Toward individualized connectomes of brain morphology

The morphological brain connectome (MBC) delineates the coordinated patterns of local morphological features (such as cortical thickness) across brain regions. While classically constructed using population-based approaches, there is a growing trend toward individualized modeling. Currently, the methods for individualized MBCs are varied, posing challenges for method selection and cross-study comparisons. Here, we summarize how individualized MBCs are modeled through low-order methods (correlation-, divergence-, distance-, and deviation-based methods) describing relations in brain morphology, as well as high-order methods capturing similarities in these low-order relations. We discuss the merits and limitations of different methods, examining them in the context of robustness, reproducibility, and reliability. We highlight the importance of elucidating the cellular and molecular mechanisms underlying the individualized connectome, and establishing normative benchmarks to assess individual variation in development, aging, and neuropsychiatric disorders.

The evaluation of eye-catching effect in freeway tunnel entrance zone based on fixation behavior characteristics

OBJECTIVE

The visual attraction of the freeway tunnel entrance zone will affect the driver's visual performance and visual workload, and then affect the driving safety. The purpose of this study is to explore the influence of different visual attraction conditions in the entrance zone of the freeway tunnel on driver's fixation behavior, and then evaluate the impact of eye-catching effect on driving safety.

METHODS

Thirty-five participants were recruited for the naturalistic driving experiment. Four different visually attractive driving scenarios (baseline, landscape-style architecture, tip slogan, and billboard) were selected. Participants' fixation behavior data were collected using an eye-tracking device. The effects of the visual attraction conditions in the freeway tunnel entrance zones were analyzed on driver fixation duration, number of fixations, fixation deviation, and pupil diameter.

RESULTS

The results demonstrated significant effects of different visual attractions in the entrance zone of the freeway tunnel on drivers' fixation behavior. Under the visual attraction of the billboard, drivers exhibited the most number of fixations. And under the visual attraction of tip slogan, drivers had the longest average fixation duration, the smallest horizontal fixation deviation, the largest vertical fixation deviation, and the highest pupil diameter and its coefficient of variation.

CONCLUSIONS

It can be concluded that different visual attractions in the freeway tunnel entrance zone have different effects on the eye-catching effect of drivers, by influencing the fixation behavior characteristics of drivers. Billboard is most effective in capturing drivers' visual attention, and tip slogan requires greater attention allocation and visual cognitive effort from drivers, resulting in the highest visual cognitive workload. This study highlights the complex relationship between visual attraction and its performance on driver fixation behavior. The insights from this study can provide valuable references for the design and optimization of the visual environment in the entrance zone of freeway tunnels.

Assessing the Impact of a 1.5 T Transverse Magnetic Field in Radiotherapy for Esophageal Cancer Patients

Purpose: Magnetic resonance (MR)-guided radiotherapy enables visualization of static anatomy, capturing tumor motion, and extracting quantitative image features for treatment verification and outcome monitoring. However, magnetic fields in online MR imaging (MRI) require efforts to ensure accurate dose measurements. This study aimed to assess the dosimetric impact of a 1.5 T magnetic field in esophageal cancer radiotherapy using MR-linac, exploring treatment adaptation potential and personalized medicine benefits. Methods: A prospective cohort study enrolled 100 esophageal squamous cell carcinoma patients undergoing 4DCT and 3DCT scans before radiotherapy. The heart was contoured on 3DCT, 4DCT end expiration (EE), and 4DCT end inhalation (EI) images by the same radiation oncologist. Reference RT plans were designed on 3DCT, with adjustments for different phases generating 5 plan types per patient. Variations in dose-volume parameters for organs at risk and the target area among different plans were compared using Monaco 5.40.04. Results: Slight dose distortions at air-tissue interfaces were observed in the magnetic field's presence. Dose at air-tissue interfaces (chest wall and heart wall) was slightly higher in some patients (3.0% tissue increased by 4.3 Gy on average) compared to nonmagnetic conditions. Average clinical target volume coverage V100 dropped from 99% to 95% compared to reference plans (planEI and planEE). Dose-volume histogram variation between the original plan and reference plans was within 2.3%. Superior-inferior (SI) direction displacement was significantly larger than lateral and anterior-posterior directions (P < .05). Conclusion: Significant SI direction shift in lower esophageal cancerous regions during RT indicates the magnetic field's dosimetric impact, including the electron return effect at tissue-air boundaries. Changes in OAR dose could serve as valuable indicators of organ impairment and target dose alterations, especially for cardiac tissue when using the 1.5 T linac method. Reoptimizing the plan with the magnetic field enhances the feasibility of achieving a clinically acceptable treatment plan for esophageal cancer patients.

An exploratory investigation into the influence of risk factors on driver injury severity in angle crashes: A random parameter bivariate ordered probit model approach

OBJECTIVE

Angle crashes have been acknowledged as a concerning issue in the traffic safety field, though there is limited understanding of the contributions of risk factors to injury severity. This article aims to examine the impact of risk factors and unobserved heterogeneity on the severity of driver injuries in angle collisions by utilizing angle crash data in the United States from 2016 to 2021.

METHODS

The relationship between risk factors and driver injury severities in angle crashes was investigated using a random parameter bivariate ordered probit model (RPBOP) with 4 categories of injury severity classified as outcome variables, including no injury, possible injury, minor injury, and serious jury. Risk factors were considered as explanatory variables, classified as driver characteristics, vehicle characteristics, road characteristics, environmental characteristics, time characteristics, and crash characteristics. Bayesian inference was used to assess the unobserved heterogeneity in risk factors, and marginal effects were computed to analyze the effect of each factor on injury outcomes.

RESULTS

The findings demonstrate that risk factors have varying effects on driver involvement in angle crashes. Certain factors exhibited unobserved heterogeneity, including young drivers (ages 25-44), older drivers (over age 59), road grade, and collision point orientation. On the other hand, other factors, such as female gender, motorcycles, intersections, speed limit (>50 mph), poor lighting conditions, adverse weather, urban areas, and workdays, were shown to significantly increase the likelihood of driver injury in angle collisions, as well as increase susceptibility to fatal injury.

CONCLUSIONS

This article offers new insights into reducing driver injuries in angle crashes and has the potential to inform policy development aimed at preventing such incidents. Further research could utilize multisource data fusion and investigate the spatiotemporal stability of risk factors to enhance the generalizability of angle collision prevention strategies.

Isopsoralen ameliorates rheumatoid arthritis by targeting MIF

BACKGROUND

Isopsoralen (IPRN), one of the active ingredients of Psoralea corylifolia Linn, has anti-inflammatory properties. We attempted to investigate the inhibitory effects of IPRN on rheumatoid arthritis (RA) and characterize its potential mechanism.

METHODS

RA fibroblast-like synoviocytes (FLSs) and mice with collagen-induced arthritis (CIA) were used as in vitro and in vivo models to analyze the antiarthritic effect of IPRN. Histological analysis of the inflamed joints from mice with CIA was performed using microcomputed tomography (micro-CT) and hematoxylin-eosin (HE) staining. RNA sequencing (RNA-Seq), network pharmacology analysis, molecular docking, drug affinity responsive target stability (DARTS) assay, and cellular thermal shift assay (CETSA) were performed to evaluate the targets of IPRN.

RESULTS

IPRN ameliorated the inflammatory phenotype of RA FLSs by inhibiting their cytokine production, migration, invasion, and proangiogenic ability. IPRN also significantly reduced the severity of CIA in mice by decreasing paw thickness, arthritis score, bone damage, and serum inflammatory cytokine levels. A mechanistic study demonstrated that macrophage migration inhibitory factor (MIF), a key protein in the inflammatory process, was the specific target by which IPRN exerted its anti-inflammatory effects in RA FLSs.

CONCLUSION

Our study demonstrates the antiarthritic effect of IPRN, which suggests the therapeutic potential of IPRN in RA.

Upregulated microRNA let-7a accelerates apoptosis and inhibits proliferation in uterine junctional zone smooth muscle cells in adenomyosis under conditions of a normal activated hippo-YAP1 axis

BACKGROUND

Let-7a is a small non-coding RNA that has been found to take part in cell proliferation and apoptosis. The hippo-YAP1 axis, known as a tumour suppressor pathway, also plays an important role in cell proliferation and apoptosis. YAP1, TAZ, and phospho-YAP1 play key roles in actions of the hippo-YAP1 axis. Adenomyosis (ADS) is a proliferative disease leading to a large uterus in patients with prolonged illness. Abnormal proliferation of smooth muscle cells (SMCs) in the uterine endometrial-myometrial junctional zone (JZ) is an important reason for developing ADS. This study aimed to explore the expression levels of let-7a and components of the hippo-YAP1 axis in SMCs in the uterine endometrial-myometrial JZ in ADS and to explore the roles of let-7a and the hippo-YAP1 axis of JZ SMC proliferation and apoptosis in ADS.

METHODS

We collected JZ tissues for the primary culture of SMCs from 25 women diagnosed with ADS and 27 women without ADS. We used quantitative real-time polymerase chain reaction and western blotting to measure the mRNA and protein expression levels of let-7a, YAP1, TAZ, and phospho-YAP1 in ADS JZ SMCs. A CCK-8 assay and flow cytometry analysis of apoptosis were utilized to test the proliferation and apoptosis of JZ SMCs. The let-7a overexpression lentiviral vector GV280 was used to increase the expression level of let-7a. We added verteporfin to block the phosphorylation of components of the hippo-YAP1 axis.

RESULTS

We found that the let-7a level was decreased, while the YAP1 and TAZ levels were increased in ADS JZ SMCs. Upregulated let-7a affected the expression levels of components of the hippo-YAP1 axis, accelerated apoptosis, and inhibited proliferation in JZ SMCs. Furthermore, accumulated YAP1 led to increasing proliferation of JZ SMCs after verteporfin treatment to block the phosphorylation of components of the hippo-YAP1 axis. If components of the hippo-YAP1 axis were unphosphorylated, upregulated let-7a could not inhibit the proliferation of ADS JZ SMCs. Upregulated let-7a could not activate the hippo-YAP1 axis in verteporfin treatment.

CONCLUSIONS

Our findings suggest that the let-7a and hippo-YAP1 axis may act as important regulators of JZ SMCs proliferation, and upregulated let-7a may be an effective method to treat ADS.

Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

BACKGROUND

Rice, which serves as a staple food for more than half of the world's population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined.

RESULTS

In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together.

CONCLUSIONS

This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

Ultrasound-targeted microbubble destruction promotes myocardial angiogenesis and functional improvements in rat model of diabetic cardiomyopathy

BACKGROUND

Microvascular insufficiency plays an important role in the development of diabetic cardiomyopathy (DCM), therapeutic angiogenesis has been mainly used for the treatment of ischemic diseases. This study sought to verify the preclinical performance of SonoVue microbubbles (MB) combined ultrasound (US) treatment on myocardial angiogenesis in the rat model of DCM and investigate the optimal ultrasonic parameters.

METHODS

The male Sprague-Dawley (SD) rats were induced DCM by streptozotocin through intraperitoneal injecting and fed with high-fat diet. After the DCM model was established, the rats were divided into the normal group, DCM model group, and US + MB group, while the US + MB group was divided into four subsets according to different pulse lengths (PL) (8 cycles;18 cycle;26 cycle; 36 cycle). After all interventions, all rats underwent conventional echocardiography to examine the cardiac function. The rats were sacrificed and myocardial tissue was examined by histology and morphometry evaluations to detect the myocardial protective effect of SonoVue MBs using US techniques.

RESULTS

From morphologic observation and echocardiography, the DCM rats had a series of structural abnormalities of cardiac myocardium compared to the normal rats. The US-MB groups exerted cardioprotective effect in DCM rats, improved reparative neovascularization and increased cardiac perfusion, while the 26 cycle group showed significant therapeutic effects on the cardiac functions in DCM rats.

CONCLUSION

This strategy using SonoVue MB and US can improve the efficacy of angiogenesis, even reverse the progress of cardiac dysfunction and pathological abnormalities, especially using the 26 cycle parameters. Under further study, this combined strategy might provide a novel approach for early intervention of DCM in diabetic patients.

Identification and characterization of regulatory pathways involved in early flowering in the new leaves of alfalfa (Medicago sativa L.) by transcriptome analysis

BACKGROUND

Alfalfa (Medicago sativa L.) is a perennial legume extensively planted throughout the world as a high nutritive value livestock forage. Flowering time is an important agronomic trait that contributes to the production of alfalfa hay and seeds. However, the underlying molecular mechanisms of flowering time regulation in alfalfa are not well understood.

RESULTS

In this study, an early-flowering alfalfa genotype 80 and a late-flowering alfalfa genotype 195 were characterized for the flowering phenotype. Our analysis revealed that the lower jasmonate (JA) content in new leaves and the downregulation of JA biosynthetic genes (i.e. lipoxygenase, the 12-oxophytodienoate reductase-like protein, and salicylic acid carboxyl methyltransferase) may play essential roles in the early-flowering phenotype of genotype 80. Further research indicated that genes encode pathogenesis-related proteins [e.g. leucine rich repeat (LRR) family proteins, receptor-like proteins, and toll-interleukin-like receptor (TIR)-nucleotide-binding site (NBS)-LRR class proteins] and members of the signaling receptor kinase family [LRR proteins, kinases domain of unknown function 26 (DUF26) and wheat leucine-rich repeat receptor-like kinase10 (LRK10)-like kinases] are related to early flowering in alfalfa. Additionally, those involved in secondary metabolism (2-oxoglutarate/Fe (II)-dependent dioxygenases and UDP-glycosyltransferase) and the proteasome degradation pathway [really interesting new gene (RING)/U-box superfamily proteins and F-box family proteins] are also related to early flowering in alfalfa.

CONCLUSIONS

Integrated phenotypical, physiological, and transcriptomic analyses demonstrate that hormone biosynthesis and signaling pathways, pathogenesis-related genes, signaling receptor kinase family genes, secondary metabolism genes, and proteasome degradation pathway genes are responsible for the early flowering phenotype in alfalfa. This will provide new insights into future studies of flowering time in alfalfa and inform genetic improvement strategies for optimizing this important trait.

A novel effector CfEC92 of Colletotrichum fructicola contributes to glomerella leaf spot virulence by suppressing plant defences at the early infection phase

The ascomycete fungus Colletotrichum fructicola causes diseases on a broad range of plant species. On susceptible cultivars of apple, it induces severe early defoliation and fruit spots, named glomerella leaf spot (GLS), but the mechanisms of pathogenicity have remained elusive. Phytopathogens exhibit small secreted effectors to advance host infection by manipulating host immune reactions. We report the identification and characterization of CfEC92, an effector required for C. fructicola virulence. CfEC92 is a Colletotrichum-specific small secreted protein that suppresses BAX-triggered cell death in Nicotiana benthamiana. Accumulation of the gene transcript was barely detectable in conidia or vegetative hyphae, but was highly up-regulated in appressoria formed during early apple leaf infection. Gene deletion mutants were not affected in vegetative growth, appressorium formation, or appressorium-mediated cellophane penetration. However, the mutants were significantly reduced in virulence toward apple leaves and fruits. Microscopic examination indicated that infection by the deletion mutants elicited elevated deposition of papillae at the penetration sites, and formation of infection vesicles and primary hyphae was retarded. Signal peptide activity, subcellular localization, and cell death-suppressive activity (without signal peptide) assays suggest that CfEC92 could be secreted and perform virulence functions inside plant cells. RNA sequencing and quantitative reverse transcription PCR results confirmed that the deletion mutants triggered elevated host defence reactions. Our results strongly support the interpretation that CfEC92 contributes to C. fructicola virulence as a plant immunity suppressor at the early infection phase.

Transgenerational memory of gene expression changes induced by heavy metal stress in rice (Oryza sativa L.)

BACKGROUND

Heavy metal toxicity has become a major threat to sustainable crop production worldwide. Thus, considerable interest has been placed on deciphering the mechanisms that allow plants to combat heavy metal stress. Strategies to deal with heavy metals are largely focused on detoxification, transport and/or sequestration. The P_1B subfamily of the Heavy Metal-transporting P-type ATPases (HMAs) was shown to play a crucial role in the uptake and translocation of heavy metals in plants. Here, we report the locus-specific expression changes in the rice HMA genes together with several low-copy cellular genes and transposable elements upon the heavy metal treatment and monitored the transgenerational inheritance of the altered expression states. We reveal that plants cope with heavy metal stress by making heritable changes in gene expression and further determined gene-specific responses to heavy metal stress.

RESULTS

We found most HMA genes were upregulated in response to heavy metal stress, and furthermore found evidence of transgenerational memory via changes in gene regulation even after the removal of heavy metals. To explore whether DNA methylation was also altered in response to the heavy metal stress, we selected a Tos17 retrotransposon for bisulfite sequencing and studied its methylation state across three generations. We found the DNA methylation state of Tos17 was altered in response to the heavy metal stress and showed transgenerational inheritance.

CONCLUSIONS

Collectively, the present study elucidates heritable changes in gene expression and DNA methylation in rice upon exposure to heavy metal stress and discusses implications of this knowledge in breeding for heavy metal tolerant crops.

RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)

BACKGROUND

Sweet potato (Ipomoea batatas L.) is the sixth most important food crop in the world. The formation and development of storage roots in sweet potato is a highly complicated and genetically programmed process. However, the underlying mechanisms of storage root development have not yet been elucidated.

RESULTS

To better understand the molecular mechanisms involved in storage root development, a combined analysis of the transcriptome and proteome of sweet potato fibrous roots (F) and storage roots at four different stages (D1, D3, D5 and D10) was performed in the present study. A total of 26,273 differentially expressed genes were identified in a comparison between the fibrous root library and four storage root libraries, while 2558 proteins showed a 1.0-fold or greater expression difference as indicated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis. The combination of the transcriptome and proteome analyses and morphological and physiological data revealed several critical pathways involved in storage root formation and development. First, genes/proteins involved in the development of meristems/cambia and starch biosynthesis were all significantly upregulated in storage roots compared with fibrous roots. Second, multiple phytohormones and the genes related to their biosynthesis showed differential expression between fibrous roots and storage roots. Third, a large number of transcription factors were differentially expressed during storage root initiation and development, which suggests the importance of transcription factor regulation in the development of storage roots. Fourth, inconsistent gene expression was found between the transcriptome and proteome data, which indicated posttranscriptional regulatory activity during the development of storage roots.

CONCLUSION

Overall, these results reveal multiple events associated with storage root development and provide new insights into the molecular mechanisms underlying the regulatory networks involved in storage root development.

Comparative proteomic investigation of drought responses in foxtail millet

BACKGROUND

Foxtail millet (Setaria italica L. P. Beauv) has been considered as a tractable model crop in recent years due to its short growing cycle, lower amount of repetitive DNA, inbreeding nature, small diploid genome, and outstanding abiotic stress-tolerance characteristics. With modern agriculture facing various adversities, it's urgent to dissect the mechanisms of how foxtail millet responds and adapts to drought and stress on the proteomic-level.

RESULTS

In this research, a total of 2474 differentially expressed proteins were identified by quantitative proteomic analysis after subjecting foxtail millet seedlings to drought conditions. 321 of these 2474 proteins exhibited significant expression changes, including 252 up-regulated proteins and 69 down-regulated proteins. The resulting proteins could then be divided into different categories, such as stress and defense responses, photosynthesis, carbon metabolism, ROS scavenging, protein synthesis, etc., according to Gene Ontology annotation. Proteins implicated in fatty acid and amino acid metabolism, polyamine biosynthesis, hormone metabolism, and cell wall modifications were also identified. These obtained differential proteins and their possible biological functions under drought stress all suggested that various physiological and metabolic processes might function cooperatively to configure a new dynamic homeostasis in organisms. The expression patterns of five drought-responsive proteins were further validated using western blot analysis. The qRT-PCR was also carried out to analyze the transcription levels of 21 differentially expressed proteins. The results showed large inconsistency in the variation between proteins and the corresponding mRNAs, which showed once again that post-transcriptional modification performs crucial roles in regulating gene expression.

CONCLUSION

The results offered a valuable inventory of proteins that may be involved in drought response and adaption, and provided a regulatory network of different metabolic pathways under stress stimulation. This study will illuminate the stress tolerance mechanisms of foxtail millet, and shed some light on crop germplasm breeding and innovation.

Identification of cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing

BACKGROUND

Low temperature is a major abiotic stress affecting the production of rapeseed in China by impeding plant growth and development. A comprehensive knowledge of small-RNA expression pattern in Brassica rapa under cold stress could improve our knowledge of microRNA-mediated stress responses.

RESULTS

A total of 353 cold-responsive miRNAs, 84 putative novel and 269 conserved miRNAs, were identified from the leaves and roots of two winter turnip rape varieties 'Longyou 7' (cold-tolerant) and 'Tianyou 4' (cold-sensitive), which were stressed under - 4 °C for 8 h. Eight conserved (miR166h-3p-1, miR398b-3p, miR398b-3p-1, miR408d, miR156a-5p, miR396h, miR845a-1, miR166u) and two novel miRNAs (Bra-novel-miR3153-5p and Bra-novel-miR3172-5p) were differentially expressed in leaves of 'Longyou 7' under cold stress. Bra-novel-miR3936-5p was up-regulated in roots of 'Longyou 7' under cold stress. Four and five conserved miRNAs were differentially expressed in leaves and roots of 'Tianyou 4' after cold stress. Besides, we found two conserved miRNAs (miR319e and miR166m-2) were down-regulated in non-stressed roots of 'Longyou 7' compared with 'Tianyou 4'. After cold stress, we found two and eight miRNAs were differentially expressed in leaves and roots of 'Longyou 7' compared with 'Tianyou 4'. The differentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR166 and miR319 families. A total of 211 target genes for 15 known miRNAs and two novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Five differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR, and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR166e, miR319, and Bra-novel-miR3936-5p) may play important roles in plant response to cold stress.

CONCLUSIONS

Our work indicates that miRNA and putative target genes mediated metabolic processes and stress responses are significant to cold tolerance in B. rapa.