Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin

The T-loop motif is an important recurrent RNA structural building block consisting of a U-turn sub-motif and a UA trans Watson–Crick/Hoogsteen base pair. In the presence of a hairpin stem, the UA non-canonical base pair becomes part of the UA-handle motif. To probe the hierarchical organization and energy landscape of the T-loop, we performed replica exchange molecular dynamics (REMD) simulations of the T-loop in isolation and as part of a hairpin. Our simulations reveal that the isolated T-loop adopts coil conformers stabilized by base stacking. The T-loop hairpin shows a highly rugged energy landscape featuring multiple local minima with a transition state for folding consisting of partially zipped states. The U-turn displays a high conformational flexibility both when the T-loop is in isolation and as part of a hairpin. On the other hand, the stability of the UA non-canonical base pair is enhanced in the presence of the UA-handle. This motif is apparently a key component for stabilizing the T-loop, while the U-turn is mostly involved in long-range interaction. Our results suggest that the stability and folding of small RNA motifs are highly dependent on local context

A feedforward air-conditioning energy management method for high-speed railway sleeper compartment

In this paper, we propose a feedforward air conditioning temperature control method for high-speed railway locomotives with sleeper compartments to improve energy efficiency. First, we construct the geometric model of two typical types of compartments and three types of passengers. Then, based on the analysis of possible passenger layout patterns in each compartment, we utilize computational fluid dynamics simulations to calculate the optimal air volume for each pattern. The optimal air volume is calculated to guarantee the passenger comfort level and reduce the energy cost. In addition, we adopt an image recognition method to detect the number and types of passengers in each compartment. Passenger layout patterns serve as independent variables to determine the corresponding optimal air volume. Finally, numerical simulations were conducted to verify the effectiveness of the proposed method

A Heat and Mass Transfer Model of Peanut Convective Drying Based on a Two-Component Structure

In order to optimize the convective drying process parameters of peanuts and to provide a theoretical basis for the scientific use of energy in the drying process, this study took single-particle peanuts as the research object and analyzed the heat and mass transfer process during convective drying. In addition, a 3D two-component moisture heat transfer model for peanuts was constructed based on the mass balance and heat balance theorem. Moreover, the changes in the internal temperature and concentration fields of peanut pods during the whole drying process were investigated by simulations using COMSOL Multiphysics. The model was validated by thin-layer drying experiments, compared with the one-component model, and combined with low-field NMR technology to further analyze the internal moisture distribution state of peanut kernel drying process. The results show that both models can effectively simulate the peanut thin-layer drying process, and consistency is found between the experimental and simulated values, with the maximum errors of 10.25%, 9.10%, and 7.60% between the simulated moisture content and the experimental values for the two-component model, peanut shell, and peanut kernel models, respectively. Free water and part of the weakly bound water was the main water lost by peanuts during the drying process, the change in oil content was small, and the bound water content was basically unchanged. The results of the study provide a theoretical basis to accurately predict the moisture content within different components of peanuts and reveal the mechanism of moisture and heat migration during the drying process of peanut pods

An extended research of crossmodal correspondence between color and sound in psychology and cognitive ergonomics

Based on the existing research on sound symbolism and crossmodal correspondence, this study proposed an extended research on cross-modal correspondence between various sound attributes and color properties in a group of non-synesthetes. In Experiment 1, we assessed the associations between each property of sounds and colors. Twenty sounds with five auditory properties (pitch, roughness, sharpness, tempo and discontinuity), each varied in four levels, were used as the sound stimuli. Forty-nine colors with different hues, saturation and brightness were used to match to those sounds. Result revealed that besides pitch and tempo, roughness and sharpness also played roles in sound-color correspondence. Reaction times of sound-hue were a little longer than the reaction times of sound-lightness. In Experiment 2, a speeded target discrimination task was used to assess whether the associations between sound attributes and color properties could invoke natural cross-modal correspondence and improve participants’ cognitive efficiency in cognitive tasks. Several typical sound-color pairings were selected according to the results of Experiment 1. Participants were divided into two groups (congruent and incongruent). In each trial participants had to judge whether the presented color could appropriately be associated with the sound stimuli. Result revealed that participants responded more quickly and accurately in the congruent group than in the incongruent group. It was also found that there was no significant difference in reaction times and error rates between sound-hue and sound-lightness. The results of Experiment 1 and 2 indicate the existence of a robust crossmodal correspondence between multiple attributes of sound and color, which also has strong influence on cognitive tasks. The inconsistency of the reaction times between sound-hue and sound-lightness in Experiment 1 and 2 is probably owing to the difference in experimental protocol, which indicates that the complexity of experiment design may be an important factor in crossmodal correspondence phenomena

Genome-Wide Identification and Expression Analysis Reveal bZIP Transcription Factors Mediated Hormones That Functions during Early Somatic Embryogenesis in <i>Dimocarpus longan</i>

The basic leucine zip (bZIP) transcription factors (TFs) are a group of highly conserved gene families that play important roles in plant growth and resistance to adversity stress. However, studies on hormonal regulatory pathways and functional analysis during somatic embryogenesis (SE) in Dimocarpus longan is still unavailable. In this study, a total of 51 bZIP family members were systematically identified in the whole genome of longan, a comprehensive bioinformatics analysis of DlbZIP (bZIP family members of D. longan) was performed, and subcellular localization and profiles patterns after transiently transformed DlbZIP60 were analyzed. The combined analysis of RNA-seq, ATAC-seq and ChIP-seq showed that four members have different H3K4me1 binding peaks in early SE and differentially expressed with increased chromatin accessibility. Comparative transcriptome analysis of bZIPs expression in early SE, different tissues and under 2,4-D treatment revealed that DlbZIP family might involved in growth and development during longan early SE. The qRT-PCR results implied that DlbZIP family were subjected to multiple hormonal responses and showed different degrees of up-regulated expression under indole-3-acetic acid (IAA), abscisic acid (ABA) and methyl jasmonate (MeJA) treatments, which indicated that they played an important role in the hormone synthesis pathways associated with the early SE of longan. Subcellular localization showed that DlbZIP60 was located in the nucleus, and the contents of endogenous IAA, MeJA and ABA were up-regulated in transiently DlbZIP60 overexpressed cell lines. These results suggest that DlbZIP60 may mediate hormones pathways that functions the development during early SE in longan

Structure, Antioxidant, and Hypoglycemic Activities of Arabinoxylans Extracted by Multiple Methods from Triticale

Different methods of isolating arabinoxylans (AXs) from triticale were performed to investigate the extraction methods&rsquo; effects on the physiological functions of the AXs. Structural, antioxidant, and hypoglycemic activities were determined. The molecular weights (MWs) of enzyme- or water-extracted AXs were lower than those of alkali-extracted AXs. Opposite trends were shown by the arabinose&ndash;xylose ratio. Enzyme-extracted AXs exhibited higher glucose adsorption capacity and hydroxyl radical-scavenging efficiency than alkali-extracted AXs. The &alpha;-amylase inhibition ability, DPPH radical-scavenging capacity, and metal-chelating activity of alkali-extracted AXs were higher than those of enzyme-extracted AXs. Water-extracted AXs had the highest glucose dialysis retardation index. In conclusion, extraction methods can influence the physiological function of AXs through their structural features. AXs with higher MWs and esterified ferulic acid (FA) levels had higher antioxidant ability, whereas AXs with higher solubility and free FA level exhibited higher hypoglycemic activity

CD39-Expressing CD8⁺ T Cells as a New Molecular Marker for Diagnosis and Prognosis of Esophageal Squamous Cell Carcinoma

We aimed to explore the effect of CD39 expression on CD8+ T cells and on the diagnosis and prognosis of esophageal squamous cell carcinoma (ESCC). The independent prognostic factors for the surgical specimens of the 95 ESCC patients were screened by multivariate Cox regression analysis. Differential gene expression analysis was performed by the NetworkAnalyst platform based on data from the Gene Expression Omnibus (GEO). The expression of CD39 on CD8+ T cells in the CK+ region was higher in cancer tissue than in paracancerous tissue (p = 0.011), and high CD39-expressing CD8+ T cells in the CK+ region (HR, 2.587; p = 0.033) and high CD39-expressing CD8+ T cells in the CK− region (HR, 3.090; p = 0.008) were independent risk factors for prognosis in ESCC patients; the expression of ENTPD1 was upregulated in ESCC tissues compared to normal tissues (adjusted p 2 fold change = 1.99), and its expression was significantly positively correlated with the expression of PDCD1, CTLA4, and HAVCR2. High CD39-expressing CD8+ T cells can be used as a new molecular marker for the diagnosis and prognosis of ESCC, and the restoration of partially exhausted CD8+ T cells by inhibiting CD39 may be a new strategy for treating ESCC

Noninvasively Imaging Subcutaneous Tumor Xenograft by a Handheld Raman Detector, with the Assistance of an Optical Clearing Agent

A handheld Raman detector with operational convenience, high portability, and rapid acquisition rate has been applied in clinics for diagnostic purposes. However, the inherent weakness of Raman scattering and strong scattering of the turbid tissue restricts its utilization to superficial locations. To extend the applications of a handheld Raman detector to deep tissues, a gold nanostar-based surface-enhanced Raman scattering (SERS) nanoprobe with robust colloidal stability, a fingerprint-like spectrum, and extremely high sensitivity (5.0 fM) was developed. With the assistance of FPT, a multicomponent optical clearing agent (OCA) efficiently suppressing light scattering from the turbid dermal tissues, the handheld Raman detector noninvasively visualized the subcutaneous tumor xenograft with a high target-to-background ratio after intravenous injection of the gold nanostar-based SERS nanoprobe. To the best of our knowledge, this work is the first example to introduce the optical clearing technique in assisting SERS imaging in vivo. The combination of optical clearing technology and SERS is a promising strategy for the extension of the clinical applications of the handheld Raman detector from superficial tissues to subcutaneous or even deeper lesions that are usually “concealed” by the turbid dermal tissue