Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations.

Accurate subgenome phasing is crucial for understanding the origin, evolution and adaptive potential of polyploid genomes. SubPhaser and WGDI software are two common methodologies for subgenome phasing in allopolyploids, particularly in scenarios lacking known diploid progenitors. Triggered by a recent debate over the subgenomic origins of the cultivated octoploid strawberry, we examined four well-documented complex allopolyploidy cases as benchmarks, to evaluate and compare the accuracy of the two software. Our analysis demonstrates that the subgenomic structure phased by both software is in line with prior research, effectively tracing complex allopolyploid evolutionary trajectories despite the limitations of each software. Furthermore, using these validated methodologies, we revisited the controversial issue regarding the progenitors of the octoploid strawberry. The results of both methodologies reaffirm Fragaria vesca and Fragaria iinumae as progenitors of the octoploid strawberry. Finally, we propose recommendations for enhancing the accuracy of subgenome phasing in future studies, recognizing the potential of integrated tools for advanced complex allopolyploidy research and offering a new roadmap for robust subgenome-based phylogenetic analysis.

High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

Precise Synthesis of Organic Cocrystal Alloys with Full-Spectrum Emission Characteristics for the Stepless Color Changing Display.

Organic luminescent materials are indispensable in optoelectronic displays and solid-state luminescence applications. Compared with single-component, multi-component crystalline materials can improve optoelectronic characteristics. This work forms a series of full-spectrum tunable luminescent charge-transfer (CT) cocrystals ranging from 400 to 800 nm through intermolecular collaborative self-assembly. What is even more interesting is that o-TCP-Cor(x)-Pe(1-x), p-TCP-Cor(x)-Pe(1-x), and o-TCP-AN(x)-TP(1-x) alloys are prepared based on cocrystals by doping strategies, which correspondingly achieve the stepless color change from blue (CIE [0.22, 0.44]) to green (CIE [0.16, 0.14]), from green (CIE [0.27, 0.56]) to orange (CIE [0.58, 0.42]), from yellow (CIE [0.40, 0.57]) to red (CIE [0.65, 0.35]). The work provides an efficient method for precisely synthesizing new luminescent organic semiconductor materials and lays a solid foundation for developing advanced organic solid-state displays.

Gap-free X and Y chromosome assemblies of Salix arbutifolia reveal an evolutionary change from male to female heterogamety in willows, without a change in the position of the sex-determining locus.

In the Vetrix clade of Salix, a genus of woody flowering plants, sex determination involves chromosome 15, but an XY system has changed to a ZW system. We studied the detailed genetic changes involved. We used genome sequencing, with chromosome conformation capture (Hi-C) and PacBio HiFi reads to assemble chromosome level gap-free X and Y of Salix arbutifolia, and distinguished the haplotypes in the 15X- and 15Y-linked regions, to study the evolutionary history of the sex-linked regions (SLRs). Our sequencing revealed heteromorphism of the X and Y haplotypes of the SLR, with the X-linked region being considerably larger than the corresponding Y region, mainly due to accumulated repetitive sequences and gene duplications. The phylogenies of single-copy orthogroups within the SLRs indicate that S. arbutifolia and Salix purpurea share an ancestral SLR within a repeat-rich region near the chromosome 15 centromere. During the change in heterogamety, the X-linked region changed to a W-linked one, while the Z was derived from the Y.

Pulmonary microbial spectrum in late-stage SARS-CoV-2 infection: a case series.

Coronavirus disease 2019 (COVID-19), a kind of respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), primarily spreads through the respiratory tract from human to human. Its extensive and rapid spread has led to a global pandemic, causing great harm to human health and economic development all over the world. Current known evidence indicates that SARS-CoV-2 has evolved accumulating multiple mutations, with altered infectivity and viral replication capacity. A better understanding of the complications of COVID-19 and its relationship with underlying diseases is crucial for the prevention and treatment of SARS-CoV-2. This case series reviewed case data of our 4 recent patients with severe or critical COVID-19, including treatment plan, status of pulmonary infection and their microbiology workup with metagenomic next-generation sequencing with bronchoalveolar lavage fluid. This report shed light on the significance of rapid and accurate clinical diagnosis and treatment on COVID-19.

The association of prealbumin, transferrin, and albumin with immunosenescence among elderly males.

OBJECTIVE: As people get older, the innate and acquired immunity of the elderly are affected, resulting in immunosenescence. Prealbumin (PAB), transferrin (TRF), and albumin (ALB) are commonly used markers to monitor protein energy malnutrition (PEM). However, their relationship with the immune system has not been fully explored. METHODS: In our study, a total of 93 subjects (≥65 years) were recruited from Tongji Hospital between January 2015 and February 2017. According to the serum levels of these proteins (PAB, TRF, and ALB), we divided the patients into the high serum protein group and the low serum protein group. Then, we compared the percent expression of lymphocyte subsets between two groups. RESULTS: All the low serum protein groups (PAB, TRF, and ALB) had significant decreases in the percentage of CD4+ cells, CD3+CD28+ cells, CD4+CD28+ cells and significant increases in the percentage of CD8+ cells, CD8+CD28- cells. PAB, TRF, and ALB levels revealed positive correlations with CD4/CD8 ratio, proportions of CD4+ cells, CD3+CD28+ cells, CD4+CD28+ cells, and negative correlation with proportions of CD8+ cells, CD8+CD28- cells. CONCLUSIONS: This study suggested PAB, TRF, and ALB could be used as immunosenescence indicators. PEM might accelerate the process of immunosenescence in elderly males.

Gut microbiota dysbiosis links chronic apical periodontitis to liver fibrosis in nonalcoholic fatty liver disease: Insights from a mouse model.

AIM: In this study, we investigated the systemic implications of chronic apical periodontitis (CAP). CAP may contribute to the nonalcoholic fatty liver disease (NAFLD) progression through the gut microbiota and its metabolites, which are related to the degree of fibrosis. METHODOLOGY: Sixteen 7-week-old male apolipoprotein E knockout (apoE-/-) mice were randomly divided into two groups: the CAP and Con groups. A CAP model was established by sealing the first- and second-maxillary molars with bacterium-containing cotton balls. Apical lesions were evaluated by micro-CT. Histological evaluations of NAFLD were performed using second harmonic generation/two-photon excitation fluorescence (SHG/TPEF) assays. Additionally, we comprehensively analyzed the gut microbiota using 16S rRNA gene sequencing and explored metabolic profiles by liquid chromatography-mass spectrometry (LC-MS). Immunofluorescence analysis was used to examine the impact of CAP on tight junction proteins and mucin expression. Transcriptome assays have elucidated gene expression alterations in liver tissues. RESULTS: Micro-CT scans revealed an evident periapical bone loss in the CAP group, and the total collagen percentage was increased (Con, 0.0361 ± 0.00510%, CAP, 0.0589 ± 0.00731%, p < .05). 16S rRNA sequencing revealed reduced diversity and distinct taxonomic enrichment in the CAP group. Metabolomic assessments revealed that differentially enriched metabolites, including D-galactosamine, were enriched and that 16-hydroxyhexadecanoic acid and 3-methylindole were depleted in the CAP group. Immunofluorescence analyses revealed disruptions in tight junction proteins and mucin production, indicating intestinal barrier integrity disruption. Liver transcriptome analysis revealed upregulation of Lpin-1 expression in the CAP group. CONCLUSION: This study provides comprehensive evidence of the systemic effects of CAP on liver fibrosis in NAFLD patients by elucidating alterations in the gut microbiota composition and metabolism.

Transcriptomic-based analysis to identify candidate genes for blue color rose breeding.

KEY MESSAGE: Analysis of the flower color formation mechanism of 'Rhapsody in Blue' by BF and WF transcriptomes reveals that RhF3'H and RhGT74F2 play a key role in flower color formation. Rosa hybrida has colorful flowers and a high ornamental value. Although rose flowers have a wide range of colors, no blue roses exist in nature, and the reason for this is unclear. In this study, the blue-purple petals (BF) of the rose variety 'Rhapsody in Blue' and the white petals (WF) of its natural mutant were subjected to transcriptome analysis to find genes related to the formation of the blue-purple color. The results showed that the anthocyanin content was significantly higher in BF than in WF. A total of 1077 differentially expressed genes (DEGs) were detected by RNA-Seq analysis, of which 555 were up-regulated and 522 were down-regulated in the WF vs. BF petals. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the DEGs revealed that a single gene up-regulated in BF was related to multiple metabolic pathways including metabolic process, cellular process, protein-containing complex, etc. Additionally, the transcript levels of most of the structural genes related to anthocyanin synthesis were significantly higher in BF than in WF. Selected genes were analyzed by qRT-PCR and the results were highly consistent with the RNA-Seq results. The functions of RhF3'H and RhGT74F2 were verified by transient overexpression analyses, and the results confirmed that both affect the accumulation of anthocyanins in 'Rhapsody in Blue'. We have obtained comprehensive transcriptome data for the rose variety 'Rhapsody in Blue'. Our results provide new insights into the mechanisms underlying rose color formation and even blue rose formation.

Diagnostic performance of a novel automated CT-derived FFR technology in detecting hemodynamically significant coronary artery stenoses: A multicenter trial in China.

BACKGROUND AND AIMS: Computed tomography-derived fractional flow reserve (CT-derived FFR) algorithms have emerged as promising noninvasive methods for identifying hemodynamically significant coronary artery disease (CAD). However, its broad adaption is limited by the complex workflow, slow processing, and supercomputer requirement. Therefore, CT-derived FFR solutions capable of producing fast and accurate results could help deliver time-sensitive results rapidly and potentially alter patient management. The current study aimed to determine the diagnostic performance of a novel CT-derived FFR algorithm, esFFR, on patients with CAD was evaluated. METHODS: 329 patients from 6 medical centers in China were included in this prospective study. CT-derived FFR calculations were performed on 350 vessels using the esFFR algorithm using patients' presenting coronary computed tomography angiography (CCTA) images, and results and processing speed were recorded. Using invasive FFR measurements from direct coronary angiography as the reference standard, the diagnostic performance of esFFR and CCTA in detecting hemodynamically significant lesions were compared. Post-hoc analyses were performed for patients with calcified lesions or stenoses within the CT-derived FFR diagnostic "gray zone." RESULTS: The esFFR values correlated well with invasive FFR. The sensitivity, specificity, accuracy, positive and negative predictive value for esFFR were all above 90%. The overall performance of esFFR was superior to CCTA. Coronary calcification had minimal effects on esFFR's diagnostic performance. It also maintained 85% of diagnostic accuracy for "gray zone" lesions, which historically was <50%. The average esFFR processing speed was 4.6 ± 1.3 minutes. CONCLUSIONS: The current study demonstrated esFFR had high diagnostic efficacy and fast processing speed in identifying hemodynamically significant CAD.

Dehydroaromatization of Indolines and Cyclohexanones with Thiol Access to Aryl Sulfides under Basic Conditions.

Aryl sulfides are common and ubiquitous motifs in natural products and pharmaceuticals. Presented herein is the first example of the synthesis of diaryl sulfide derivatives via dehydroaromatization under simple basic conditions. Dehydroaromatization reactions between indolines or cyclohexanones with aryl thiols are performed in an environmentally benign manner by the use of air (molecular oxygen) as the oxidant, with producing water as the only byproduct. The methodology provides a simple and practical route to diaryl sulfides with wide functional groups in good to excellent yields. Preliminary mechanistic studies suggest that a radical process is involved in the transformation.

Cytochalasans with Inhibitory Activity against NPC1L1 from the Endophytic Fungus Chaetomium nigricolor F5.

Mass spectrometry (MS)-based metabolic profiling of the endophytic fungus Chaetomium nigricolor F5 guided the isolation of five novel cytochalasans, chamisides B-F (1-5), and two known ones, chaetoconvosins C and D (6 and 7). Their structures including stereochemistry were unambiguously determined by MS, nuclear magnetic resonance, and single-crystal X-ray diffraction analyses. Compounds 1-3 share a new 5/6/5/5/7-fused pentacyclic skeleton in cytochalasans and are appropriately proposed to be the key biosynthetic precursors of co-isolated cytochalasans with a 6/6/5/7/5, 6/6/5/5/7, or 6/6/5 ring system. Remarkably, compound 5 with a relatively flexible side chain showed promising inhibition activity against the cholesterol transporter protein Niemann-Pick C1-like 1 (NPC1L1), expanding the function of cytochalasans.

Photomodulation of Proton Conductivity by Nitro-Nitroso Transformation in a Metal-Organic Framework.

The design of a highly and photomodulated proton conductor is important for advanced potential applications in chemical sensors and bioionic functions. In this work, a metal-organic framework (MOF; Gd-NO2) with high proton conductivity is synthesized with a photosensitive ligand of 5-nitroisophthalic acid (BDC-NO2), and it provides remote-control photomodulated proton-conducting behavior. The proton conduction of Gd-NO2 reaches 3.66 × 10-2 S cm-1 at 98% relative humidity (RH) and 25 °C, while it decreases by ∼400 times after irradiation with a 355 nm laser. The newly generated and disappearing FT-IR characteristic peaks reveal that this photomodulated process is realized by the photoinduced transformation from BDC-NO2 to 5-nitroso-isophthalic acid (BDC-NO). According to density functional theory, the smaller electronegativity of the -NO group, the longer distance of the hydrogen bond between BDC-NO and H2O molecules, and the lower water adsorption energy of BDC-NO indicate that the irradiated sample possesses a poorer hydrophilicity and has difficulty forming rich hydrogen-bonded networks, which results in the remarkable decrease of proton conductivity.

Histopathological features of glandular atrophy of the lamina propria of the gastric mucosa during its occurrence and development.

OBJECTIVE: To explore the histopathological features of glandular atrophy of the lamina propria of gastric mucosa during its occurrence and development. METHOD: We performed detailed histological observation and immunohistochemical examination on the endoscopic biopsy and ESD endoscopic resection specimens of 896 patients with glandular atrophy of the lamina propria of gastric mucosa. The EnVision two-step method was used for immunohistochemical staining, and the slices were incubated with primary antibody CK7, CK20, villin, CDX2, MUC5AC, MUC6, p53 and ki-67. Hematoxylin staining was performed and observed under the microscope and statistically analyzed. RESULTS: In the initial stage of glandular atrophy of the lamina propria, the proliferation area of the deep gastric pits, and the isthmus and neck of the gastric glands are characterized by roughly normal structure of the glandular structure, increased mesenchyme, and widened space between glands. Subsequently, the gland becomes smaller in volume and less in number, especially at the base, in the gastric glandular part of the gastric unit. The disease at this stage has higher incidence, and occurs more often in the elderly who account for 64.0% (573/896) of our study group. The disease in this stage may exhibit some lesions that are physiologic (age-related degeneration) while others are pathological. Therefore, this condition is called simple glandular atrophy of the lamina propria of the gastric mucosa. When the gastric mucosal epithelium is subjected to infection or repeated infections, chemical stimuli, immune factors, and genetic factors, it can lead to the proliferation and transformation of stem cells in the proliferation area of the deep gastric pits, and the isthmus and neck of the gastric glands, forming single ducts, multiple ducts, or a proliferation of patchy cells. Then, atypical hyperplasia (intraepithelial neoplasia) presents, finally leading to gastric adenocarcinoma. CONCLUSION: Understanding the histopathological characteristics of glandular atrophy of the lamina propria of gastric mucosa is of great significance in controlling the occurrence and development of gastric cancer.

An integrated PK/PD model investigating the impact of tumor size and systemic safety on animal survival in SW1990 pancreatic cancer xenograft.

Survival is one of the most important endpoints in cancer therapy, and parametric survival analysis could comprehensively reveal the overall result of disease progression, drug efficacy, toxicity as well as their interactions. In this study we investigated the efficacy and toxicity of dexamethasone (DEX) combined with gemcitabine (GEM) in pancreatic cancer xenograft. Nude mice bearing SW1990 pancreatic cancer cells derived tumor were treated with DEX (4 mg/kg, i.g.) and GEM (15 mg/kg, i.v.) alone or in combination repeatedly (QD, Q3D, Q7D) until the death of animal or the end of study. Tumor volumes and net body weight (NBW) were assessed every other day. Taking NBW as a systemic safety indicator, an integrated pharmacokinetic/pharmacodynamic (PK/PD) model was developed to quantitatively describe the impact of tumor size and systemic safety on animal survival. The PK/PD models with time course data for tumor size and NBW were established, respectively, in a sequential manner; a parametric time-to-event (TTE) model was also developed based on the longitudinal PK/PD models to describe the survival results of the SW1990 tumor-bearing mice. These models were evaluated and externally validated. Only the mice with good tumor growth inhibition and relatively stable NBW had an improved survival result after DEX and GEM combination therapy, and the simulations based on the parametric TTE model showed that NBW played more important role in animals' survival compared with tumor size. The established model in this study demonstrates that tumor size was not always the most important reason for cancer-related death, and parametric survival analysis together with safety issues was also important in the evaluation of oncology therapies in preclinical studies.

DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools.

Essential genes refer to genes that are required by an organism to survive under specific conditions. Studies of the minimal-gene-set for bacteria have elucidated fundamental cellular processes that sustain life. The past five years have seen a significant progress in identifying human essential genes, primarily due to the successful use of CRISPR/Cas9 in various types of human cells. DEG 15, a new release of the Database of Essential Genes (www.essentialgene.org), has provided major advancements, compared to DEG 10. Specifically, the number of eukaryotic essential genes has increased by more than fourfold, and that of prokaryotic ones has more than doubled. Of note, the human essential-gene number has increased by more than tenfold. Moreover, we have developed built-in analysis modules by which users can perform various analyses, such as essential-gene distributions between bacterial leading and lagging strands, sub-cellular localization distribution, enrichment analysis of gene ontology and KEGG pathways, and generation of Venn diagrams to compare and contrast gene sets between experiments. Additionally, the database offers customizable BLAST tools for performing species- and experiment-specific BLAST searches. Therefore, DEG comprehensively harbors updated human-curated essential-gene records among prokaryotes and eukaryotes with built-in tools to enhance essential-gene analysis.

Clinical application of spinal robot in cervical spine surgery: safety and accuracy of posterior pedicle screw placement in comparison with conventional freehand methods.

The novel robot-assisted (RA) technique has been utilized increasingly to improve the accuracy of cervical pedicle screw placement. Although the clinical application of the RA technique has been investigated in several case series and comparative studies, the superiority and safety of RA over conventional freehand (FH) methods remain controversial. Meanwhile, the intra-pedicular accuracy of the two methods has not been compared for patients with cervical traumatic conditions. This study aimed to compare the rate and risk factors of intra-pedicular accuracy of RA versus the conventional FH approach for posterior pedicle screw placement in cervical traumatic diseases. A total of 52 patients with cervical traumatic diseases who received cervical screw placement using RA (26 patients) and FH (26 patients) techniques were retrospectively included. The primary outcome was the intra-pedicular accuracy of cervical pedicle screw placement according to the Gertzbin-Robbins scale. Secondary outcome parameters included surgical time, intraoperative blood loss, postoperative drainage, postoperative hospital stay, and complications. Moreover, the risk factors that possibly affected intra-pedicular accuracy were assessed using univariate analyses. Out of 52 screws inserted using the RA method, 43 screws (82.7%) were classified as grade A, with the remaining 7 (13.5%) and 2 (3.8%) screws classified as grades B and C. In the FH cohort, 60.8% of the 79 screws were graded A, with the remaining screws graded B (21, 26.6%), C (8, 10.1%), and D (2, 2.5%). The RA technique showed a significantly higher rate of optimal intra-pedicular accuracy than the FH method (P = 0.008), but there was no significant difference between the two groups in terms of clinically acceptable accuracy (P = 0.161). Besides, the RA technique showed remarkably longer surgery time, less postoperative drainage, shorter postoperative hospital stay, and equivalent intraoperative blood loss and complications than the FH technique. Furthermore, the univariate analyses showed that severe obliquity of the lateral atlantoaxial joint in the coronal plane (P = 0.003) and shorter width of the lateral mass at the inferior margin of the posterior arch (P = 0.014) were risk factors related to the inaccuracy of C1 screw placement. The diagnosis of HRVA (P < 0.001), severe obliquity of the lateral atlantoaxial joint in the coronal plane (P < 0.001), short pedicle width (P < 0.001), and short pedicle height (P < 0.001) were risk factors related to the inaccuracy of C2 screw placement. RA cervical pedicle screw placement was associated with a higher rate of optimal intra-pedicular accuracy to the FH technique for patients with cervical traumatic conditions. The severe obliquity of the lateral atlantoaxial joint in the coronal plane independently contributed to high rates of the inaccuracy of C1 and C2 screw placements. RA pedicle screw placement is safe and useful for cervical traumatic surgery.

Characteristics and evaluation of C1 posterior arch variation for transpedicular screw placement between patients with and without basilar invagination.

BACKGROUND: C1 transpedicular screw (C1TS) placement provided satisfactory pullout resistance and 3D stability, but its application might be limited in patients with basilar invagination (BI) due to the high incidences of the atlas anomaly and vertebral artery (VA) variation. However, no study has explored the classifications of C1 posterior arch variations and investigated their indications and ideal insertion trajectories for C1TS in BI. PURPOSE: To investigate the bony and surrounding arterial characteristics of the atlas, classify posterior arch variations, identify indications for C1TS, evaluate ideal insertion trajectories for C1TS in BI patients without atlas occipitalization (AO), and compare them with those without BI and AO as control. METHODS: A total of 130 non-AO patients with and without BI (52 patients and 78 patients, respectively) from two medical centers were included at a 1:1.5 ratio. The posterior arch variations were assessed using a modified C1 morphological classification. Comparisons regarding the bony and surrounding arterial characteristics, morphological classification distributions, and ideal insertion trajectories between BI and control groups were performed. The subgroup analyses based on different morphological classifications were also conducted. In addition, the factors possibly affecting the insertion parameters were investigated using multiple linear regression analyses. RESULTS: The BI group was associated with significantly smaller lateral mass height and width, sagittal length of posterior arch, pedicle height, vertical height of posterior arch, and distance between VA and VA groove (VAG) than control group. Four types of posterior arch variations with indications for different screw placement techniques were classified; Classifications I and II were suitable for C1TS. The BI cohort showed a significantly lower rate of Classification I than the control cohort. In the BI group, the subgroup of Classification I had significantly larger distance between the insertion point (IP) and inferior aspect of the posterior arch. In addition, it had the narrowest width along ideal screw trajectory, but a significantly more lateral ideal mediolateral angle than the subgroup of Classification II. Multiple linear regression indicated that the cephalad angle was significantly associated with the diagnosis of BI (B = 3.708, P < 0.001) and sagittal diameter of C1 (B = 3.417, P = 0.027); the ideal mediolateral angle was significantly associated with BMI (B = 0.264, P = 0.031), sagittal diameter of C1 (B = - 4.559, P = 0.002), and pedicle height (B = - 2.317, P < 0.001); the distance between the IP and inferior aspects of posterior arch was significantly associated with age (B = - 0.002, P = 0.035), BMI (B = - 0.007, P = 0.028), sagittal length of posterior arch (B = - 0.187, P = 0.032), pedicle height (B = - 0.392, P < 0.001), and middle and lower parts of posterior arch (B = 0.862, P < 0.001). CONCLUSION: The incidence of posterior arch variation in BI patients without AO was remarkably higher than that in control patients. The insertion parameters of posterior screws were different between the morphological classification types in BI and control groups. The distance between VA V3 segments and VAG in BI cohort was substantially smaller than that in control cohort. Preoperative individual 3D computed tomography (CT), CT angiography and intraoperative navigation are recommended for BI patients receiving posterior screw placement.

Gut microbiota may mediate the impact of chronic apical periodontitis on atherosclerosis in apolipoprotein E-deficient mice.

AIM: There are growing evidences linking chronic apical periodontitis (CAP) to atherosclerosis. Gut microbiota is found to be involved in the development of atherosclerosis. Recent studies have shown that CAP could change the diversity and composition of the gut microbiota. It was therefore, we hypothesized that gut microbiota and its metabolites could mediate the impact of CAP on atherosclerosis. METHODOLOGY: Twenty-four 5-week-old lipoprotein E knockout (apoE-/- ) mice were randomly divided into four groups: the CAP group, Con group, Co-CAP (cohoused with CAP) and Co-Con (cohoused with Con) group. In the CAP group, sterile cotton wool containing P. gingivalis was placed into the exposed pulp chamber, followed by coronal resin-based composite restoration of the bilateral maxillary first and second molars. In the Con group, a sham operation was performed. Biweekly, mice in the CAP group were anaesthetised to check the sealing of coronal access. Meanwhile, the animals in the Con group were anaesthetised. The cohousing approach was used to introduce gut microbiota from the CAP and Con groups into the Co-CAP and Co-Con groups, respectively. Alterations in the abundance and diversity of the gut microbiota were detected using 16S rRNA sequencing, Oil-red O staining was used to demonstrate the extent of lesions, and serum levels of trimethylamine N-oxide (TMAO), and immunohistochemistry of flavin-containing monooxygenase 3 (FMO3) in liver were used to assess TMAO-related metabolic alterations. RESULTS: Alterations of alpha and beta diversity were shown both in the CAP and the Co-CAP groups. Moreover, the percentage of atherosclerotic lesion area increased in the CAP and Co-CAP groups (p < .05). Linear discriminant analysis effect size (LEfSe) at the family level found the increases of Lachnospiraceae and Ruminococcaceae (p < .05), which were positively correlated with serum TMAO levels (p < .05). In the redundancy analysis technique (RDA), serum levels of TMAO were positively associated with the atherosclerotic lesions. Co-occurrence analysis revealed that the relative abundances of Lachnospiraceae and Porphyromonadacae were positively correlated with both the percentage of lesion area and TMAO level (p < .05). CONCLUSION: Thus, within the limitations of this study, the data suggest that the gut microbiota can mediate the effects of CAP on atherosclerosis.

Medium and long-term radiographic and clinical outcomes of Dynesys dynamic stabilization versus instrumented fusion for degenerative lumbar spine diseases.

BACKGROUND: Dynesys stabilization (DS) is utilized to preserve mobility at the instrumental segments and prevent adjacent segment pathology in clinical practice. However, the advantages of DS method in medium and long-term follow-up remain controversial. OBJECTIVE: To compare the radiographic and clinical outcomes between DS and instrumented fusion in the treatment of degenerative lumbar spine disease with or without grade I spondylolisthesis with a minimum follow-up period of 2 years. METHODS: We conducted a comprehensive search of PubMed, EMBASE, Cochrane, and Web of Science databases, Chinese National Knowledge Databases, and Wanfang Database for potentially eligible articles. Clinical outcomes were assessed in terms of VAS and ODI scores, screw loosening and breakage, and surgical revision. Radiographic outcomes were assessed in terms of postoperative range of movement (ROM) and disc heigh. Moreover, adjacent segment degeneration (ASDeg) and adjacent segment disease (ASDis) were evaluated. RESULTS: Seventeen studies with 1296 patients were included in the meta-analysis. The DS group was associated with significantly lower postoperative VAS scores for low-back and leg pain, and lower rate of surgical revision than the fusion group. Moreover, the Dynesys group showed significantly less ASDeg than the fusion group but showed no significant advantage over the fusion group in terms of preventing ASDis. Additionally, the ROM at the stabilized segments of the fusion group decreased significantly and that at the adjacent segments increased significantly compared with those of the DS group. CONCLUSION: DS showed comparable clinical outcomes and provided benefits in preserving the motion at the stabilized segments, thus limiting the hypermobility at the adjacent segments and preventing ASDeg compared with the fusion method in degenerative disease with or without grade I spondylolisthesis.

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers.

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.