transcription. Accurate identification of promoters is essential for understanding gene expression studies. Traditional sequencing techniques for identifying promoters are costly and time-consuming. Therefore, the development of computational methods to identify promoters has become critical. Since deep learning methods show great potential in identifying promoters, this study proposes a new promoter prediction model, called iPro2L-DG. The iPro2L-DG predictor, based on an improved Densely Connected Convolutional Network (DenseNet) and a Global Attention Mechanism (GAM), is constructed to achieve the prediction of promoters. The promoter sequences are combined feature encoding using C2 encoding and nucleotide chemical property (NCP) encoding. An improved DenseNet extracts advanced feature information from the combined feature encoding. GAM evaluates the importance of advanced feature information in terms of channel and spatial dimensions, and finally uses a Full Connect Neural Network (FNN) to derive prediction probabilities. The experimental results showed that the accuracy of iPro2L-DG in the first layer (promoter identification) was 94.10% with Matthews correlation coefficient value of 0.8833. In the second layer (promoter strength prediction), the accuracy was 89.42% with Matthews correlation coefficient value of 0.7915. The iPro2L-DG predictor significantly outperforms other existing predictors in promoter identification and promoter strength prediction. Therefore, our proposed model iPro2L-DG is the most advanced promoter prediction tool. The source code of the iPro2L-DG model can be found in https://github.com/leirufeng/iPro2L-DG.

The vibration of the micro-milling tool presents a significant chaotic vibration phenomenon, which has a great influence on the tool life and part machining precision, and is one of the basic problems restricting the improvement of machining efficiency and machining accuracy in micro-milling. To overcome the difficulty of the traditional vibration measurement method with the online measurement of micro-milling tool multi-dimensional vibration, a three-dimensional (3D) measurement method of the micro-milling tool is proposed based on multi-fiber array coding, which converts the tool space motion into a decoding process of the optical coding array employing the tool modulating the multi-fiber array encoding. A 6 × 6 optical fiber array was designed, and a 3D motion platform for micro-milling tools was built to verify the characteristics of the optical fiber measurement system. The measurement results show that the measuring accuracy of the system reached 1 µm, and the maximum linear error in x-, y-, and z-direction are 1.5%, 2.58%, and 2.43%, respectively; the tool space motion position measurement results show that the maximum measurement error of the measuring system was 3.4%. The designed system has unique coding characteristics for the tool position in the space of 100 µm3. It provides a new idea and realization means for the online vibration measurement of micro-milling tools.

OBJECTIVE: While high concentrations of toluene are known to affect multiple human organ systems, research concerning the influence of immediate, short-term exposure to toluene indoors and at low concentrations is scarce. Here, we studied effects of indoor toluene exposure on neural network alterations during working memory (WM) encoding.
METHODS: A total of 23 healthy college students were recruited. All participants were situated in a closed environmental chamber with a full fresh air system. Each participant was subjected to four exposure experiments with different toluene concentrations (0, 17.5, 35, and 70 ppb, named Group A, B, C and D, respectively), with at least one week between each experiment. WM Behavioral and 19-channel electroencephalogram (EEG) recordings in a pre-set environmental chamber were conducted simultaneously during each toluene exposure experiment. Neural networks relevant to WM encoding were visualized analyzing the obtained data.
RESULTS: 1. No significant difference in WM behavioral performance among the four groups was found. However, a significant increase in whole brain neural network functional connectivity was noted, especially in the frontal region. 2. An outflow directional transfer function (DTFoutflow) revealed higher frontal region values among Group D (the 70 ppb group) as compared to Group A, B and C (the0, 17.5 ppb and 35 ppb groups, respectively), although no differences in frontal region DTFinflow values among the four groups were noted. 3. The DTFFZ-F7, DTFFZ-T5, DTFFZ-P4, DTFFZ-P3, DTFFP2-O2, DTFP3-T4, DTFP3-F4, DTFP4-CZ and DTFP4-T4 values of Group D were found to be higher as compared to those of Group A and B. Furthermore, DTFFZ-F7 and DTFP4-T4 values of Group C were higher as compared to those of Group A. The DTFFZ-F7 values of Group D were higher as compared to those of the Group C.
CONCLUSIONS: Short-term toluene exposure significantly influences neural networks during cognitive processes such as WM encoding, even at low concentration.

In the cellular response to stresses, the tumor suppressor p53 is activated to maintain genomic integrity and fidelity. As a transcription factor, p53 exhibits rich dynamics to allow for discrimination of the type and intensity of stresses and to direct the selective activation of target genes involved in different processes including cell cycle arrest and apoptosis. In this review, we focused on how stresses are encoded into p53 dynamics and how the dynamics are decoded into cellular outcomes. Theoretical modeling may provide a global view of signaling in the p53 network by coupling the encoding and decoding processes. We discussed the significance of modeling in revealing the mechanisms of the transition between p53 dynamic modes. Moreover, we shed light on the crosstalk between the p53 network and other signaling networks. This review may advance the understanding of operating principles of the p53 signaling network comprehensively and provide insights into p53 dynamics-based cancer therapy.

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Evading or escaping from predators is one of the most crucial issues for survival across the animal kingdom. The timely detection of predators and the initiation of appropriate fight-or-flight responses are innate capabilities of the nervous system. Here we review recent progress in our understanding of innate visually-triggered defensive behaviors and the underlying neural circuit mechanisms, and a comparison among vinegar flies, zebrafish, and mice is included. This overview covers the anatomical and functional aspects of the neural circuits involved in this process, including visual threat processing and identification, the selection of appropriate behavioral responses, and the initiation of these innate defensive behaviors. The emphasis of this review is on the early stages of this pathway, namely, threat identification from complex visual inputs and how behavioral choices are influenced by differences in visual threats. We also briefly cover how the innate defensive response is processed centrally. Based on these summaries, we discuss coding strategies for visual threats and propose a common prototypical pathway for rapid innate defensive responses.

We propose a multidimensional reconciliation encoding algorithm based on a field-programmable gate array (FPGA) with variable data throughput that enables quantum key distribution (QKD) systems to be adapted to different throughput requirements. Using the circulatory structure, data flow in the most complex pipeline operation in the same time interval, which enables the structural multiplexing of the algorithm. We handle the calculation and storage of eight-dimensional matrices cleverly to conserve resources and increase data processing speed. In order to obtain the syndrome more efficiently, we designed a simplified algorithm according to the characteristics of the FPGA and parity-check matrix, which omits the unnecessary operation of matrix multiplication. The simplified algorithm could adapt to different rates. We validated the feasibility and high speed of the algorithm by implementing the multidimensional reconciliation encoding algorithm on a Xilinx Virtex-7 FPGA. Our simulation results show that the maximum throughput could reach 4.88 M symbols/s.

It is generally believed that working memory (WM) is dysfunctional in depression. However, whether this impaired performance originates from impaired encoding, maintenance or both stages is still unclear. Here, we aimed to decompose the abnormal characteristics of encoding and maintenance in patients with recurrent major depressive disorder (MDD). Thirty patients and thirty-nine healthy controls completed a spatial working memory task where the encoding time and the retention time could vary under different load levels. Encoding performance was assessed by comparing accuracies between short and long encoding times, and maintenance performance was assessed by comparing accuracies between short and long retention times. The results show a lower performance in depression than the controls. However, while the decreased accuracy by long retention (vs. short retention) was increased by a short encoding time in the control group, the retention performance of the depression group did not further suffer from the short encoding time. The generally impaired encoding, together with limited maintenance of immunity against the constrained encoding time, suggests a common bias for fixed internal processing over external processing in recurrent MDD. The paradigm provided in this study can be a convenient and efficient clinical test for assessing the WM encoding and maintenance function.

One critical approach for promoting the efficiency of memory is to adopt selective encoding strategies to prioritize more valuable information. Past neuroimaging studies have shown that value-directed modulation of verbal memory depends heavily on the engagement of left-lateralized semantic processing regions, particularly in the ventrolateral prefrontal cortex (VLPFC). In the present study, we used high-definition transcranial direct current stimulation (HD-tDCS) to seek evidence for a causal role of left VLPFC in supporting the memory advantage for high-value items. Three groups of healthy young adult participants were presented with lists of words to remember, with each word accompanied by an arbitrarily assigned point value. During the first session, all participants received sham stimulation as they encoded five lists of 30 words each. Two of these lists were immediately tested with free recall, with feedback given to allow participants to develop metacognitive insight and strategies to maximize their point total. The second session had the exact same structure as the first, but the groups differed in whether they received continued sham stimulation (N = 22) or anodal stimulation of the left VLPFC (N = 21) or right VLPFC (N = 20). Those lists not tested with immediate recall were tested with recognition judgments after a one-day delay. Since no brain stimulation was applied during this Day 2 test, any performance differences can be attributed to the effects of stimulation on Day 1 encoding processes. Anodal stimulation of left VLPFC significantly boosted participants\' memory encoding selectivity. In comparison, no such effect was seen in participants who received right VLPFC or sham stimulation. Estimates of recollection- and familiarity-based responding revealed that left VLPFC stimulation specifically amplified the effects of item value on recollection. These results demonstrate a causal role for left VLPFC in the implementation of selective value-directed encoding strategies, putatively by boosting deep semantic processing of high-value words. Our findings also provide further evidence on the hemispheric lateralization of value-directed verbal memory encoding.

Although memory has long been recognized as a generative process, neural research of memory in recent decades has been predominantly influenced by Tulving\'s \"mental time traveling\" perspective and focused on the reactivation and consolidation of encoded memory representations. With the development of multiple powerful analytical approaches to characterize the contents and formats of neural representations, recent studies are able to provide detailed examinations of the representations at various processing stages and have provided exciting new insights into the transformative nature of episodic memory. These studies have revealed the rapid, substantial, and continuous transformation of memory representation during the encoding, maintenance, consolidation, and retrieval of both single and multiple events, as well as event sequences. These transformations are characterized by the abstraction, integration, differentiation, and reorganization of memory representations, enabling the long-term retention and generalization of memory. These studies mark a significant shift in perspective from remembering to reconstruction, which might better reveal the nature of memory and its roles in supporting more effective learning, adaptive decision-making, and creative problem solving.