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Coronavirus disease 2019 (COVID-19) is currently a global concern, and the psychological impact cannot be overlooked. Our purpose was to evaluate the anxiety and depression in spinocerebellar ataxia (SCA) patients during the pandemic and to analyse the influencing factors. We conducted an online questionnaire survey among 307 SCA patients from China and selected 319 healthy people matched by sex and age as the control group. The questionnaire included general information, the self-rating anxiety scale (SAS), and the self-rating depression scale (SDS). The relevant factors included COVID-19 risk factors, age, sex, body mass index (BMI), educational background, disease course, score on the scale for the assessment and rating of ataxia (SARA), Mini-mental State Examination (MMSE) and International Cooperative Ataxia Rating Scale (ICARS). The proportion of SCA patients with anxiety was 34.9%, and the proportion with depression was 56.7%. The SAS and SDS scores of the SCA patients were significantly higher than those of the control group (SAS: 45.8 ± 10.1 vs. 40.6 ± 8.9, P

Exploring the driving forces promoting speciation is a key question in evolutionary biology. Cycas bifida and C. micholitzii are two leaflets dichotomously divided Cycas species that have morphological similarities. Their distribution areas are separated by the RRFZ, a biogeographical barrier for Cycas species. The hypothesis for explaining their divergence is geographical isolation or convergent evolution. Three chloroplast DNA fragments, five low copy nuclear genes and 16 microsatellite loci were used to test this hypothesis and also to reveal their population genetics. The two species had high genetic differentiation but low gene flow with a deep divergence occurred in the late Miocene. The long-term geographical isolation not convergent evolution could explain for the divergence of the two species revealed from significant IBD testing, Barrier analysis and Niche consistency detection. Subsequently, each species made its own response to the Pleistocene climate fluctuations: a weak bottleneck effect in C. bifida and a population expansion in C. micholitzii. These findings imply that the role of geographic isolation rather than convergent evolution facilitates them divergence by constraining gene flow. Maybe they have gene flow or introgression with their neighboring distribution of Cycas species, making them genetically closer to neighboring Cycas species.

Perovskite quantum dots (PQDs) require ligands on their surfaces to passivate defects and prevent aggregation. However, the ligands construct the interface relationship between the PQDs, which may seriously hinder the carrier transport. Hence, we propose a molecular engineering strategy of using 3,4-ethylenedioxythiophene (EDOT) to perfectly solve this problem, benefiting from its high conjugation and passivation ability to CsPbBr3 PQDs. Furthermore, EDOT on the surface of PQDs can be in-situ polymerized under the photocurrent of the photodetector, thus interconnecting the PQDs which enhanced the performance of the photodetectors up to 178% of its initial performance. We have thoroughly investigated the electropolymerization process of EDOT and its passivation effect on PQDs. The simple lateral photodetector based on EDOT PQDs exhibits a high responsivity of 11.96 A/W, which is 104 times higher than that of oleic acid caped PQDs. Due to the protection of poly(3,4-ethylenedioxythiophene) (PEDOT), the photodetector prepared from EDOT PQDs exhibited very high stability, retaining 94% of its performance after six months in air. This strategy provides a solution for the application of PQDs in high performances and stable optoelectronic devices.

Background and Aims Cycads are regarded as an ancient lineage of living seed plants, and hold important clues to understand the early evolutionary trends of seed plants. The molecular phylogeny and spatio-temporal diversification of one of the species-rich genera of cycads, Macrozamia, have not been well reconstructed. Methods We analysed a transcriptome dataset of 4740 single-copy nuclear genes (SCGs) of 39 Macrozamia species and two outgroup taxa. Based on concatenated (maximum parsimony, maximum likelihood) and multispecies coalescent analyses, we first establish a well-resolved phylogenetic tree of Macrozamia. To identify cyto-nuclear incongruence, the plastid protein coding genes (PCGs) from transcriptome data are extracted using the software HybPiper. Furthermore, we explore the biogeographical history of the genus and shed light on the pattern of floristic exchange between three distinct areas of Australia. Six key diagnostic characters are traced on the phylogenetic framework using two comparative methods, and infra-generic classification is investigated. Key Results The tree topologies of concatenated and multi-species coalescent analyses of SCGs are mostly congruent with a few conflicting nodes, while those from plastid PCGs show poorly supported relationships. The genus contains three major clades that correspond to their distinct distributional areas in Australia. The crown group of Macrozamia is estimated to around 11.80 Ma, with a major expansion in the last 5–6 Myr. Six morphological characters show homoplasy, and the traditional phenetic sectional division of the genus is inconsistent with this current phylogeny. Conclusions This first detailed phylogenetic investigation of Macrozamia demonstrates promising prospects of SCGs in resolving phylogenetic relationships within cycads. Our study suggests that Macrozamia, once widely distributed in Australia, underwent major extinctions because of fluctuating climatic conditions such as cooling and mesic biome disappearance in the past. The current close placement of morphologically distinct species in the phylogenetic tree may be related to neotenic events that occurred in the genus.

Cycads represent one of the most ancient lineages of living seed plants. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. Here, we report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. We found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. The male-specific region of the Y chromosome of C. panzhihuaensis contains a MADS-box transcription factor expressed exclusively in male cones that is similar to a system reported in Ginkgo, suggesting that a sex determination mechanism controlled by MADS-box genes may have originated in the common ancestor of cycads and Ginkgo. The C. panzhihuaensis genome provides an important new resource of broad utility for biologists. The study assembled a chromosome-level genome of Cycas panzhihuaensis, the last major lineage of seed plants for which a high-quality genome assembly was lacking. The study closes an important gap in our understanding of genome structure and evolution in seed plants.

Large eddy simulations (LESs) are performed for turbulent flow through and around a porous patch of thin vertical plates at a plate Reynolds number of Rep=5,800. The plates are arranged in a staggered pattern, presenting an elliptical planform and mimicking streamwise‐oriented blades of emergent vegetation. The immersed boundary method is employed to explicitly resolve the interaction between flow and plates. Three flow cases, each with a different number of plates within the same planform area, that is, different patch density, are studied. The Reynolds number based on freestream velocity and plate length is the same in all cases. Inspection of the distribution of velocity and vorticity in the horizontal plane reveals that downstream plates are significantly impacted by the wakes from upstream plates. It is therefore proposed that the plates can be divided into two groups based on the local flow characteristics, which are a function of position within the patch: a free group and a wake group. This classification is subsequently used in the quantitative analysis of boundary layer development and drag force at plate scale. The thickness and character of the simulated boundary layers on the plates differ significantly from predictions based on analytical or empirical relationships, which is due to wake effects and the finite length of the plates. The simulations demonstrate the so‐called sheltering effect; that is, the drag forces acting on downstream plates (in the wake group) are significantly lower than those acting on upstream plates, a result of the lower approach flow speed. Although the front‐area‐to‐lateral‐area ratio of the plates is low (1/40), pressure drag is observed to be larger than friction drag for each plate. The ratio of pressure drag to the total drag at patch scale shows only very little dependence on the plate density of the patch.

Spur dikes provide significant control for flow regimes in river regulation engineering, which can help in the regeneration of stream habitats. However, the narrowing of the flow by spur dike changes the turbulence characteristics. To clarify the turbulence characteristics around the spur dike, the method of large eddy simulation (LES) was used to investigate the horizontal turbulence structure around spur dikes with different discharges in an open-channel flume. The simulations were an exact reproduction of large-scale laboratory experiments, which showed agreement with the experimental results. The distributions of time-averaged streamwise velocity, bed shear stress, and second-order turbulence statistics obtained from the LES were analyzed. An examination of the time series of velocity fluctuation as the probability density function, quadrant analysis, the power density spectra, flow instability, and the vortex separation created in the detached shear layer were estimated. The results accurately revealed the flow field under flow separation, the turbulence statistics inside the separated shear layer, and the vortex structure and emphasized the variation in the different water depths. The results demonstrated that the form of turbulence was not significantly affected by discharge. Moreover, vortex and energy transmission displayed the same periodicity, despite variances in the structural form of turbulence at different water depths. Overall, the results of the study provide an efficient basis for understanding the turbulence around spur dikes, which is crucial for their safe design.

Magnolia biondii Pamp. (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China. Determining the genome sequence of M. biondii would help resolve the phylogenetic uncertainty of magnoliids and improve the understanding of individual trait evolution within the Magnolia genus. We assembled a chromosome-level reference genome of M. biondii using ~67, ~175, and ~154 Gb of raw DNA sequences generated via Pacific Biosciences single-molecule real-time sequencing, 10X Genomics Chromium, and Hi-C scaffolding strategies, respectively. The final genome assembly was ~2.22 Gb, with a contig N50 value of 269.11 kb and a BUSCO complete gene percentage of 91.90%. Approximately 89.17% of the genome was organized into 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 47,547 protein-coding genes, accounting for 23.47% of the genome length, whereas 66.48% of the genome length consisted of repetitive elements. We confirmed a WGD event that occurred very close to the time of the split between the Magnoliales and Laurales. Functional enrichment of the Magnolia-specific and expanded gene families highlighted genes involved in the biosynthesis of secondary metabolites, plant–pathogen interactions, and responses to stimuli, which may improve the ecological fitness and biological adaptability of the lineage. Phylogenomic analyses revealed a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence of M. biondii could lead to trait improvement, germplasm conservation, and evolutionary studies on the rapid radiation of early angiosperms.

Background：Spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) is a progressive autosomal dominant neurodegenerative disease caused by abnormal CAG repeats in exon 10 of ATXN3. The accumulation of the mutant ataxin3 proteins carrying polyglutamine (polyQ) lead to selective degeneration of neurons. Therapeutic strategies were used to inhibit mutant ATXN3 expression, including antisense oligonucleotides, RNA interference and more recently CRISPR/Cas9 genome-editing based approaches. Since the pathogenesis of SCA3 has not been fully elucidated, and no effective therapies can be used, it is crucial to investigate the pathogenesis and seek new therapeutic strategies of SCA3/MJD. Methods: Here we used the paired sgRNA/Cas9 nickases and Cre-loxP mediated homologous recombination (HR) strategy to precisely modify the abnormal CAG expansions in the ATXN3 of SCA3/MJD patient derived induced pluripotent stem cells (SCA3/MJD-iPSCs). Meanwhile, we investigated the disease related phenotypes in differentiated neurons, including electrophysiological characteristics, IC2-positive aggregations, mitochondrial membrane potentials (MMPs), glutathione (GSH) expressions, intracellular reactive oxygen species (ROS), Ca2+ concentrations and malondialdehyde (MDA) levels. Results: SCA3/MJD-iPSCs can be corrected by the replacement of the abnormal CAG expansions with normal repeats using HR. Besides, corrected SCA3/MJD-iPSCs retained pluripotent and normal karyotype, which could be differentiated into neuron cells (NCs) and maintained electrophysiological characteristics. The expression of differentiation markers and electrophysiological characteristics were similar among the control individuals, SCA3/MJD patients and isogenic control SCA3/MJD groups. Furthermore, this study proved that the phenotypic abnormalities in SCA3/MJD-iPSCs derived NCs, including aggregated polyQ toxic protein, decreased MMPs and GSH expressions, increased ROS, Ca2+ concentrations and MDA levels, all were rescued in the corrected SCA3/MJD-NCs. Conclusion: The present study firstly suggested that the genetically corrected SCA3/MJD-iPSCs and associated phenotypic abnormalities, which will provide an ideal models for molecular mechanism research and autologous stem cell therapy.

ObjectivesThe aim of this study was to develop an appropriate parametric survival model to predict patient's age at onset (AAO) for spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) populations from mainland China.MethodsWe compared the efficiency and performance of 6 parametric survival analysis methods (exponential, weibull, log-gaussian, gaussian, log-logistic, and logistic) based on cytosine-adenine-guanine (CAG) repeat length at ATXN3 to predict the probability of AAO in the largest cohort of patients with SCA3/MJD. A set of evaluation criteria, including −2 log-likelihood statistic, Akaike information criterion (AIC), bayesian information criterion (BIC), Nagelkerke R-squared (Nagelkerke R^2), and Cox-Snell residual plot, were used to identify the best model.ResultsAmong these 6 parametric survival models, the logistic model had the lowest −2 log-likelihood (6,560.12), AIC (6,566.12), and BIC (6,566.14) and the highest value of Nagelkerke R^2 (0.54), with the closest graph to the bisector Cox-Snell residual graph. Therefore, the logistic survival model was the best fit to the studied data. Using the optimal logistic survival model, we indicated the age-specific probability distribution of AAO according to the CAG repeat size and current age.ConclusionsWe first demonstrated that the logistic survival model provided the best fit for AAO prediction in patients with SCA3/MJD from mainland China. This optimal model can be valuable in clinical and research. However, the rigorous clinical testing and practice of other independent cohorts are needed for its clinical application. A unified model across multiethnic cohorts is worth further exploration by identifying regional differences and significant modifiers in AAO determination.

COVID-19 is a global concern nowadays, and the psychological impact of the pandemic cannot be overlooked. People are under insurmountable pressure, which may lead to psychological problems such as anxiety and depression. The purpose of this study was to evaluate the mental health of spinocerebellar ataxia (SCA) patients during COVID-19 pandemic and to analyze its influencing factors. We conducted an online questionnaire survey among 307 SCA patients from China. The contents of the questionnaire included general information, the self-rating anxiety scale (SAS), the self-rating depression scale (SDS). The relevant influencing factors included COVID-19 risk factors, age, gender, BMI (body mass index), educational background, disease course, and score of the scale for the assessment and rating of ataxia (SARA). Results indicate the 307 SCA patients had an anxiety rate of 34.9%, along with a depression rate of 56.7%. Their SAS and SDS scores were significantly higher than those of the Chinese norm group (SAS: 45.8±10.1 vs. 37.2±12.6, P < 0.01; SDS: 55.1±12.2 vs. 41.9±10.6, P < 0.01). Risks of exposure to COVID-19, educational level, and disease course may be factors affecting mental health status. The existence of a positive correlation among the scores of SARA, SAS and SDS scale was demonstrated, the higher the SARA score, the higher the risk of anxiety and depression. Anxiety and depression were more prevalent in SCA patients compared with the normal population, and depression was more common than anxiety during this pandemic. More psychological attention should be paid to SCA patients during COVID-19 pandemic.

Background In polyglutamine (polyQ) disease, the investigation of the prediction of a patient's age at onset (AAO) facilitates the development of disease-modifying intervention and underpins the delay of disease onset and progression. Few polyQ disease studies have evaluated AAO predicted by machine-learning algorithms and linear regression methods. Objective The objective of this study was to develop a machine-learning model for AAO prediction in the largest spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) population from mainland China. Methods In this observational study, we introduced an innovative approach by systematically comparing the performance of 7 machine-learning algorithms with linear regression to explore AAO prediction in SCA3/MJD using CAG expansions of 10 polyQ-related genes, sex, and parental origin. Results Similar prediction performance of testing set and training set in each models were identified and few overfitting of training data was observed. Overall, the machine-learning-based XGBoost model exhibited the most favorable performance in AAO prediction over the traditional linear regression method and other 6 machine-learning algorithms for the training set and testing set. The optimal XGBoost model achieved mean absolute error, root mean square error, and median absolute error of 5.56, 7.13, 4.15 years, respectively, in testing set 1, with mean absolute error (4.78 years), root mean square error (6.31 years), and median absolute error (3.59 years) in testing set 2. Conclusion Machine-learning algorithms can be used to predict AAO in patients with SCA3/MJD. The optimal XGBoost algorithm can provide a good reference for the establishment and optimization of prediction models for SCA3/MJD or other polyQ diseases. © 2020 International Parkinson and Movement Disorder Society.

A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN (duplex-specific nuclease) normalization method combined with the SMART (Switching Mechanism At 5′ end of the RNA Transcript) technique. The titer of the original cDNA library was about 1.5 × 106 cfu·mL−1 and the average insertion size was about 1 kb with a high recombination rate (97%). The 5011 high-quality expressed sequence tags (ESTs) were obtained from 5393 randomly picked cDNA clones. Clustering and assembly of ESTs resulted in 2984 unique sequences, consisting of 618 contigs and 2366 singlets. EST sequence annotation revealed that 2333 and 1901 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 1495 (50.1%) unigenes were associated with 4082 Gene Ontology (GO) terms. A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups (COG) functional categories. Based on the EST dataset, 22 ESTs that encoded putative receptor-like protein kinase (RLK) genes were screened. Furthermore, a total of 94 simple sequence repeats (SSRs) were discovered, of which 20 loci were successfully amplified in C. debaoensis. This study is the first EST analysis for the coralloid roots of C. debaoensis and provides a valuable genomic resource for novel gene discovery, gene expression and comparative genomics, conservation and management studies as well as applications in C. debaoensis and related cycad species. Keywords: Cycas debaoensis, Coralloid root, cDNA library, Expressed sequence tags, Symbiosis and defense, SSRs