BCI Toolbox: An open-source python package for the Bayesian causal inference model.

Psychological and neuroscientific research over the past two decades has shown that the Bayesian causal inference (BCI) is a potential unifying theory that can account for a wide range of perceptual and sensorimotor processes in humans. Therefore, we introduce the BCI Toolbox, a statistical and analytical tool in Python, enabling researchers to conveniently perform quantitative modeling and analysis of behavioral data. Additionally, we describe the algorithm of the BCI model and test its stability and reliability via parameter recovery. The present BCI toolbox offers a robust platform for BCI model implementation as well as a hands-on tool for learning and understanding the model, facilitating its widespread use and enabling researchers to delve into the data to uncover underlying cognitive mechanisms.

The overlooked role of unisensory precision in multisensory research.

Zhu et al. present an alternative explanation for the weaker multisensory illusions in football goalkeepers compared with outfielders and non-athletes, showing that better unisensory precision in goalkeepers can also account for this effect.

Zonal demand-controlled ventilation strategy to minimize infection probability and energy consumption: A coordinated control based on occupant detection.

Due to the outbreak of COVID-19, an increased risk of airborne transmission has been experienced in buildings, particularly in confined public places. The need for ventilation as a means of infection prevention has become more pronounced given that some basic precautions (like wearing masks) are no longer mandatory. However, ventilating the space as a whole (e.g., using a unified ventilation rate) may lead to situations where there is either insufficient or excessive ventilation in localized areas, potentially resulting in localized virus accumulation or large energy consumption. It is of urgent need to investigate real-time control of ventilation systems based on local demands of the occupants to strike a balance between infection risk and energy saving. In this work, a zonal demand-controlled ventilation (ZDCV) strategy was proposed to optimize the ventilation rates in sub-zones. A camera-based occupant detection method was developed to detect occupants (with eight possible locations in sub-zones denoted as 'A' to 'H'). Linear ventilation model (LVM), dimension reduction, and artificial neural network (ANN) were integrated for rapid prediction of pollutant concentrations in sub-zones with the identified occupants and ventilation rates as inputs. Coordinated ventilation effects between sub-zones were optimized to improve infection prevention and energy savings. Results showed that rapid prediction models achieved an average prediction error of 6 ppm for CO2 concentration fields compared with the simulation under different occupant scenarios (i.e., occupant locations at ABH, ABCFH, and ABCDEFH). ZDCV largely reduced the infection risk to 2.8% while improved energy-saving efficiency by 34% compared with the system using constant ventilation rate. This work can contribute to the development of building environmental control systems in terms of pollutant removal, infection prevention, and energy sustainability.

Prime editing using CRISPR-Cas12a and circular RNAs in human cells.

Genome editing with prime editors based on CRISPR-Cas9 is limited by the large size of the system and the requirement for a G/C-rich protospacer-adjacent motif (PAM) sequence. Here, we use the smaller Cas12a protein to develop four circular RNA-mediated prime editor (CPE) systems: nickase-dependent CPE (niCPE), nuclease-dependent CPE (nuCPE), split nickase-dependent CPE (sniCPE) and split nuclease-dependent CPE (snuCPE). CPE systems preferentially recognize T-rich genomic regions and possess a potential multiplexing capacity in comparison to corresponding Cas9-based systems. The efficiencies of the nuclease-based systems are up to 10.42%, whereas niCPE and sniCPE reach editing frequencies of up to 24.89% and 40.75% without positive selection in human cells, respectively. A derivative system, called one-sniCPE, combines all three RNA editing components under a single promoter. By arraying CRISPR RNAs for different targets in one circular RNA, we also demonstrate low-efficiency editing of up to four genes simultaneously with the nickase prime editors niCPE and sniCPE.

Involvement of IGF1 in endoplasmic reticulum stress contributes to cataract formation through regulating Nrf2/NF-κB signaling.

Endoplasmic reticulum (ER) stress is reportedly involved in the development of ophthalmic diseases. This study aimed to investigate the role and potential mechanism of insulin-like growth factor 1 (IGF1) in ER stress. A mouse cataract model was constructed by subcutaneous injection of sodium selenite, and sh-IGF1 was used to evaluate the effect of silencing IGF1 on cataract progression. Slit-lamp and histological examination of the lens were performed to examine lens damage. The regulatory effects of IGF1 on inflammatory responses, oxidative stress, and ER stress were evaluated using ELISA, reverse transcription-quantitative PCR (RT-qPCR), and immunoblotting analysis. Tunicamycin was used to induce ER stress in the lens of epithelial cells. The NF-E2 related factor-2 (Nrf2) inhibitor ML385 and nuclear factor-κB (NF-κB) agonist diprovocim were used to confirm whether IGF1 regulates inflammation and ER stress through Nrf2/NF-κB signaling. Silencing IGF1 alleviated lens damage and reduced lens turbidity in the cataract mice. Silencing IGF1 inhibited inflammatory response, oxidative stress and ER stress response. Meanwhile, IGF1 was highly expressed in sodium selenite-treated lens epithelial cells. The ER stress agonist tunicamycin suppressed cell viability as well as induced ER stress, oxidative stress and inflammation. Silencing IGF1 increased cell viability, EdU-positive rate and migration. Also, silencing of IGF1 reduced inflammation and ER stress via regulating Nrf2/NF-κB pathway. This study reveals silencing IGF1 attenuated cataract through regulating Nrf2/NF-κB signaling, which shares novel insights into the underlying mechanism of cataract and provides potential therapeutic target for cataract.

Intelligent operation, maintenance, and control system for public building: Towards infection risk mitigation and energy efficiency.

During the post-COVID-19 era, it is important but challenging to synchronously mitigate the infection risk and optimize the energy savings in public buildings. While, ineffective control of ventilation and purification systems can result in increased energy consumption and cross-contamination. This paper is to develop intelligent operation, maintenance, and control systems by coupling intelligent ventilation and air purification systems (negative ion generators). Optimal deployment of sensors is determined by Fuzzy C-mean (FCM), based on which CO2 concentration fields are rapidly predicted by combing the artificial neural network (ANN) and self-adaptive low-dimensional linear model (LLM). Negative oxygen ion and particle concentrations are simulated with different numbers of negative ion generators. Optimal ventilation rates and number of negative ion generators are decided. A visualization platform is established to display the effects of ventilation control, epidemic prevention, and pollutant removal. The rapid prediction error of LLM-based ANN for CO2 concentration was below 10% compared with the simulation. Fast decision reduced CO2 concentration below 1000 ppm, infection risk below 1.5%, and energy consumption by 27.4%. The largest removal efficiency was 81% when number of negative ion generators was 10. This work can promote intelligent operation, maintenance, and control systems considering infection prevention and energy sustainability.

Audiovisual illusion training improves multisensory temporal integration.

When we perceive external physical stimuli from the environment, the brain must remain somewhat flexible to unaligned stimuli within a specific range, as multisensory signals are subject to different transmission and processing delays. Recent studies have shown that the width of the 'temporal binding window (TBW)' can be reduced by perceptual learning. However, to date, the vast majority of studies examining the mechanisms of perceptual learning have focused on experience-dependent effects, failing to reach a consensus on its relationship with the underlying perception influenced by audiovisual illusion. The sound-induced flash illusion (SiFI) training is a reliable function for improving perceptual sensitivity. The present study utilized the classic auditory-dominated SiFI paradigm with feedback training to investigate the effect of a 5-day SiFI training on multisensory temporal integration, as evaluated by a simultaneity judgment (SJ) task and temporal order judgment (TOJ) task. We demonstrate that audiovisual illusion training enhances multisensory temporal integration precision in the form of (i) the point of subjective simultaneity (PSS) shifts to reality (0 ms) and (ii) a narrowing TBW. The results are consistent with a Bayesian model of causal inference, suggesting that perception learning reduce the susceptibility to SiFI, whilst improving the precision of audiovisual temporal estimation.

SnRK2 subfamily I protein kinases regulate ethylene biosynthesis by phosphorylating HB transcription factors to induce ACO1 expression in apple.

Ethylene (ETH) controls climacteric fruit ripening and can be triggered by osmotic stress. However, the mechanism regulating ETH biosynthesis during fruit ripening and under osmotic stress is largely unknown in apple (Malus domestica). Here, we explored the roles of SnRK2 protein kinases in ETH biosynthesis related to fruit ripening and osmoregulation. We identified the substrates of MdSnRK2-I using phosphorylation analysis techniques. Finally, we identified the MdSnRK2-I-mediated signaling pathway for ETH biosynthesis related to fruit ripening and osmoregulation. The activity of two MdSnRK2-I members, MdSnRK2.4 and MdSnRK2.9, was significantly upregulated during ripening or following mannitol treatment. Overexpression of MdSnRK2-I increased ETH biosynthesis under normal and osmotic conditions in apple fruit. MdSnRK2-I phosphorylated the transcription factors MdHB1 and MdHB2 to enhance their protein stability and transcriptional activity on MdACO1. MdSnRK2-I also interacted with MdACS1 and increased its protein stability through two phosphorylation sites. The increased MdACO1 expression and MdACS1 protein stability resulted in higher ETH production in apple fruit. In addition, heterologous expression of MdSnRK2-I or manipulation of SlSnRK2-I expression in tomato (Solanum lycopersicum) fruit altered fruit ripening and ETH biosynthesis. We established that MdSnRK2-I functions in fruit ripening and osmoregulation, and identified the MdSnRK2-I-mediated signaling pathway controlling ETH biosynthesis.

Author Correction: Applications of CRISPR-Cas in agriculture and plant biotechnology.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Publisher Correction: Applications of CRISPR-Cas in agriculture and plant biotechnology.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Establishment of a PEG-mediated protoplast transformation system based on DNA and CRISPR/Cas9 ribonucleoprotein complexes for banana.

BACKGROUND: To date, CRISPR/Cas9 RNP editing tools have not been applied to the genetic modification of banana. Here, the establishment of a PEG-mediated banana protoplast transformation system makes it possible to build an efficient DNA-free method for a site-directed mutagenesis system. RESULTS: Protoplasts constitute a versatile platform for transient expression in plant science. In this study, we established a PEG-mediated banana protoplast transformation system. This system was further optimized for successfully delivering CRISPR/Cas9 and CRISPR/Cas12a plasmids and CRISPR/Cas9 ribonucleoproteins (RNPs) for targeted delivery of the PDS gene into banana protoplasts. Specific bands were observed in PCR-Restriction Enzyme Digestion (PCR-RE) assays, and Sanger sequencing of single clones further confirmed the occurrence of indels at target sites. Deep amplicon sequencing results showed that the editing efficiency of the CRISPR/Cas9 system was higher than that of the other two systems. CONCLUSIONS: The PEG-mediated banana protoplast transformation system can serve as a rapid and effective tool for transient expression assays and sgRNA validation in banana. The application of the CRISPR/Cas9 RNP system enables the generation of banana plants engineered by DNA-free gene editing.

Applications of CRISPR-Cas in agriculture and plant biotechnology.

The prokaryote-derived CRISPR-Cas genome editing technology has altered plant molecular biology beyond all expectations. Characterized by robustness and high target specificity and programmability, CRISPR-Cas allows precise genetic manipulation of crop species, which provides the opportunity to create germplasms with beneficial traits and to develop novel, more sustainable agricultural systems. Furthermore, the numerous emerging biotechnologies based on CRISPR-Cas platforms have expanded the toolbox of fundamental research and plant synthetic biology. In this Review, we first briefly describe gene editing by CRISPR-Cas, focusing on the newest, precise gene editing technologies such as base editing and prime editing. We then discuss the most important applications of CRISPR-Cas in increasing plant yield, quality, disease resistance and herbicide resistance, breeding and accelerated domestication. We also highlight the most recent breakthroughs in CRISPR-Cas-related plant biotechnologies, including CRISPR-Cas reagent delivery, gene regulation, multiplexed gene editing and mutagenesis and directed evolution technologies. Finally, we discuss prospective applications of this game-changing technology.

Fine-tuning sugar content in strawberry.

Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33.9-83.6% higher than that of the wild-type. We also recover a series of transgene-free mutants with 35 novel genotypes containing a continuum of sugar content. All the novel genotypes could be immediately fixed in subsequent generations by asexual reproduction. Genome editing coupled with asexual reproduction offers tremendous opportunities for quantitative trait improvement.

SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds.

We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using paired sgRNAs, SWISS can produce insertions/deletions in addition to base editing. Rice mutants are generated using the SWISS system with efficiencies of cytosine conversion of 25.5%, adenine conversion of 16.4%, indels of 52.7%, and simultaneous triple mutations of 7.3%. The SWISS system provides a powerful tool for multi-functional genome editing in plants.