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Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from ~ 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.

BackgroundImmunotherapy plays an important role in the treatment of triple-negative breast cancer (TNBC). This study aimed to identify immune-related genes that are associated with the prognosis of patients with TNBC as possible targets of immunotherapy, alongside their related tumor-infiltrating lymphocytes (TILs).MethodsThe clinical data and gene expression profiles of patients with breast cancer were extracted from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and divided into training (n = 1,053) and verification (n = 508) groups. CIBERSORT was used to predict the differences in immune cell infiltration in patient subsets that were stratified according to risk. Gene Ontology (GO) enrichment analysis was used to identify pathways associated with immune-related genes in patient subsets that were stratified according to risk. The clinical data and insulin-like growth factor 2 receptor (IGF2R) expression profiles of patients with breast cancer were extracted from METABRIC. The expression of IGF2R and TILs were evaluated in a cohort containing 282 untreated patients with TNBC. The correlations of IGF2R expression, TILs, and clinicopathological parameters with patient prognosis were analyzed in the whole cohort.ResultsThe prognostic model, which was composed of 26 immune-related gene pairs, significantly distinguished between high- and low-risk patients. Univariate and multivariate analyses indicated that the model was an independent prognostic factor for breast cancer. Among the identified genes, the expression of IGF2R significantly distinguished between high- and low-risk patients in TCGA (P = 0.008) and in METABRIC patients (P < 0.001). The expression of IGF2R was significantly associated with clinical risk factors such as TNBC, estrogen receptor (ER)–negative expression, human epidermal growth factor receptor 2 (HER2)–positive expression, and age ≤60 years old in METABRIC patients. In addition, the patients with IGF2R-positive expression had lower disease-free survival (DFS) rates than those with IGF2R-negative expression in the TNBC cohort (67.8% vs. 78.5%, P = 0.023). IGF2R expression also was significantly negatively correlated with TILs, particularly with CD8+ TILs and CD19+ TILs in the cohort of patients with TNBC.ConclusionIGF2R can be used as an indicator of a poor prognosis in patients with TNBC and as a potential target and research direction for TNBC immunotherapy in the future.

Abstract Understanding the spatial distribution characteristics and formation mechanism of urban facilities (city functional components) constitutes the basis of urban layout optimization. Currently, research on the overall distribution of the various types of city functional components is lacking. In this study, by applying the gradient analysis method common in ecology, we considered 13 types of city functional components (80,214 individuals in total) in large, medium and small Chinese cities (9 cities in total) to carry out quantitative analysis of the distribution of components along urban–rural gradients through density distribution curves. The results indicated that: (1) a higher density of city functional components near the city centre revealed an obvious aggregated distribution; (2) the spatial distribution dynamics of city functional components were related to the city size, providing a reference for the rational distribution of components in cities of different sizes; (3) the distribution of city functional components was affected by their ecosystem services. This study offers a new perspective for the application of ecological methods in the examination of the distribution of city functional components.

Measurement(s) LTR_retrotransposon • genome Technology Type(s) bioinformatics method • digital curation Factor Type(s) Species Sample Characteristic - Organism Rhodophyta • Chlorophyta • Bryophyta • Tracheophyta Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.14684877

Abstract Long noncoding ribonucleic acids (LncRNAs) have been found to be involved in the proliferation, apoptosis, invasion, migration, and other pathological processes of triple-negative breast cancer (TNBC). Expression of the lncRNA actin filament-associated protein 1 antisense RNA1 (AFAP1-AS1) has been found to be significantly higher in TNBC than in other subtypes or in normal tissue samples, but the specific mechanism by which AFAP1-AS1 affects the occurrence and development of TNBC is yet to be revealed. In this study, we used Cell Counting Kit-8 (CCK-8), colony formation, wound healing migration, Transwell invasion, and nude mouse xenograft assays to confirm the role of AFAP1-AS1 in the proliferation, migration of TNBC cells in vitro and in vivo. In addition, we performed bioinformatics analyses, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR), western blot (WB), and dual-luciferase reporter assays (dual-LRA) to confirm interaction among AFAP1-AS1, micro-RNA 2110 (miR-2110), and Sp1 transcription factor (Sp1). We found that silencing AFAP1-AS1 and Sp1 or upregulating miR-2110 suppressed the proliferation, migration, and invasion of MDA–MB-231 and MDA–MB-468 cells in vitro as well as tumor growth in vivo. Mechanistically, the dual-LRA highlighted that miR-2110 was an inhibitory target of AFAP1-AS1, and that AFAP1-AS1 functioned as a miR-2110 sponge to increase Sp1 expression. AFAP1-AS1 silencing led to a reduction in Sp1 mRNA and protein levels, which could be reversed by joint transfection with miR-2110 inhibitor. Our findings demonstrated that AFAP1-AS1 could modulate the progression of breast cancer cells and affect tumorigenesis in mice by acting as a miR-2110 sponge, resulting in regulation of Sp1 expression. Therefore, AFAP1-AS1 could play a pivotal role in the treatment of TNBC.

Abstract Background Antegrade intramedullary nailing (AIMN) with Kirschner wire (K-wire) is a minimally invasive osteosynthesis technique. This procedure has been widely performed to treat the fifth metacarpal neck fracture (FMNF) in adults. This study was performed to determine whether using AIMN with a single K-wire to treat FMNF in adolescents would have good clinical and radiographic outcomes. Methods In this retrospective study, 21 children (aged 11–16 years) with FMNF were treated using AIMN with a single K-wire from May 2017 to January 2020 in our hospital. Indications for intervention were severe displacement with malrotation deformity, apex dorsal angulation of greater than 40°, or both. Collected data included apex dorsal angulation, range of motion (ROM) in the fifth metacarpophalangeal (MCP) joint, Visual Analog Scale (VAS) for pain, grip strength, and Disabilities of the Arm, Shoulder, and Hand (DASH) score. Results All patients were followed up for 12–24 months (average, 16.57 months), and all patients obtained anatomical reduction postoperatively. The healing time was 2.69 ± 0.83 months (range, 2–4 months). Average apex dorsal angulation was reduced significantly from 44.49°±2.64° to 15.74°±2.47° (P

Taxis are an important component of the transportation system, and empty taxis represent a significant waste of transportation resources. To alleviate the imbalance between supply and demand and relieve traffic congestion, real-time prediction of taxi trajectories is necessary. Most existing trajectory prediction studies focus on extracting time-series information but do not capture spatial information sufficiently. In this paper, we focus on the construction of an urban network and propose an urban topology-encoding spatiotemporal attention network (UTA) to address destination prediction problems. Firstly, this model discretizes the production and attraction units of transportation, combining them with key nodes in the road network to form an urban topological network. Secondly, GPS records are matched to the urban topological map to construct a topological trajectory, which significantly improves trajectory consistency and endpoint certainty, helping to model destination prediction problems. Thirdly, semantic information concerning surrounding space is attached to effectively mine the spatial dependencies of trajectories. Finally, after the topological encoding of city space and trajectories, this algorithm proposes a topological graph neural network to model the attention calculation with the trajectory context, comprehensively considering the spatiotemporal characteristics of the trajectories and improving prediction accuracy. We solve the prediction problems with the UTA model and also compare it with some other classical models, such as the HMM, RNN, LSTM, and transformer. The results suggest that all the models work well in combination with the proposed urban model (with a rough increase of 2%), while the UTA model is less affected by data sparsity.

European hornbeam (Carpinus betulus L.) is widely planted in landscaping. In October 2021 and August 2022, leaf spot was observed on C. betulus in Xuzhou, Jiangsu Province, China. To identify the causal agent of anthracnose disease on C. betulus, 23 isolates were obtained from the symptomatic leaves. Based on ITS sequences and colony morphology, these isolates were divided into four Colletotrichum groups. Koch’s postulates of four Colletotrichum species showed similar symptoms observed in the field. Combining the morphological characteristics and multi-gene phylogenetic analysis of the concatenated sequences of the internal transcribed spacer (ITS) gene, Apn2-Mat1-2 intergenic spacer (ApMat) gene, the calmodulin (CAL) gene, glyceraldehyde3-phosphate dehydrogenase (GAPDH) gene, Glutamine synthetase (GS) gene, and beta-tubulin 2 (TUB2) genes, the four Colletotrichum groups were identified as C. gloeosporioides, C. fructicola, C. aenigma, and C. siamense. This study is the first report of four Colletotrichum species causing leaf spot on European hornbeam in China, and it provides clear pathogen information for the further evaluation of the disease control strategies.

Steatohepatitic hepatocellular carcinoma (SH-HCC) is a distinctive histologic variant of HCC for the presence of steatohepatitis. This study intended to evaluate the contrast-enhanced imaging features and clinicopathological characteristics of 26 SH-HCCs in comparison with 26 age-and-sex-matched non-SH-HCCs. The frequency of obesity (34.6%, p = 0.048) and type 2 diabetes mellitus (23.1%, p = 0.042) were significantly higher in SH-HCC patients. As seen via B-mode ultrasound (BMUS), SH-HCCs were predominantly hyperechoic (65.4%, p = 0.002) lesions, while non-SH-HCCs were mainly hypo-echoic. As seen via contrast-enhanced ultrasound (CEUS), 96.2% of SH-HCCs exhibited hyperenhancement in the arterial phase. During the portal venous and late phase, 88.5% of SH-HCCs showed late and mild washout. Consequently, most SH-HCCs and all non-SH-HCCs were categorized as LR-4 or LR-5. As seen via magnetic resonance imaging (MRI), a signal drop in the T1WI opposed-phase was observed in 84.6% of SH-HCCs (p = 0.000). Notably, diffuse fat in mass was detected in 57.7% (15/26) SH-HCCs (p < 0.001). As seen via contrast-enhanced MRI (CEMRI), most of the SH-HCCs and non-SH-HCCs exhibited heterogeneous hyperenhancement in the arterial phase (80.8% versus 69.2%, p = 0.337). During the delayed phase, 76.9% SH-HCCs and 88.5% non-SH-HCCs exhibited hypo-enhancement. Histopathologically, the rate of microvascular invasion (MVI) was significantly lower in SH-HCCs than non-SH-HCCs (42.3% versus 73.1%, p = 0.025). The frequency of hepatic steatosis >5% in non-tumoral liver parenchyma of SH-HCCs was significantly higher than in non-SH-HCCs (88.5% versus 26.9%, p = 0.000). Additionally, the fibrotic stages of S0, S1 and S2 in SH-HCCs were significantly higher than in non-SH-HCCs (p = 0.044). During follow-up, although the PFS of SH-HCC patients was significantly longer than non-SH-HCC patients (p = 0.046), for the overall survival rate of SH-HCC and non-SH-HCC patients there was no significant difference (p = 0.162). In conclusion, the frequency of metabolism-related diseases in SH-HCC patients was significantly higher than in non-SH-HCC patients. The imaging features of SH-HCCs combined the fatty change and typical enhancement performance of standard HCC as seen via CEUS/CEMRI.

Verticillium dahliae is a soil-borne fungal pathogen that can cause severe vascular wilt in many plant species. Kelch repeat proteins are essential for fungal growth, resistance, and virulence. However, the function of the Kelch repeat protein family in V. dahliae is unclear. In this study, a Kelch repeat domain-containing protein DK185_4252 (VdLs.17 VDAG_08647) included in the conserved VdPKS9 gene cluster was identified and named VdKeR1. Phylogenetic analysis demonstrated a high degree of evolutionary conservation of VdKeR1 and its homologs among fungi. The experimental results showed that the absence of VdKeR1 impaired vegetative growth, microsclerotia development, and pathogenicity of V. dahliae. Osmotic and cell wall stress analyses suggested that VdKeR1-deleted mutants were more tolerant to NaCl, sorbitol, CR, and CFW, while more sensitive to H2O2 and SDS. In addition, analyses of the relative expression level of sqe and the content of squalene and ergosterol showed that VdKeR1 mediates the synthesis of squalene and ergosterol by positively regulating the activity of squalene epoxidase. In conclusion, these results indicated that VdKeR1 was involved in the growth, stress resistance, pathogenicity, and ergosterol metabolism of V. dahliae. Investigating VdKeR1 provided theoretical and experimental foundations for subsequent control of Verticillium wilt. [ABSTRACT FROM AUTHOR]

Bile acids are synthesized from cholesterol in hepatocytes and play an important role in the absorption, transport and distribution of fat and fat soluble vitamins. They also act as important signal molecules to regulate metabolism and inflammatory response. The accumulation of bile acids in the body and the activation of bile acid related receptors can aggravate or alleviate the complications of liver cirrhosis such as hepatic encephalopathy, portal hypertension and peritonitis.

46,XY disorders of sex development (DSD) is characterized by incomplete masculinization genitalia, with gonadal dysplasia and with/without the presence of Müllerian structures. At least 30 genes related to 46,XY DSD have been found. However, the clinical phenotypes of patients with different gene mutations overlap, and accurate diagnosis relies on gene sequencing technology. Therefore, this study aims to determine the prevalence of pathogenic mutations in a Chinese cohort with 46,XY DSD by the targeted next-generation sequencing (NGS) technology. Eighty-seven 46,XY DSD patients were enrolled from the Peking Union Medical College Hospital (Beijing, China). A total of fifty-four rare variants were identified in 60 patients with 46,XY DSD. The incidence of these rare variants was approximately 69.0% (60/87). Twenty-five novel variants and 29 reported variants were identified. Based on the American College of Medical Genetics and Genomics (ACMG) guidelines, thirty-three variants were classified as pathogenic or likely pathogenic variants and 21 variants were assessed as variants of uncertain significance. The overall diagnostic rate was about 42.5% based on the pathogenic and likely pathogenic variants. Androgen receptor (AR), steroid 5-alpha-reductase 2 (SRD5A2) and nuclear receptor subfamily 5 Group A member 1 (NR5A1) gene variants were identified in 21, 13 and 13 patients, respectively. The incidence of these three gene variants was about 78.3% (47/60) in patients with rare variants. It is concluded that targeted NGS is an effective method to detect pathogenic mutations in 46,XY DSD patients and AR, SRD5A2, and NR5A1 genes were the most common pathogenic genes in our cohort.

Kato, Abdollahi et al. identify a redox protein thioredoxin and mitochondrial fission-1 (FIS1) protein as miR-379 targets in mouse kidney. They find that miR-379 knockout mice are protected from diabetic kidney disease by enhancing mitophagy via FIS1, suggesting miR-379 as a potential therapeutic target for diabetic kidney disease.

BackgroundThe tightly controlled activity of EGFR is important for the homeostasis of self-renewal of human tissue. Mutations in the extracellular domain of EGFR are frequent and function as a novel mechanism for oncogenic EGFR activation in GBM, and impact the response of patients to small-molecule inhibitors.MethodsWe constructed glioblastoma cell lines stably expressing wild-type EGFR and the mutant of EGFR S645C. We detected cell growth in vitro and in vivo. We evaluated the anti-tumor activity and effectiveness of gefitinib and osimertinib in cells.ResultsIn the present study, we identified an oncogenic substituted mutation of EGFR—S645C. The mutation can promote the proliferation and colony formation of glioblastoma in vitro and in vivo. Mechanistically, the EGFR S645C mutation potentially changes the formation of hydrogen bonds within dimerized EGFR and inhibits the degradation of EGFR to prolong downstream signaling. The mutation induces resistance to gefitinib but presents an opportunity for osimertinib treatment.ConclusionThe study indicated a novel oncogenic mutation and advises on the precise treatment of individual patients with the EGFR S645C mutation.

Cyclocarya paliurus is an endemic Chinese tree species with considerable medicinal, timber, and horticultural value. The anthracnose disease of C. paliurus is caused by the fungal pathogen Colletotrichum fructicola, which results in great losses in yield and quality. Here, resistance evaluation of six cultivars of C. paliurus exhibited varying degrees of resistance to C. fructicola infection, where Wufeng was the most resistant and Jinggangshan was the most susceptive. Physiological measurements and histochemical staining assays showed that the Wufeng cultivar exhibits intense reactive oxygen species accumulation and defense capabilities. A multiomics approach using RNA sequencing and metabolome analyses showed that resistance in C. paliurus (Wufeng) is related to early induction of reprogramming of the flavonoid biosynthesis pathway. In vitro antifungal assays revealed that the flavonoid extracts from resistant cultivars strongly inhibited C. fructicola hyphal growth than susceptible cultivars. Relative gene expression analysis further demonstrated the pivotal antifungal role of C. paliurus flavonoids in targeting Colletotrichum appressorium formation. Together, these results represent a novel resistance mechanism of C. paliurus against anthracnose through the reprogramming of flavonoids, which will lay a foundation for breeding anthracnose-resistant varieties and the application of flavonoid extraction of C. paliurus as a natural antifungal treatment.

BackgroundThe prognostic and clinical value of tumor-associated macrophages (TAMs) in patients with breast cancer (BCa) remains unclear. We conducted the current meta-analysis to systematically evaluate the association of CD68+ and CD163+ TAM density with the prognosis and clinicopathologic features of BCa patients.MethodsSearches of Web of Science, PubMed, and EMBASE databases were performed up to January 31, 2022. The meta-analysis was conducted using hazard risks (HRs) and 95% confidence intervals (CIs) for survival data including overall survival (OS), disease-free survival (DFS), and BCa specific survival. Sensitivity and meta-regression analyses were also conducted to identify the robustness of the pooled estimates.ResultsOur literature search identified relevant articles involving a total of 8,496 patients from 32 included studies. Our analysis indicates that a high CD68+ TAM density in the tumor stoma was significantly linked with poor OS (HR 2.46, 95% CI, 1.83–3.31, P

Glioblastoma is the most common primary malignant tumor in the brain and has a dismal prognosis despite patients accepting standard therapies. Alternation of genes and deregulation of proteins, such as receptor tyrosine kinase, PI3K/Akt, PKC, Ras/Raf/MEK, histone deacetylases, poly (ADP-ribose) polymerase (PARP), CDK4/6, branched-chain amino acid transaminase 1 (BCAT1), and Isocitrate dehydrogenase (IDH), play pivotal roles in the pathogenesis and progression of glioma. Simultaneously, the abnormalities change the cellular biological behavior and microenvironment of tumor cells. The differences between tumor cells and normal tissue become the vulnerability of tumor, which can be taken advantage of using targeted therapies. Small molecule inhibitors, as an important part of modern treatment for cancers, have shown significant efficacy in hematologic cancers and some solid tumors. To date, in glioblastoma, there have been more than 200 clinical trials completed or ongoing in which trial designers used small molecules as monotherapy or combination regimens to correct the abnormalities. In this review, we summarize the dysfunctional molecular mechanisms and highlight the outcomes of relevant clinical trials associated with small-molecule targeted therapies. Based on the outcomes, the main findings were that small-molecule inhibitors did not bring more benefit to newly diagnosed glioblastoma, but the clinical studies involving progressive glioblastoma usually claimed “noninferiority” compared with historical results. However, as to the clinical inferiority trial, similar dosing regimens should be avoided in future clinical trials.

Yiqi Huoxue Decoction (abbreviated as YH in this paper) is a well-accepted traditional Chinese medicine formula used for the treatment of lumbar disc herniation (LDH). The main components of YH, such as tetrandrine, astragaloside IV and ferulic acid, have the effects of regulating inflammation and immunity as well as analgesia. Our lab previously reported that YH could promote the accumulation of reactive oxygen species (ROS) in the nucleus pulposus cells. This study was to determine the effect and mechanism of YH on both ruptured and non-ruptured intervertebral disc (IVD). First, we isolated human primary nucleus pulposus cells, then incubated them with 10 μM H2O2 to imitate the condition of oxidative stress in vivo. We found that YH-containing serum could promote the apoptosis and autophagy of nucleus pulposus cells in vitro. Next, we constructed rat models of both ruptured and unruptured disc herniation. The in vivo results showed that YH significantly could promote the number of autophagosomes, proportion of apoptotic cells, and expression levels of autophagy/apoptosis-related proteins in the nucleus pulposus of ruptured IVD. Also, YH could promote the resorption and degeneration of the ruptured IVD. Further, we investigated the molecular mechanism of YH-enhanced resorption of ruptured IVD. The in vitro data suggested that YH could activate ERK/mTOR in nucleus pulposus cells, leading to excessive autophagy and apoptosis while ERK inhibitor U0126 reversed the effect of YH on the ROS content, proportion of apoptotic cells and expression levels of autophagy. Overall, this study has demonstrated that the traditional Chinese medicine Yiqi Huoxue decoction promotes the resorption of herniated IVD via regulating ERK/mTOR-mediated apoptosis/autophagy in the nucleus pulposus cells, which highlights traditional Chinese medicine has a great potential for clinical conservative treatment for lumbar disc herniation.

However evanescent coupling between acoustic waveguides has been well studied by the mode-matching method in the literature, a proposed physical model based on the tunnelling concept is used to explain such coupling. Based on phonons being one type of quasi-particles, the Schrödinger equation for a phonon has been built by introducing a virtual mass and potential for phonons. This proposed model is physically intuitive and analytical. It can well explain the exponential dependence of the coupling length on the guide separation distances and the frequency of acoustic waves reported in the literature. The exponential dependent relationship between the coupling coefficients predicted by the proposed model agrees well with the experimental data reported in the literature. The model provides a new idea for understanding and studying coupling between acoustic waveguides.

BackgroundFirst-line surveillance on hepatitis B virus (HBV)-infected populations with B-mode ultrasound is relatively limited to identifying hepatocellular carcinoma (HCC) without elevated α-fetoprotein (AFP). To improve the present HCC surveillance strategy, the state of the art of artificial intelligence (AI), a deep learning (DL) approach, is proposed to assist in the diagnosis of a focal liver lesion (FLL) in HBV-infected liver background.MethodsOur proposed deep learning model was based on B-mode ultrasound images of surgery that proved 209 HCC and 198 focal nodular hyperplasia (FNH) cases with 413 lesions. The model cohort and test cohort were set at a ratio of 3:1, in which the test cohort was composed of AFP-negative HBV-infected cases. Four additional deep learning models (MobileNet, Resnet50, DenseNet121, and InceptionV3) were also constructed as comparative baselines. To evaluate the models in terms of diagnostic power, sensitivity, specificity, accuracy, confusion matrix, F1-score, and area under the receiver operating characteristic curve (AUC) were calculated in the test cohort.ResultsThe AUC of our model, Xception, achieved 93.68% in the test cohort, superior to other baselines (89.06%, 85.67%, 83.94%, and 78.13% respectively for MobileNet, Resnet50, DenseNet121, and InceptionV3). In terms of diagnostic power, our model showed sensitivity, specificity, accuracy, and F1-score of 96.08%, 76.92%, 86.41%, and 87.50%, respectively, and PPV, NPV, FPR, and FNR calculated from the confusion matrix were respectively 80.33%, 95.24%, 23.08%, and 3.92% in identifying AFP-negative HCC from HBV-infected FLL cases. Satisfactory robustness of our proposed model was shown based on 5-fold cross-validation performed among the models above.ConclusionsOur DL approach has great potential to assist B-mode ultrasound in identifying AFP-negative HCC from FLL found in surveillance of HBV-infected patients.

Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.

Among the three genomes in plant cells, the mitochondrial genome (mitogenome) is the least studied due to complex recombination and intergenomic transfer. In gymnosperms only ∼20 mitogenomes have been released thus far, which hinders a systematic investigation into the tempo and mode of mitochondrial DNA evolution in seed plants. Here, we report the complete mitogenome sequence of Platycladus orientalis (Cupressaceae). This mitogenome is assembled as two circular-mapping chromosomes with a size of ∼2.6 Mb and which contains 32 protein-coding genes, three rRNA and seven tRNA genes, and 1,068 RNA editing sites. Repetitive sequences, including dispersed repeats, transposable elements (TEs), and tandem repeats, made up 23% of the genome. Comparative analyses with 17 other mitogenomes representing the five gymnosperm lineages revealed a 30-fold difference in genome size, 80-fold in repetitive content, and 230-fold in substitution rate. We found dispersed repeats are highly associated with mitogenome expansion (r = 0.99), and most of them were accumulated during recent duplication events. Syntenic blocks and shared sequences between mitogenomes decay rapidly with divergence time (r = 0.53), with the exceptions of Ginkgo and Cycads which retained conserved genome structure over long evolutionary time. Our phylogenetic analysis supports a sister group relationship of Cupressophytes and Gnetophytes; both groups are unique in that they lost 8–12 protein-coding genes, of which 4–7 intact genes are likely transferred to nucleus. These two clades also show accelerated and highly variable substitution rates relative to other gymnosperms. Our study highlights the dynamic and enigmatic evolution of gymnosperm mitogenomes.

IntroductionAcquired resistance to endocrine therapy (ET) remains a big challenge in the management of metastatic breast cancer (MBC). A novel therapeutic agent, histone deacetylase inhibitors (HDACi), targets the abnormal epigenetic modification and may overcome acquired resistance. However, HDACi efficacy and the safety profile for hormone receptor (HoR)-positive/human epidermal growth factor receptor 2 (HER2)-negative MBC remain controversial.MethodsTwo independent reviewers searched PubMed, Embase, and Cochrane Central Register of Controlled Trials databases for relevant studies on HDACi and HoR+/HER2- MBC. Demographic and clinicopathological parameters were extracted and presented as means and proportions, and between-group differences were assessed by Pearson chi-square test. Fixed- or random-effects models were used for meta-analysis based on inter-study heterogeneity. Pooled results were presented as L’Abbé plot and forest plot. Funnel plot and Egger’s test were employed for evaluation of publication bias.ResultsFour studies with 1,457 patients were included for meta-analysis. The overall objective response rates (ORRs) of HDACi + ET (HE) and placebo + ET (PE) groups were 11.52% and 6.67%, respectively. The HE regimen significantly increased ORR (odds ratio [OR] 1.633, 95% confidence interval [CI] = 1.103–2.418, p < 0.05) and showed higher clinical benefit rate (CBR) than the PE regimen (HE vs. PE groups: 38.82% vs. 30.58%, OR 1.378, 95% CI = 1.020–1.861, p < 0.05). Additionally, the HE regimen was associated with prolonged progression-free survival (PFS) (hazard ratio [HR] 0.761, 95% CI = 0.650–0.872, p < 0.001) and overall survival (OS) (HR 0.849, 95% CI = 0.702–0.996, p < 0.001). Regarding safety profile, the HE regimen had increasing toxicity in terms of higher overall adverse event (AE), Grade ≥3 AE, dose modification, and discontinuation rate.ConclusionsThis meta-analysis validated that the HE regimen had superior efficacy over control in terms of ORR, CBR, PFS, and OS, but was accompanied with increasing toxicity. HDACi plus ET could serve as an important option in managing HoR+/HER2- MBC. Future studies may focus on the clinical difference among different HDACi and AE managements to enhance tolerability.

Abstract Background Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. Results Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. Conclusions The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.

Sentiment analysis of e-commerce reviews is the hot topic in the e-commerce product quality management, from which manufacturers are able to learn the public sentiment about products being sold on e-commerce websites. Meanwhile, customers can know other people's attitudes about the same products. This paper proposes the deep learning model of Bert-BiGRU-Softmax with hybrid masking, review extraction and attention mechanism, which applies sentiment Bert model as the input layer to extract multi-dimensional product feature from e-commerce reviews, Bidirectional GRU model as the hidden layer to obtain semantic codes and calculate sentiment weights of reviews, and Softmax with attention mechanism as the output layer to classify the positive or negative nuance. A series of experiments are conducted on the large-scale dataset involving over 500 thousand product reviews. The results show that the proposed model outperforms the other deep learning models, including RNN, BiGRU, and Bert-BiLSTM, which can reach over 95.5% of accuracy and retain a lower loss for the e-commerce reviews.

It is well known that different racial groups have significantly different incidence and mortality rates for certain cancers. It has been suggested that biological factors play a major role in these cancer racial disparities. Previous studies on the biological factors contributing to cancer racial disparity have generated a very large number of candidate factors, although there is modest agreement among the results of the different studies. Here, we performed an integrative analysis using genomic data of 21 cancer types from TCGA, GTEx, and the 1000 Genomes Project to identify biological factors contributing to racial disparity in cancer. We also built a companion website with additional results for cancer researchers to freely mine. Our study identified genes, gene families, and pathways displaying similar differential expression patterns between different racial groups across multiple cancer types. Among them, XKR9 gene expression was found to be significantly associated with overall survival for all cancers combined as well as for several individual cancers. Our results point to the interesting hypothesis that XKR9 could be a novel drug target for cancer immunotherapy. Bayesian network modeling showed that XKR9 is linked to important cancer‐related genes, including FOXM1, cyclin B1, and RB1CC1 (RB1 regulator). In addition, metabolic pathways, neural signaling pathways, and several cancer‐related gene families were found to be significantly associated with cancer racial disparities for multiple cancer types. Single nucleotide polymorphisms (SNPs) discovered through integrating data from the TCGA, GTEx, and 1000 Genomes databases provide biologists the opportunity to test highly promising, targeted hypotheses to gain a deeper understanding of the genetic drivers of cancer racial disparity and cancer biology in general.

Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.

Abstract Background HER2 dual-blockade combined with aromatase inhibitors (AI) is a promising strategy to improve progression-free survival (PFS) in hormone receptor (HR) positive, metastatic breast cancer (MBC). Pyrotinib is a novel irreversible epidermal growth factor receptor/HER2 dual tyrosine kinase inhibitor. However, there is scarcity of data on the effectiveness and safety of pyrotinib combined with trastuzumab and AI as first-line treatment in a metastatic setting. Methods/design The present study is a prospective, randomized, open-label trial. 198 patients with HER2+/HR+ MBC will be recruited. Eligible patients will be allocated (2:1) to either an experimental group (pyrotinib + trastuzumab + AI) or a control group (trastuzumab + AI). Allocation will be stratified by 1) time since adjuvant hormone therapy (≤ 12 months/> 12 months/no prior hormone therapy); 2) lesion sites (visceral / non-visceral). The primary endpoint is PFS. Discussion To our knowledge, this is the first prospective randomized controlled trial to assess dual HER2-blockade with pyrotinib in the metastatic setting. This study will provide valuable evidence regarding the efficacy and safety of pyrotinib when combined with trastuzumab and an AI as first-line treatment for MBC. Moreover, it will also evaluate the feasibility of endocrine therapy as an alternative to chemotherapy in providing de-escalation therapy with less toxicity for advanced HR+/HER2+ patients. Trial registration ClinicalTrials.gov, ID: NCT03910712 . Registered on 10 Apr. 2019.

Abstract Background RFA is designed to produce localized tumor destruction by heating the tumor and surrounding liver tissue, especially suitable for patients who do not qualify for hepatic resection. Many studies have reported that RFA was inferior to hepatectomy in the treatment of recurrent colorectal liver metastases. However, strong evidence is lacking in the literature. This study aimed to investigate the effect and clinical outcome of percutaneous ultrasound-guided RFA and repeat hepatic resection for recurrent colorectal liver metastases after hepatectomy. Methods From January 2007 to January 2014, 194 patients with recurrent colorectal liver metastases after hepatectomy diagnosed in our hospital was performed, and then divided into two groups based on different regimens: repeat hepatic resection group and RFA group. The clinical data of the two groups were analyzed. After treatment, the liver function-related indexes, complication rate, survival rate, and tumor recurrence of the two groups were recorded. The difference in short-term and long-term effects between repeat hepatic resection and RFA was identified by propensity score analysis. Results The number of metastases and the proportion of left and right lobe involved by tumor and preoperative chemotherapy in the RFA group were higher than those in the repeat hepatic resection group. The clinical data showed no significant difference between the two groups after using propensity score analysis. Compared with the RFA group, the liver function of the repeat hepatic resection group was significantly improved. After adjustment for potential confounders, no significant difference in liver function-related indexes was found between RFA and repeat hepatic resection, and the incidence of complications in the RFA group was lower. In survival analysis, there was no significant difference in OS and DFS between the two groups. Conclusions RFA is a safe and effective therapeutic option for patients with recurrent colorectal liver metastases after hepatectomy.

Abstract Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome‐wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high‐quality variants from Platycladus orientalis range‐wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature‐related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.

Because thermionic emission or tunneling occurs when carriers overcome or tunneling through the barrier for any Schottky diode, hot carriers caused by the applied electric field can enhance carrier thermionic emission or carrier tunneling. An analytical and physical organic diode current equation that includes hot-carriers effect on the diode current equation has been proposed. When organic diode current equation has the same mathematical expression as Shockley diode current equation does, hot-carrier effects in organic semiconductor diodes can be a physical origin of the ideality factor and can reduce the barrier height for both band-like conduction mechanism and hopping conduction mechanism. The voltage-dependent ideality factor and temperature-dependent ideality factor predicted by the proposed model agree well with experimental data of organic semiconductor diodes reported in the literature. The proposed model can also physically explain the experimental relation between the ideality factor and the effective barrier height. The proposed model is useful in better physically understanding the carrier transport in organic semiconductor diodes. It also benefits to better optimize the organic semiconductor diode performance by tuning material properties.

Partial congenital hypogonadotropic hypogonadism (PCHH) is caused by an insufficiency in, but not a complete lack of, gonadotropin secretion. This leads to reduced testosterone production, mild testicular enlargement, and partial pubertal development. No studies have shown the productivity of spermatogenesis in patients with PCHH. We compared the outcomes of gonadotropin-induced spermatogenesis between patients with PCHH and those with complete congenital hypogonadotropic hypogonadism (CCHH). This retrospective study included 587 patients with CHH who were treated in Peking Union Medical College Hospital (Beijing, China) from January 2008 to September 2016. A total of 465 cases were excluded from data analysis for testosterone or gonadotropin-releasing hormone treatment, cryptorchidism, poor compliance, or incomplete medical data. We defined male patients with PCHH as those with a testicular volume of ≥4 ml and patients with a testicular volume of

The Asplenium coenobiale complex is distributed in Eastern Asia and Southeast Asia with its distribution center in southwestern China. In this study, we carried out a detailed morphological, cytological, and phylogenetic study by adding two samples from Danxia landform in Guangdong. The sequences of five chloroplast markers and one nuclear marker of the A. coenobiale complex were analyzed with maximum likelihood and Bayesian inference, respectively. The morphological and phylogenetic analyses support the recognition of a new species (A. danxiaense K.W.Xu sp. nov.) of the A. coenobiale complex from a cave of Danxia mountain, Guangdong province, southern China. This new species can be distinguished from A. coenobiale and A. pulcherrimum by having scales narrowly triangular to lanceolate, apex ending in a short apical tail, basal basiscopic pinnule usually largest, fertile segment scarce, and exospore length usually more than 50 μm and shows significant molecular differences from other species in this complex. A detailed description and illustrations are presented.

Verticillium dahliae is a destructive soil-borne pathogen of many economically important dicots. The genetics of pathogenesis in V. dahliae has been extensively studied. Spt-Ada-Gcn5 acetyltransferase complex (SAGA) is an ATP-independent multifunctional chromatin remodeling complex that contributes to diverse transcriptional regulatory functions. As members of the core module in the SAGA complex in Saccharomyces cerevisiae, Ada1, together with Spt7 and Spt20, play an important role in maintaining the integrity of the complex. In this study, we identified homologs of the SAGA complex in V. dahliae and found that deletion of the Ada1 subunit (VdAda1) causes severe defects in the formation of conidia and microsclerotia, and in melanin biosynthesis and virulence. The effect of VdAda1 on histone acetylation in V. dahliae was confirmed by western blot analysis. The deletion of VdAda1 resulted in genome-wide alteration of the V. dahliae transcriptome, including genes encoding transcription factors and secreted proteins, suggesting its prominent role in the regulation of transcription and virulence. Overall, we demonstrated that VdAda1, a member of the SAGA complex, modulates multiple physiological processes by regulating global gene expression that impinge on virulence and survival in V. dahliae.

The global impact of coronavirus disease 2019 (COVID-19) is unprecedented, and many control and prevention measures have been implemented to test for and trace COVID-19. However, invisible-spreaders, who are associated with nucleic acid detection and asymptomatic infections, have received insufficient attention in the current COVID-19 control efforts. In this paper, we analyze the time series infection data for Italy, Germany, Brazil, India and Sweden since the first wave outbreak to address the following issues through a series of experiments. We conclude that: 1) As of June 1, 2020, the proportion of invisible-spreaders is close to 0.4% in Sweden, 0.8% in early Italy and Germany, and 0.4% in the middle and late stages. However, in Brazil and India, the proportion still shows a gradual upward trend; 2) During the spread of this pandemic, even a slight increase in the proportion of invisible-spreaders could have large implications for the health of the community; and 3) On resuming work, the pandemic intervention measures will be relaxed, and invisible-spreaders will cause a new round of outbreaks.

Owing to its capacity to eliminate a long-standing methodological limitation, fiber photometry can assist research gaining novel insight into neural systems. Fiber photometry can reveal artifact-free neural activity under deep brain stimulation (DBS). Although evoking neural potential with DBS is an effective method for mediating neural activity and neural function, the relationship between DBS-evoked neural Ca2+ change and DBS-evoked neural electrophysiology remains unknown. Therefore, in this study, a self-assembled optrode was demonstrated as a DBS stimulator and an optical biosensor capable of concurrently recording Ca2+ fluorescence and electrophysiological signals. Before the in vivo experiment, the volume of tissue activated (VTA) was estimated, and the simulated Ca2+ signals were presented using Monte Carlo (MC) simulation to approach the realistic in vivo environment. When VTA and the simulated Ca2+ signals were combined, the distribution of simulated Ca2+ fluorescence signals matched the VTA region. In addition, the in vivo experiment revealed a correlation between the local field potential (LFP) and the Ca2+ fluorescence signal in the evoked region, revealing the relationship between electrophysiology and the performance of neural Ca2+ concentration behavior. Concurrent with the VTA volume, simulated Ca2+ intensity, and the in vivo experiment, these data suggested that the behavior of neural electrophysiology was consistent with the phenomenon of Ca2+ influx to neurons.

Objective: This study seeks to evaluate the value of the high-frame-rate vector flow imaging technique in assessing the hemodynamic changes of carotid atherosclerotic stenosis in aging people (>60 years old). Methods: Aging patients diagnosed with carotid atherosclerotic stenosis who underwent carotid high-frame-rate vector flow imaging examination were prospectively enrolled. A Mindray Resona7s ultrasound machine equipped with high-frame-rate vector flow function was used for ultrasound evaluation. First, B mode ultrasound and color Doppler flow imaging were used to evaluate carotid stenosis. Then, the vector arrows and flow streamline detected by V Flow were analyzed and the wall shear stress values (Pa) at the carotid stenosis site were measured. All patients were divided into symptomatic and asymptomatic groups according to whether they had acute/subacute stroke or other clinical symptoms within 2 weeks before ultrasound examination. The results of digital subtraction angiography or computed tomography angiography were used as the gold standard. The stenosis rate was calcified, according to North American Symptomatic Carotid Endarterectomy Trial criteria. The diagnostic values of wall shear stress, conventional ultrasound, and the combined diagnosis in carotid atherosclerotic stenosis were compared. Results: Finally, 88 patients with carotid atherosclerotic plaque were enrolled (71 males (80.7%), mean age 67.6 ± 5.4 years). The success rate of high-frame-rate vector flow imaging was 96.7% (88/91). The WSS value of symptomatic carotid stenosis (1.4 ± 0.15 Pa) was significantly higher than that of asymptomatic carotid stenosis (0.80 ± 0.08 Pa) (p < 0.05). Taking the wall shear stress value > 0.78 Pa as the diagnostic criteria for symptomatic carotid atherosclerotic plaque, the area under receiver operating characteristic curves was 0.79 with 87.1% sensitivity and 69.6% specificity. The area under receiver operating characteristic curves of the combined diagnosis (0.966) for differentiating severe carotid atherosclerotic stenosis was significantly higher than that of conventional ultrasound and WSS value, with 89.7% sensitivity and 93.2% specificity (p < 0.05). Conclusion: As a non-invasive imaging method, the high-frame-rate vector flow imaging technique showed potential value in the preoperative assessment of the symptomatic carotid atherosclerotic stenosis and diagnosing carotid atherosclerotic stenosis in aging patients.

Pinus bungeana, an endangered and native coniferous tree species in China, has considerable timber and horticulture value. However, little is known about needle diseases in P. bungeana. A needle blight of P. bungeana has been observed in Hebei Province, China. P. bungeana inoculated with mycelial plugs of fungal isolates presented symptoms similar to those observed under field conditions. Ten virulent fungal isolates were identified as a small-spored Alternaria species based on morphological observations. Maximum likelihood and Bayesian phylogenetic analyses carried out with multilocus sequence typing of eight regions (SSU, LSU, ITS, gapdh, tef1, Alt a 1, endoPG, OPA10-2) assigned the pathogen to Alternaria alternata. This is the first report of A. alternata causing needle blight on P. bungeana in China.