Exploring the Structural Plasticity Mechanism of Corticospinal Tract during Stroke Rehabilitation Based Automated Fiber Quantification Tractography.

BACKGROUND: Corticospinal tract (CST) is the principal motor pathway; we aim to explore the structural plasticity mechanism in CST during stroke rehabilitation. METHODS: A total of 25 patients underwent diffusion tensor imaging before rehabilitation (T1), 1-month post-rehabilitation (T2), 2 months post-rehabilitation (T3), and 1-year post-discharge (T4). The CST was segmented, and fractional anisotropy (FA), axial diffusion (AD), mean diffusivity (MD), and radial diffusivity (RD) were determined using automated fiber quantification tractography. Baseline level of laterality index (LI) and motor function for correlation analysis. RESULTS: The FA values of all segments in the ipsilesional CST (IL-CST) were lower compared with normal CST. Repeated measures analysis of variance showed time-related effects on FA, AD, and MD of the IL-CST, and there were similar dynamic trends in these 3 parameters. At T1, FA, AD, and MD values of the mid-upper segments of IL-CST (around the core lesions) were the lowest; at T2 and T3, values for the mid-lower segments were lower than those at T1, while the values for the mid-upper segments gradually increased; at T4, the values for almost entire IL-CST were higher than before. The highest LI was observed at T2, with a predominance in contralesional CST. The LIs for the FA and AD at T1 were positively correlated with the change rate of motor function. CONCLUSIONS: IL-CST showed aggravation followed by improvement from around the lesion to the distal end. Balance of interhemispheric CST may be closely related to motor function, and LIs for FA and AD may have predictive value for mild-to-moderate stroke rehabilitation. Clinical Trial Registration. URL: http://www.chictr.org.cn; Unique Identifier: ChiCTR1800019474.

quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification.

A high-quality genome is the basis for studies on functional, evolutionary, and comparative genomics. The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences, along with the emergence of a new 'telomere-to-telomere (T2T) assembly' era. However, the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited. Here, we developed a user-friendly web toolkit, quarTeT, which currently includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner. First, AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome. Then, GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences. Finally, TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome. These four modules can be used alone or in combination with each other for T2T genome assembly and characterization. As a case study, by adopting the entire modular functions of quarTeT, we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0, which was assembled with the addition of manual handling. Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods. Collectively, quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration.

Abnormal gray matter volume and functional connectivity patterns in social cognition-related brain regions of young children with autism spectrum disorder.

Autism spectrum disorder (ASD) is associated with abnormal brain imaging findings, but descriptions thereof are inconsistent. The aim of the present study was to investigate brain abnormalities in young children with ASD using a combination of structural and functional brain magnetic resonance imaging (MRI). Structural and resting-state functional MRI was performed in 67 children with ASD (aged 2-7 years) and 39 age-matched typically developing (TD) controls. Voxel-based morphometry was used to evaluate differences in brain structure between groups. Topologic parameters of the functional brain network were compared by graph theoretic analysis and network connectomes were compared with network-based statistics. A support vector machine (SVM) was used to discriminate between ASD and TD groups. Results demonstrated young children with ASD had increased gray matter volumes (GMVs) in the right medial superior frontal gyrus and left fusiform gyrus compared with the TD group. The ASD group had altered subnetwork connectivity in frontal and temporal lobes and other social cognition-related brain regions. Functional connectivity in the left superior temporal gyrus and left temporal pole of the middle temporal gyrus was positively correlated with adaptability and language developmental quotient (DQ) in children with ASD. The combination of the brain structural and functional features had 86.2% accuracy in discriminating between ASD and TD. The present study shows that young children with ASD have altered GMVs and functional networks in social cognition-related brain regions, which are potential neuroimaging biomarkers for ASD.

[Soil Enzyme Activity in Picea schrenkiana and Its Relationship with Environmental Factors in the Tianshan Mountains, Xinjiang].

Nitrogen deposition may affect forest soil traits and metabolic activity. We would like to further understand the mechanisms of soil biochemical processes and habitat interactions under conditions of nitrogen deposition in forests and to investigate the characteristics of soil enzyme activities and soil environmental factors in response to nitrogen deposition in Picea schrenkiana forests in the Tianshan Mountains. In this study, nitrogen application tests were carried out using the nitrogen sedimentation gradient method on Picea schrenkiana forest soils in the Tianshan Mountains. We analyzed the characteristics of soil enzyme activity and soil environmental factors at different nitrogen application levels and discussed the correlation between soil enzyme activity and soil environmental factors in conjunction with a redundancy analysis. The study showed that:① Soil enzyme activities showed a tendency to increase and then decrease with the increase in nitrogen application. With the exception of soil acid phosphatase, all enzyme levels reached maximums in the low nitrogen treatment. ② Exogenous nitrogen addition led to low soil pH values, and in the low or medium nitrogen treatments, soil conductivity and the content of organic carbon, ammonium nitrogen, ammonium nitrogen, and total phosphorus increases, along with the C/N ratio, while the N/P ratio showed an irregular decline. ③ Soil enzymes and their correlation with soil environmental factors showed that soil water content, organic carbon content, ammonium nitrogen content, total phosphorus content, and the C/N ratio were all significantly correlated with soil enzymes activity. Only the C/N ratio was negatively correlated with soil enzyme activity, while all other environmental factors were positively correlated with soil enzyme activity. There was no significant correlation between pH and the N/P ratio and soil enzyme activity. The important factors influencing soil enzyme activity were soil organic carbon and ammonium nitrogen with nitrogen application in Picea schrenkiana, Xinjiang.