Genomes of multicellular algal sisters to land plants illuminate signaling network evolution

Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.

Three de novo assembled wild cacao genomes from the Upper Amazon

Theobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Recent advancement in plant genomics highlights the importance of de novo sequencing of multiple reference genomes to capture the genome diversity present in different cacao populations. In this study, three high-quality chromosome-level genomes of wild cacao were constructed, de novo assembled with HiFi long reads sequencing, and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. The five cacao genetic clusters were inferred to have diverged in the early and middle Pleistocene period, approximately 1.83-0.69 million years ago. The results shown here serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying genetic diversity and advancing genetic improvement of this species.

A Choline-Based Antifreezing Complexing Agent with Selective Compatibility for Zn-Br2 Flow Batteries

The high freezing point of polybromides, charging products, is a significant obstacle to the rapid development of zinc-bromine flow batteries (Zn-Br2 FBs). Here, a choline-based complexing agent (CCA) is constructed to liquefy the polybromides at low temperatures. Depending on quaternary ammonium group, choline can effectively complex with polybromide anions and form dense oil-phase that has excellent antifreezing property. Benefiting from indispensable strong ion-ion interaction, the highly selectively compatible CCA, consisting of choline and N-methyl-N-ethyl-morpholinium salts (CCA-M), can be achieved to further enhance bromine fixing ability. Interestingly, the formed polybromides with CCA-M are able to keep liquid even at -40 °C. The CCA-M endows Zn-Br2 FBs at 40 mA cm-2 with unprecedented long cycle life (over 150 cycles) and high Coulombic efficiency (CE, average ≈98.8%) at -20 °C, but also at room temperature (over 1200 cycles, average CE: ≈94.7%). The CCA shows a promising prospect of application and should be extended to other antifreezing bromine-based energy storage systems.

AZGP1 Aggravates Macrophage M1 Polarization and Pyroptosis in Periodontitis

Periodontal tissue destruction in periodontitis is a consequence of the host inflammatory response to periodontal pathogens, which could be aggravated in the presence of type 2 diabetes mellitus (T2DM). Accumulating evidence highlights the intricate involvement of macrophage-mediated inflammation in the pathogenesis of periodontitis under both normal and T2DM conditions. However, the underlying mechanism remains elusive. Alpha-2-glycoprotein 1 (AZGP1), a glycoprotein featuring an MHC-I domain, has been implicated in both inflammation and metabolic disorders. In this study, we found that AZGP1 was primarily colocalized with macrophages in periodontitis tissues. AZGP1 was increased in periodontitis compared with controls, which was further elevated when accompanied by T2DM. Adeno-associated virus-mediated overexpression of Azgp1 in the periodontium significantly enhanced periodontal inflammation and alveolar bone loss, accompanied by elevated M1 macrophages and pyroptosis in murine models of periodontitis and T2DM-associated periodontitis, while Azgp1-/- mice exhibited opposite effects. In primary bone marrow-derived macrophages stimulated by lipopolysaccharide (LPS) or LPS and palmitic acid (PA), overexpression or knockout of Azgp1 markedly upregulated or suppressed, respectively, the expression of macrophage M1 markers and key components of the NLR Family Pyrin Domain Containing 3 (NLRP3)/caspase-1 signaling. Moreover, conditioned medium from Azgp1-overexpressed macrophages under LPS or LPS+PA stimulation induced higher inflammatory activation and lower osteogenic differentiation in human periodontal ligament stem cells (hPDLSCs). Furthermore, elevated M1 polarization and pyroptosis in macrophages and associated detrimental effects on hPDLSCs induced by Azgp1 overexpression could be rescued by NLRP3 or caspase-1 inhibition. Collectively, our study elucidated that AZGP1 could aggravate periodontitis by promoting macrophage M1 polarization and pyroptosis through the NLRP3/casapse-1 pathway, which was accentuated in T2DM-associated periodontitis. This finding deepens the understanding of AZGP1 in the pathogenesis of periodontitis and suggests AZGP1 as a crucial link mediating the adverse effects of diabetes on periodontal inflammation.

BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework

MOTIVATION

Removal of batch effect between multiple datasets from different experimental platforms has become an urgent problem, since single-cell RNA sequencing (scRNA-seq) techniques developed rapidly. Although there have been some methods for this problem, most of them still face the challenge of under-correction or over-correction. Specifically, handling batch effect in highly nonlinear scRNA-seq data requires a more powerful model to address under-correction. In the meantime, some previous methods focus too much on removing difference between batches, which may disturb the biological signal heterogeneity of datasets generated from different experiments, thereby leading to over-correction.

RESULTS

In this article, we propose a novel multi-layer adaptation autoencoder with dual-channel framework to address the under-correction and over-correction problems in batch effect removal, which is called BERMAD and can achieve better results of scRNA-seq data integration and joint analysis. First, we design a multi-layer adaptation architecture to model distribution difference between batches from different feature granularities. The distribution matching on various layers of autoencoder with different feature dimensions can result in more accurate batch correction outcome. Second, we propose a dual-channel framework, where the deep autoencoder processing each single dataset is independently trained. Hence, the heterogeneous information that is not shared between different batches can be retained more completely, which can alleviate over-correction. Comprehensive experiments on multiple scRNA-seq datasets demonstrate the effectiveness and superiority of our method over the state-of-the-art methods.

AVAILABILITY AND IMPLEMENTATION

The code implemented in Python and the data used for experiments have been released on GitHub (https://github.com/zhanglabNKU/BERMAD) and Zenodo (https://zenodo.org/records/10695073) with detailed instructions.

The American Cherimoya Genome Reveals Insights into the Intra-Specific Divergence, the Evolution of Magnoliales, and a Putative Gene Cluster for Acetogenin Biosynthesis

Annona cherimola (cherimoya) is a species renowned for its delectable fruit and medicinal properties. In this study, we developed a chromosome-level genome assembly for the cherimoya 'Booth' cultivar from the United States. The genome assembly has a size of 794 Mb with a N50 = 97.59 Mb. The seven longest scaffolds account for 87.6% of the total genome length, which corresponds to the seven pseudo-chromosomes. A total of 45,272 protein-coding genes (≥30 aa) were predicted with 92.9% gene content completeness. No recent whole genome duplications were identified by an intra-genome collinearity analysis. Phylogenetic analysis supports that eudicots and magnoliids are more closely related to each other than to monocots. Moreover, the Magnoliales was found to be more closely related to the Laurales than the Piperales. Genome comparison revealed that the 'Booth' cultivar has 200 Mb less repeats than the Spanish cultivar 'Fino de Jete', despite their highly similar (>99%) genome sequence identity and collinearity. These two cultivars were diverged during the early Pleistocene (1.93 Mya), which suggests a different origin and domestication of the cherimoya. Terpene/terpenoid metabolism functions were found to be enriched in Magnoliales, while TNL (Toll/Interleukin-1-NBS-LRR) disease resistance gene has been lost in Magnoliales during evolution. We have also identified a gene cluster that is potentially responsible for the biosynthesis of acetogenins, a class of natural products found exclusively in Annonaceae. The cherimoya genome provides an invaluable resource for supporting characterization, conservation, and utilization of Annona genetic resources.

Characterization of Variant RNAs Encapsidated during Bromovirus Infection by High-Throughput Sequencing

Previously, we described the RNA recombinants accumulating in tissues infected with the bromoviruses BMV (Brome mosaic virus) and CCMV (Cowpea chlorotic mottle virus). In this work, we characterize the recombinants encapsidated inside the purified virion particles of BMV and CCMV. By using a tool called the Viral Recombination Mapper (ViReMa) that detects recombination junctions, we analyzed a high number of high-throughput sequencing (HTS) short RNA sequence reads. Over 28% of BMV or CCMV RNA reads did not perfectly map to the viral genomes. ViReMa identified 1.40% and 1.83% of these unmapped reads as the RNA recombinants, respectively, in BMV and CCMV. Intra-segmental crosses were more frequent than the inter-segmental ones. Most intra-segmental junctions carried short insertions/deletions (indels) and caused frameshift mutations. The mutation hotspots clustered mainly within the open reading frames. Substitutions of various lengths were also identified, whereas a small fraction of crosses occurred between viral and their host RNAs. Our data reveal that the virions can package detectable amounts of multivariate recombinant RNAs, contributing to the flexible nature of the viral genomes.

Carbohydrate-active enzyme annotation in microbiomes using dbCAN

CAZymes or carbohydrate-active enzymes are critically important for human gut health, lignocellulose degradation, global carbon recycling, soil health, and plant disease. We developed dbCAN as a web server in 2012 and actively maintain it for automated CAZyme annotation. Considering data privacy and scalability, we provide run_dbcan as a standalone software package since 2018 to allow users perform more secure and scalable CAZyme annotation on their local servers. Here, we offer a comprehensive computational protocol on automated CAZyme annotation of microbiome sequencing data, covering everything from short read pre-processing to data visualization of CAZyme and glycan substrate occurrence and abundance in multiple samples. Using a real-world metagenomic sequencing dataset, this protocol describes commands for dataset and software preparation, metagenome assembly, gene prediction, CAZyme prediction, CAZyme gene cluster (CGC) prediction, glycan substrate prediction, and data visualization. The expected results include publication-quality plots for the abundance of CAZymes, CGCs, and substrates from multiple CAZyme annotation routes (individual sample assembly, co-assembly, and assembly-free). For the individual sample assembly route, this protocol takes ∼33h on a Linux computer with 40 CPUs, while other routes will be faster. This protocol does not require programming experience from users, but it does assume a familiarity with the Linux command-line interface and the ability to run Python scripts in the terminal. The target audience includes the tens of thousands of microbiome researchers who routinely use our web server. This protocol will encourage them to perform more secure, rapid, and scalable CAZyme annotation on their local computer servers.

dbAPIS: a database of anti-prokaryotic immune system genes

Anti-prokaryotic immune system (APIS) proteins, typically encoded by phages, prophages, and plasmids, inhibit prokaryotic immune systems (e.g. restriction modification, toxin-antitoxin, CRISPR-Cas). A growing number of APIS genes have been characterized and dispersed in the literature. Here we developed dbAPIS (https://bcb.unl.edu/dbAPIS), as the first literature curated data repository for experimentally verified APIS genes and their associated protein families. The key features of dbAPIS include: (i) experimentally verified APIS genes with their protein sequences, functional annotation, PDB or AlphaFold predicted structures, genomic context, sequence and structural homologs from different microbiome/virome databases; (ii) classification of APIS proteins into sequence-based families and construction of hidden Markov models (HMMs); (iii) user-friendly web interface for data browsing by the inhibited immune system types or by the hosts, and functions for searching and batch downloading of pre-computed data; (iv) Inclusion of all types of APIS proteins (except for anti-CRISPRs) that inhibit a variety of prokaryotic defense systems (e.g. RM, TA, CBASS, Thoeris, Gabija). The current release of dbAPIS contains 41 verified APIS proteins and ∼4400 sequence homologs of 92 families and 38 clans. dbAPIS will facilitate the discovery of novel anti-defense genes and genomic islands in phages, by providing a user-friendly data repository and a web resource for an easy homology search against known APIS proteins.

[Analysis of the maternal and fetal adverse outcomes of 154 pregnant women with cesarean section in the second stage of labor]

Objective: To investigate the perinatal maternal and fetal adverse outcomes of cesarean section in the different duration of the second stage of labor. Methods: A retrospective cohort study was conducted on the clinical data of 154 pregnant women with singleton head pregnancy who underwent cesarean section at different times of the second stage of labor due to maternal and fetal factors in the First Affiliated Hospital of Nanjing Medical University from January 1, 2019 to December 31, 2021. According to the duration of the second stage of labor, they were divided into <2 h group (54 cases), 2-<3 h group (61 cases), and ≥3 h group (39 cases). The general data of pregnant women and neonates, preoperative maternal and neonatal conditions related to labor stages, surgical indications, surgical procedures, and perioperative maternal and neonatal adverse outcomes were compared among the three groups. Results: (1) General Information: there were no significant differences in maternal age, gravidity and parity, proportion of primipara, gestational age at delivery, body mass index before delivery, pregnancy complications, labor analgesia rate and the duration of the first stage of labor among the three groups (all P>0.05). The differences of the gender composition, birth weight and incidence of macrosomia of the three groups were also not statistically significant (all P>0.05). (2) Maternal and fetal status and surgical indications: the incidence of intrapartum fever and type Ⅱ and Ⅲ fetal heart rate monitoring in the <2 h group were higher than those in the 2-<3 h group and the ≥3 h group, and the preoperative fetal head position in the ≥3 h group was lower than that in the 2-<3 h group, with statistically significant differences (all P<0.05). The proportion of cesarean section due to "fetal distress" was 40.7% (22/54) in the <2 h group, which was higher than that in the 2-<3 h group (4.9%, 3/61) and the ≥3 h group (2.6%, 1/39). The proportions of surgical indication of "relative cephalo-pelvic disproportion" were 98.4% (60/61) and 94.9% (37/39) in the 2-<3 h group and ≥3 h group, respectively, and the surgical indication of "fetal head descent arrest" were 41.0% (25/61) and 59.0% (23/39), respectively. Compared with <2 h group [63.0% (34/54), 13.0% (7/54)], the differences were statistically significant (all P<0.05). There were no significant difference in surgical indications between 2-<3 h group and ≥3 h group (all P>0.05). (3) Intraoperative conditions and perioperative complications of cesarean section: the puerperal morbidity rate of <2 h group was 37.0% (20/54), which was higher than those of 2-<3 h group (18.0%, 11/61) and ≥3 h group (7.7%, 3/39), the difference was statistically significant (P<0.05). There were no significant differences in operation time, intraoperative blood loss, incidence of fetal head inlay, uterine incision tear, modified B-Lynch suture for uterine atony, postpartum hemorrhage, perioperative blood transfusion, preoperative hemoglobin (Hb) level, perioperative Hb change, and postoperative hospital stay among the three groups (all P>0.05). (4) Adverse neonatal outcomes: non-hemolytic neonatal hyperbilirubinemia in ≥3 h group was 35.9% (14/39), which was significantly higher than that in <2 h group (13.0%, 7/54; P<0.05). Among the neonates admitted to neonatal intensive care unit (NICU) within 1 week after birth, the proportion of neonates admitted to NICU due to neonatal hyperbilirubinemia in ≥3 h group (15/19) was significantly higher than that in <2 h group (9/17) and 2-<3 h group (10/19), and the differences were statistically significant (all P<0.05). However, there was no significant difference between the <2 h group and the 2-<3 h group (P>0.05). There was no perinatal death in the three groups. Conclusions: The rate of puerperal morbidity is higher in patients who were transferred to cesarean section within 2 hours of the second stage of labor. In the early stage of the second stage of labor, the monitoring of fetal heart rate and amniotic fluid characteristics should be strengthened, especially the presence or absence of prenatal fever. In good maternal and neonatal conditions, conversion to cesarean section after 2 hours of the second stage of labor does not significantly increase the incidence of serious adverse maternal and neonatal outcomes. For the second stage of labor more than 3 hours before cesarean section, it is necessary to strengthen the monitoring of neonatal bilirubin.

Expression of water-soluble nucleocapsid protein of SARS-CoV-2 and analysis of its immunogenicity

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a major public health concern. Nucleocapsid (N) protein is the most abundant structural protein on SARS-CoV-2 virions and induces the production of antibodies at the early stage of infection. Large-scale preparation of N protein is essential for the development of immunoassays to detect antibodies to SARS-CoV-2 and the control of virus transmission. In this study, expression of water-soluble N protein was achieved through inducing protein expression at 25°C with 0.5 mM IPTG for 12 h. Western blot and ELISA showed that recombinant N protein could be recognized by sera collected from subjects immunized with Sinovac inactivated SARS-CoV-2 vaccine. Four monoclonal antibodies namely 2B1B1, 4D3A3, 5G1F8, and 7C6F5 were produced using hybridoma technology. Titers of all four monoclonal antibodies in ELISA reached more than 1.28×10 6.0. Moreover, all monoclonal antibodies could react specifically with N protein expressed by transfection of pcDNA3.1-N into BHK-21 cells in IPMA and IFA. These results indicated that water-soluble N protein retained high immunogenicity and possessed the same epitopes as that of native N protein on virions. In addition, the preparation of water-soluble N protein and its monoclonal antibodies laid the basis for the development of immunoassays for COVID-19 detection.

Occlusal Force Maintains Alveolar Bone Homeostasis via Type H Angiogenesis

Physiologically, teeth and periodontal tissues are exposed to occlusal forces throughout their lifetime. Following occlusal unloading, unbalanced bone remodeling manifests as a net alveolar bone (AB) loss. This phenomenon is termed alveolar bone disuse osteoporosis (ABDO), the underlying mechanism of which remains unclear. Type H vessels, a novel capillary subtype tightly coupled with osteogenesis, reportedly have a role in skeletal remodeling; however, their role in ABDO is not well studied. In the present study, we aimed to explore the pathogenesis of and therapies for ABDO. The study revealed that type H endothelium highly positive for CD31 and endomucin was identified in the periodontal ligament (PDL) but rarely in the AB of the mice. In hypofunctional PDL, the density of type H vasculature and coupled osterix+ (OSX+) osteoprogenitors declined significantly. In addition, the angiogenic factor Slit guidance ligand 3 (SLIT3) was downregulated in the disused PDL, and periodontal injection of the recombinant SLIT3 protein partially ameliorated type H vessel dysfunction and AB loss in ABDO mice. With regard to the molecular mechanism, a mechanosensory signaling circuit, PIEZO1/Ca2+/HIF-1α/SLIT3, was validated by applying cyclic compression to 3-dimensional-cultured PDL cells using the Flexcell FX-5000 compression system. In summary, PDL plays a pivotal role in mechanotransduction by translating physical forces into the intracellular signaling axis PIEZO1/Ca2+/HIF-1α/SLIT3, which promotes type H angiogenesis and OSX+ cell-related osteogenensis, thereby contributing to AB homeostasis. Our findings advance the understanding of PDL in AB disorders. Further therapies targeting SLIT3 may provide new insights into preventing bone loss in ABDO.

[Research and reflection on the diversified method system of multi-stages and multi-scenarios surveillance and early warning of infectious diseases]

With the outbreak of infectious diseases, more and more attention has been paid to surveillance and early warning work. Timely and accurate monitoring data is the basis of infectious diseases prevention and control. Effective early warning methods for infectious diseases can improve the timeliness and sensitivity of early warning work. This paper briefly introduces the intelligent early warning model of infectious diseases, summarizes the emerging surveillance and early warning methods of infectious diseases, and seeks the possibility of diversified surveillance and early warning in different epidemic stages and different outbreak scenarios of infectious diseases. This paper puts forward the idea of constructing a diversified method system of infectious diseases surveillance and early warning based on multi-stages and multi-scenarios and discusses the future development trend of infectious diseases surveillance and early warning, in order to provide reference for improving the construction level of infectious diseases surveillance and early warning system in China.

The economic burden of coronary heart disease in mainland China

OBJECTIVES

The aim of this study was to systematically evaluate the current economic burden of coronary heart disease (CHD) in mainland China and provide a reference for the formulation of policies to reduce the economic burden of CHD.

STUDY DESIGN

A systematic literature review was conducted of empirical studies on the economic burden of CHD over the past 20 years.

METHODS

PubMed, Web of Science, Embase, China Knowledge Resource Integrated Database and the WANFANG database were comprehensively searched for relevant articles published between 1 January 2000 and 22 December 2021. Content analysis was used to extract the data, and Stata 17.0 software was used for analysis. The median values were used to describe trends.

RESULTS

A total of 35 studies were included in this review. The annual median per-capita hospitalisation expense and the average expense per hospitalisation were $3544.40 ($891.64-$18,371.46) and $5407.34 ($1139.93-$8277.55), respectively. The median ratio on medical consumables expenses, drug expenses, medical examination expenses and treatment expenses were 41.59% (12.40%-63.73%), 26.90% (7.30%-60.00%), 9.45% (1.65%-33.40%) and 10.10% (2.36%-66.00%), respectively. The median per-capita hospitalisation expense in the eastern, central and western regions were $9374.45 ($2056.13-$18,371.46), $4751.5 ($2951.95-$8768.93) and $3251.25 ($891.64-$13,986.38), respectively. The median average expense per hospitalisation in the eastern and central regions were $6177.15 ($1679.15-$8277.55) and $1285.49 ($1239.93-$2197.36), respectively. The median average length of stay in the eastern, central and western regions were 9.3 days, 15.2 days and 16.1 days, respectively.

CONCLUSIONS

The economic burden of CHD is more severe in mainland China than in developed countries, especially in terms of the direct economic burden. In terms of the types of direct medical expenses, a proportion of medical examination expenses, treatment expenses and drug expenses were lowest in the eastern region, but medical consumables expenses were the highest in this region. This study provides guidance for the formulation of policies to reduce the economic burden of CHD in mainland China.

A Retrospective Analysis of Immediate Postoperative Electron Radiotherapy for Keloids

PURPOSE/OBJECTIVE(S)

The increasing incidence of keloid has seriously affected people's physical and mental health, and the postoperative recurrence rate is as high as 50-80%. Postoperative radiotherapy has been shown to significantly reduce the recurrence of keloid. Given the different treatment patterns in different institutions, we tried to analyze the data of patients in our center.

MATERIALS/METHODS

We retrospectively analyzed the clinical data of 455 patients with 498 keloids treated in our institution from 2010 to 2017. All patients received a four-fraction electron radiotherapy with single dose of 4 Gy within 24 hours of surgery. The recurrence and adverse reaction of immediate adjuvant radiotherapy in these patients was evaluated.

RESULTS

At the last follow-up date, 130 (26.5%) keloids had recurred after a middle follow-up of 68.1 months (42.6-129.9 months). The recurrence rates of 1 year, 3 years and 5 years were respectively14.5%, 18.7% and 21%. Recurrence rates vary depending on the keloid location. Among them, the recurrence rate of ear was low with 14% (43/298). Face, head neck and limbs was moderate with 38.8% (17/44) and 33.3% (8/24). Chest and Suprapubic region had a high recurrence rate of 50.8% (32/64) and 47.8% (33/69). Among the patients with recurrence, 16.9% (22/130) felt that their symptoms were better than before treatment, and 37.7% (49/130) were not worsen, which was acceptable. Multivariate analysis showed that age and duration of postoperative pruritus pain were correlated with recurrence (P = 0.036; P = 0.02). Radiotherapy combined with steroid and silicone reduced the recurrence rate compared with radiotherapy alone (P = 0.015). During treatment and follow-up, Infection occurred in 2 patients and cutaneous fibroblastoma in 1 patient.

CONCLUSION

Our radiotherapy regimen can effectively reduce the recurrence rate and improve the symptoms of patients with keloids, especially ear keloids. High recurrence sites need further improvement of radiotherapy dose and fraction. Combination of multiple treatments is better than single treatment.

Potential Predictive Value of Intravoxel Incoherent Motion Magnetic Resonance for Xerostomia of Nasopharyngeal Carcinoma

PURPOSE/OBJECTIVE(S)

Xerostomia, caused by radiation-induced parotid damage, is the most commonly reported complications of radiotherapy (RT) to nasopharyngeal carcinoma (NPC). This study aimed to evaluate the value of IVIM MR in monitoring radiation parotid gland damage and predicting the risk of xerostomia.

MATERIALS/METHODS

A total of 54 patients were enrolled and underwent IVIM MR scans at before RT, after the fifth fraction, halfway through the course of RT, and at the end of radiotherapy. The parameters of IVIM MR include pseudo-diffusion coefficient (D*), perfusion fraction (f), and pure diffusion coefficient (D). The degree of xerostomia in NPC patients was assessed before each MR examination using the acute radiation morbidity scoring criteria proposed by the Radiation Therapy Oncology Group (RTOG). Concurrently, the time when the patient first reported suffering from xerostomia was recorded. The IVIM parameters trend throughout the RT, and the relationships between IVIM parameters and xerostomia, were analyzed.

RESULTS

All of the IVIM parameters increased from pre-RT to post-RT significantly (all p < 0.001). The increase rate of D from pre-RT to halfway through the RT was 32.61%, which was significantly higher than 15.64% from halfway to post-RT (p<0.001), indicating that cell necrosis in the first half of treatment is significantly higher than that in the second half. Both D* and F had significantly increased from pre-RT to halfway through the radiotherapy (p<0.001), with an increase rate of 19.58% and 29.38%, respectively. However, no significant increase was observed from Halfway to post-RT (p>0.05), with an increase rate of 4.10% and 8.30%, respectively. This may be due to radiation-induced vasculitic dilation that is significant in the first half of the radiotherapy but plateaus in the second half. Pre-D (OR = 23.85; 95% CI = 2.39, 237.82; p = .007) and pre-D* (OR = 0.75; 95% CI = 0.63, 0.91; p = 0.003) are independent influencing factors for xerostomia at 3 months after the completion of RT. D and F were significantly higher after the fifth fraction compared with Pre-RT (both p<0.05), respectively increased 31.25% and 25.16%. D* increase by 15% (p = 0.081). IVIM scans can assess parotid gland damage early. And the average time of parotid damage underwent IVIM scan was 5.99 ± 0.84 (day), much earlier than 11.84 ± 2.74 (day) according to RTOG.

CONCLUSION

Our study indicates that IVIM MR can dynamically monitor radiotherapy-induced parotid gland damage, and much earlier and objectively than RTOG.

Long-Term Results of Induction Chemotherapy for Esophageal Squamous Cell Carcinoma Receiving Concurrent Chemoradiotherapy

PURPOSE/OBJECTIVE(S)

This study aimed to investigate the long-term clinical outcomes and toxicities of induction chemotherapy (IC) followed by concurrent chemoradiotherapy (CCRT) versus CCRT alone in patients with esophageal squamous cell carcinoma (ESCC).

MATERIALS/METHODS

Between 2008 and 2022, 271 ESCC patients who received definitive CCRT (IC followed by CCRT, n = 72; CCRT alone, n = 199) were enrolled. Radiotherapy technique included intensity modulated radiation therapy (IMRT) or volumetric modulated arc therapy (VMAT). Through a propensity score matched (PSM) method, 71 patients receiving IC and CCRT were matched 1:1 to patients who received CCRT alone, according to age, gender, performance status, tumor length, and pre-treatment TN stage. The Kaplan-Meier method and Cox proportional hazards model were applied to analyze survival and prognosis.

RESULTS

The IC + CCRT group had no improvement in 5-year overall survival (OS) rate (39.0% vs 29.3%, p = 0.360), recurrence-free survival (RFS) rate (39.0% vs 26.9%, p = 0.142), and distant metastasis-free survival (DMFS) rate (33.6% vs 27.2%, p = 0.515) compared with the CCRT group. The overall clinical response rate was 45.1% after IC in the IC + CCRT group. The IC responders (CR + PR + SD) group showed more favorable 5-year OS (41.7% vs. 14.3% vs. 29.3%, p < 0.001), RFS (41.7% vs. 14.3% vs. 26.9%, p < 0.001) and DMFS (37.3% vs. 0% vs. 27.2%, p < 0.001) compared with the IC non-responders (PD) group and the CCRT group. Besides, the 5-year OS rate (65.6% vs. 17.6% vs. 29.3%, p < 0.001), RFS rate (65.6% vs. 17.6% vs. 26.9%, p < 0.001), and DMFS rate (62.5% vs. 10.3% vs. 27.2%, p < 0.001) of the IC good responders (CR + PR) were significantly higher than that of the IC poor responders (SD + PD) and CCRT group. Multivariate analysis revealed that total radiotherapy time (≥ 49 days) and AJCC stage (Ⅲ/Ⅳ) were independent predictive factors of OS, RFS and DMFS. Besides, age was an independent predictive factor of DMFS. No significant difference was observed in the rates of grades 3-4 toxicities between both groups.

CONCLUSION

Our results showed the addition of IC to CCRT was not superior to CCRT in unselected ESCC patients, while IC responders could benefit from this regime without increase in toxicities.

Inter-fractional Assessment during MR-guided Online Adaptive Radiotherapy for Glioblastoma

PURPOSE/OBJECTIVE(S)

Magnetic resonance image (MRI) guided radiation therapy has the potential to improve outcomes for glioblastoma by adapting to tumor changes during radiation therapy. This study aimed to assess the feasibility and potential benefits of MR-guided online adaptive radiotherapy (MRgOART) for patients with glioblastoma.

MATERIALS/METHODS

Twenty consecutive patients with glioblastoma were treated with MRgOART of 60 Gy in 30 fractions by the 1.5 T MR-Linac. The MRgOART fractions employed daily MR scans and the contours were utilized to create each adapted plan. The gross tumor volume (GTV) and clinical target volume (CTV) were delineated on MRI of pre-treatment simulation (Fx0) and all fractions (Fx1, Fx2, Fx3 ... Fx30) to evaluate the inter-fractional changes. These changes were quantified using absolute/relative volume (∆V), Dice similarity coefficient (DSC) and Hausdorff distance (HD) metrics. The reference treatment plans were generated using step-and-shoot IMRT and utilized 7-9 beam groups on original CT. Before the treatment, a synthetic CT (sCT) quality assurance (QA) process was performed to assess the dose accuracy of bulk relative electron density (rED) assignment for online MRI based treatment plan in terms of gamma analysis, point dose comparison and dose volume histogram (DVH) parameters. Then, the online adaptative treatment plans were obtained by re-optimizing based on the contours on daily pre-treatment MRI by "adapt to shape" workflow. Non-adaptive plans for each patient were generated by recalculating the dose from the reference plans on daily online MRI by "adapt to position" workflow. GTV and CTV coverage and organ at risk (OAR) constraints were used to compare non-adaptive and adaptive plans.

RESULTS

For both criteria, the 1%/1mm (98.58%±0.15%) and 2%/2mm (99.88%±0.18%) gamma passing rate results were always clinically acceptable in sCT QA process. The differences on point dose and DVH parameters between the plans based on sCT and original CT were less than 1%. A total of 20 patients with 600 fractions were evaluated. The results showed that large inter-fractional changes for GTV limited the efficacy of radiation therapy (DSC: 0.78±0.08, HD: 20.94±3.64mm, ∆V: 2.92%±6.36%). The inter-fractional CTV changes were smaller (DSC: 0.91±0.04, HD: 15.31±3.09mm, ∆V: 1.41%±1.29%). GTV coverage of non-adaptive plans was below the prescribed coverage in 228/600 fractions (38%), with 90 (15%) failing by more than 10%. For CTV coverage of non-adaptive plans, the changes were less than 5%. Online adaptative plans improved GTV and CTV coverage significantly (p<0.001) to 99%. The adaptive plans also had lower dose to whole brain than non-adaptive plans (p<0.001).

CONCLUSION

Significant inter-fractional tumor changes could be found during radiotherapy in patients with glioblastoma treated by the 1.5 T MR-Linac. Daily MR-guided re-optimization of treatment plans corrected for day-to-day anatomical variations and resulted in adequate target coverage in all fractions.

Investigating Incidence of Nausea and Vomiting in Patients Receiving Concurrent Chemoradiotherapy: A Real-World Cohort Study

PURPOSE/OBJECTIVE(S)

Vomiting and nausea (VN) caused by anticancer agents and/or radiation therapy (RT) can significantly affect a patient's quality of life, leading to poor compliance with further anticancer agents and/or RT. Few studies pay attention to synergistic effect of RT and concurrent highly emetogenic chemotherapy for inducing vomiting and nausea. The aim of this real-world study is to investigate the incidence of VN in patients receiving concurrent chemoradiotherapy (CCRT).

MATERIALS/METHODS

From June 2022 to December 2022, patients receiving concurrent chemoradiotherapy in our center were consecutively enrolled in this study. Patients received moderate and low emetic agents were excluded. The antiemesis regimens were NK1 receptor antagonist plus 5-HT3 antagonist and dexamethasone (NHD) with or without olanzapine, which were recommended by guideline of National Comprehensive Cancer Network. Acute and delayed VN were analyzed in the following stratification factors: tumor site and antiemesis regimen. Acute VN usually occurred after administration of anticancer agents and commonly resolves within the first 24 hours. Delayed VN develops in patients more than 24 hours after anticancer agent administration. The grade of VN was evaluated according to Common Terminology Criteria for Adverse Events Criteria.

RESULTS

A total of 312 patients were enrolled for analysis. During the CCRT period, the incidence rate of acute VN in all patients was 28.2%, the delayed VN occurred in 139 of 312 patients (44.6%). The incidence rate of acute nausea in head and neck, thorax and abdomen were 33.8%, 28.9% and 25.2%, respectively. The incidence rate of acute vomiting in head and neck, thorax and abdomen were 7.0%, 3.9% and 5.2%, respectively. The incidence rate of delayed nausea in head and neck, thorax and abdomen were 51.1%, 35.5% and 45.9%, respectively. The incidence rate of delayed vomiting in head and neck, thorax and abdomen were 14.0%, 5.3% and 9.6%, respectively. There were not significant differences between NHD regimen and NHD plus olanzapine in VN (acute nausea, 25.5% vs. 30.3%, P = 0.356; acute vomiting, 4.4% vs. 6.8%, P = 0.352; delayed nausea, 40.1% vs. 48%, P = 0.166; delayed vomiting, 8.0% vs. 10.8%, P = 0.4). Multivariate logistic regression analysis showed age <50 years (P = 0.030. HR, 95% CI: 1.893, 1.062-3.374) and history of vomiting = 0.017, HR, 95% CI: 2.249, 1.154-4.384) were risk factor for acute nausea; female (P = 0.026, HR, 95% CI: 4.254, 1.192-15.186) and sleeping time <7 hours (p = 0.049, HR, 95% CI: 3.373, 1.003-11.344) were risk factors for acute vomiting; pregnancy (P = 0.011, HR, 95% CI: 2.424, 1.228-4.783) was risk factor for delayed nausea; pregnancy = 0.013, HR, 95% CI: 3.060, 1.269-7.380) and history of vomiting = 0.020, HR, 95% CI: 2.845, 1.182-6.844) were risk factors for delayed vomiting in patients receiving CCRT.

CONCLUSION

CCRT still contributed high incidence of delayed nausea in patients receiving standard antiemesis regimen.

CT vs. MRI: Which is More Accurate in Grading Rectal Wall Infiltration after Hydrogel Spacer Placement for Prostate Cancer Patients?

PURPOSE/OBJECTIVE(S)

The purpose of this study was to evaluate the incidence and severity of rectal wall infiltration (RWI) in prostate cancer patients after rectal hydrogel spacer implantation, a commonly used procedure to minimize rectal radiation exposure during prostate radiotherapy. The study aimed to determine correlation of RWI using computed tomography (CT) scans and magnetic resonance imaging (MRI) scans in order to determine the optimal post-placement imaging modality.

MATERIALS/METHODS

This retrospective study was conducted on 370 patients diagnosed with localized prostate cancer who underwent rectal hydrogel spacer placement from 2020 to 2022. CT scans were performed on all patients, with a smaller subset also undergoing MRI scans. The images were independently evaluated by three radiation oncologists to grade RWI levels using a standardized scoring system based on CT and MRI images after hydrogel placement. The levels were categorized as 0 (no RWI), 1 (focal RWI), 2 (moderate RWI), and 3 (significant RWI).

RESULTS

Any grade of RWI was identified in 79.8% of men with the majority (41%) being RWI grade 1. The median time for CT scans was 9 days after hydrogel spacer placement and 14.5 days for MRI scans. For the subset of patients with both CT and MRI scans after spacer (mostly SpaceOAR Vue), RWI was detected in 58.33% of patients based on CT and 61.11% of patients based on MRI. Table 1 shows the mean percentage of patients with each score of RWI for each imaging modality. MRI was more likely to lead to a designation of RWI of any grade compared to CT and more often led to detection of RWI grades 2-3.

CONCLUSION

Our findings demonstrate that the incidence and severity of RWI may be higher than previously reported in clinical trials and that MRI may be a more sensitive imaging modality. Caution is needed in the utilization of rectal spacer gels given the potential for complications with misplacement prior to radiation therapy. Further study is warranted to determine the potential impact of low-grade RWI on the safety of subsequent treatment.

Low-Dose Fractionated Radiotherapy Combined with Neoadjuvant Chemotherapy for T3-4 Nasopharyngeal Carcinoma Patients: The Preliminary Results of a Phase II Randomized Controlled Trial

PURPOSE/OBJECTIVE(S)

Over 70% of NPC patients were local advanced NPC (LANPC). The 5-year local recurrence-free survival rate is only 70% in T3-4 patients. Neoadjuvant chemotherapy (NACT) followed with concurrent chemoradiotherapy (CCRT) was recommended for LANPC patients. Low-dose fractionated radiotherapy (LDFRT), which is <100cGy, induces enhanced cell killing by the hyper-radiation sensitivity phenomenon and potentiates effects of chemotherapy. The synergy of LDFRT and NACT has not been used in the clinical practice and few studies focused on it. A single arm study found the ORR of primary site was improved to 90% for head and neck squamous carcinoma patients treated with LDFRT and NACT. Our previous study found the ORR of lymph nodes was higher in LDFRT group for high-risk LANPC patients. However, another study showed there was no significant difference between LDFRT and control group for LANPC patients. So, we aimed to investigate the potential efficacy of this novel neoadjuvant therapy for T3-4 NPC patients.

MATERIALS/METHODS

A total of 60 pathological confirmed T3-4 (UICC/AJCC8th) NPC patients were prospectively enrolled in our study. They were randomly assigned to two groups. For the LDFRT group, the patients received 3 cycles of NACT (docetaxel 75mg/m2 D1, cisplatin 80mg/m2 D1) with LDFRT, and followed with CCRT. LDFRT was delivered as 50cGy per fraction twice a day to primary site on D1,2 for each cycle of NACT. The patients in the control group only received NACT and followed with CCRT. All the patients underwent IGRT. RECIST criteria and CTCAE 5.0 was used to evaluate the ORR and toxicity at post-NACT and the completion of CCRT.

RESULTS

From February 2022 to December 2022, 60 T3-4 NPC patients were included, and 30 patients for each group. For the primary site, the median volume reduction rate and the ORR after NACT was significantly improved in LDFRT group (69.27% vs 40.10%, p<0.001;93.33% vs 73.33%, p = 0.038). For the median volume reduction rate of primary site and lymph node, it was also obviously improved in LDFRT group (86.59% vs 55.43%, p<0.001). Though there was a tendency of ORR improvement in LDFRT group, but no significant difference (96.67% vs 83.33%, p = 0.195). After the completion of CCRT, the median volume reduction rate of primary site had an increased tendency in LDFRT group (96.16% vs 88.3%, p = 0.065), but the ORR had no statistical significance (LDFRT group: CR 45.8%, PR 54.2%; control group: CR 37.5%, PR 62.5%). For the toxicity, the incidence of grade 3-4 adverse events had no difference between two groups (p = 0.786). No grade 5 adverse events occurred.

CONCLUSION

LDFRT combined with NACT could obviously improve the median volume reduction rate and ORR of primary tumor for T3-4 NPC patients, and the toxicity was similar and tolerable. This novel treatment could be a promising strategy to improve treatment response and needed to be confirmed further.

Long-Term Survival Outcome for Metastatic Nasopharyngeal Carcinoma Patients Receiving Radiation to Primary and Metastatic Sites with Palliative Chemotherapy

PURPOSE/OBJECTIVE(S)

A total of 6% - 8% of NPC patients were initial diagnosed as distant metastatic disease. The median overall survival (OS) is only 10-15 months with palliative chemotherapy for these patients. A phase III study showed that palliative chemotherapy combined with radical radiotherapy to primary site could be a newly effective treatment method for metastatic NPC. Another phase 2, RCT found that the patients who had the solid tumors with 1-5 metastases received standard palliative care plus stereotactic body radiation therapy (SABR), and the 5-year OS were improved to 42.3%. Nevertheless, there was few studies focus on the radiation to both primary site and metastatic lesions. Therefore, we aimed to investigate the potential clinical benefits for initial diagnosed metastatic NPC patients with radiation to both primary site and distant metastatic lesions plus palliative chemotherapy.

MATERIALS/METHODS

Metastatic NPC patients treated with radiation to both primary site and distant metastatic lesions plus palliative chemotherapy were retrospectively collected in our hospital from May 2008 to May 2022. For treatment group, all patients underwent IGRT according to ICRU reports 50 and 62. The prescribed dose for primary site: GTVT: ≥66Gy, GTVn: ≥66Gy, CTV1: 60-66Gy, CTV2 54-60Gy, CTVln 50-54Gy. And the prescribed dose for distant metastatic lesions was more than 30Gy. For the control group, the patients treated with palliative chemotherapy were selected by propensity score matching from our hospital. The regimen for palliative chemotherapy was cisplatin-based chemotherapy every three weeks (100mg/m2 D1) for both groups. Kaplan-Meier method was used to analyze the OS. Cox regression model was used for multivariate analysis.

RESULTS

A total of 54 metastatic NPC patients with radiation to both primary site and distant metastatic lesions were retrospectively included in the treatment group, and another 54 patients were selected as the control group. The median follow-up time was 52 months. In the treatment group, the median age was 52 years (37-82), male (68%), female (32%), the main metastatic sites were bone (36 cases, 66%), lung (18 cases, 33%) and liver (10 cases, 18%). There were 23 oligometastasis cases and 31 cases. 3-year and 5-year OS in the treatment group were both dramatically improved than control group (63.2% vs 50.6%, p<0.05; 49.6% vs 38.9%, p<0.05). Multivariate analysis showed that T stage, liver metastatic lesion and oligometastases were the independent prognostic factors for them.

CONCLUSION

Palliative chemotherapy combined with radiation to primary sites and distant metastatic lesions might improve the OS for initial diagnosed distant metastatic NPC patients. More prospective clinical trials were needed to confirm it further.

Treatment Response Prediction Using a Combination of Hematological Biomarkers and CT Deep Learning Radiomics in Locally Advanced Esophageal Squamous Cell Carcinoma

PURPOSE/OBJECTIVE(S)

To assess the complementary value of hematological biomarkers to deep learning-radiomic models for assessing esophageal squamous cell carcinoma (ESCC) pathological complete response (pCR) after neoadjuvant chemoradiotherapy (nCRT), which will help to provide a reference for the following clinical study of esophageal preservation.

MATERIALS/METHODS

A total of 157 patients with ESCC were enrolled and divided into a training cohort (n = 111) and a validation cohort (n = 47). Computed tomography (CT) was performed for all patients 2 weeks before and 6 weeks after nCRT. In addition, clinicopathological factors and hematological parameters before nCRT were collected. Deep learning and handcrafted radiomic features were extracted from segmented regions of interest (ROIs) from pretreatment (ROI1) and posttreatment (ROI2) CT, which represented the features of the pre- and posttreatment tumors, respectively. The minimum redundancy maximum relevance (mRMR) and least absolute shrinkage and selection operator (LASSO) algorithms were used for feature selection, and logistic regression (LR) was used as the classifier. The deep learning radiomic nomogram (DLRN) was then developed based on the rad-scores and independent clinicopathological risk factors. The model was assessed using area under the receiver operating characteristic (ROC) curve analysis, calibration curve analysis and decision curve analysis and verified with both 10-fold cross-validation and internal validation using bootstrap resampling with 1000 replicates.

RESULTS

Rad-scores were constructed with 8 features, which were finally selected as the most predictive features from ROI 1 and ROI 2. The neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), albumin and rad-scores were incorporated into the DLRN, which achieved good prediction performance, with areas under the ROC curve of 0.888 (95% CI, 0.824-0.951, p <0.05) for the training cohort and 0.873 (95% CI, 0.772-0.974, p <0.05) for the validation cohort. On the training set, the DLRN achieved an AUC of 0.882 in 10-fold cross-validation, and after internal validation, the area under the ROC curve still reached 0.884. The DLRN performed significantly better than the clinical model and radiomics models (p<0.05). IDI and continuous NRI showed significant improvement for the DLRN when incorporating radiomics features and hematological parameters (IDI = 0.3399, P <0.001; continuous NRI = 1.141, P <0.001; categorical NRI = 0.3836, P <0.001). Calibration curves (p > 0.05) and DCA demonstrated that the DLRN was useful for pCR prediction and produced a greater net benefit than the clinical model and radiomics models.

CONCLUSION

Incorporation of radiomics features and hematological parameters into the DLRN improved pCR prediction after nCRT in ESCC. Enhanced pCR predictability may improve patient selection before surgery, providing clinical application value for the use of active surveillance.

Verification and Mechanism Exploration of CDK4 Alterations on Influencing Radiotherapy Sensitivity in Small Cell Lung Cancer

PURPOSE/OBJECTIVE(S)

In this study, we aimed to explore the changes of functional phenotype before and after radiotherapy through vitro and vivo experiments. The potential pathway was preliminarily clarified.

MATERIALS/METHODS

Firstly, the relationships between the prognosis and the expression of CDK4 protein in SCLC patients treated with definitive chemoradiotherapy were explored. Then the stable overexpressed/knockdown CDK4 and negative control transfecting SCLC cell lines were established to monitor the changes of cell proliferation, migration, invasion, apoptosis and cell cycle after increasing radiation doses according to a cell counting kit assay, transwell cell migration and invasion assay, apoptosis cell cycle assay and BALB/c mouse model of subcutaneously transplanted tumor. The potential signal pathways were confirmed via KEGG pathway enrichment analysis and western blot.

RESULTS

Compared with patients with lower CDK4 protein expression, prognosis of those with high CDK4 protein expression was decreased significantly (p < 0.05). The cell activity, migration and invasion ability of overexpression/knockdown CDK4 and negative control group were all decreased with increasing radiation doses, but the activity, migration and invasion ability of cells with overexpression CDK4 was stronger after same dose X-ray irradiation (p<0.01). For group with knockdown CDK4, it showed lower cell activity, migration and invasion than negative control group. After X-ray irradiation, the apoptotic ratio of all groups increased. And cells with overexpressed CDK4 displayed significantly reduced apoptosis, less G0/G1 phase cells, and improved M phase cells than the control group. In addition, compared with negative control group, gross tumor volume of overexpression CDK4 group decreased much smaller after X-ray irradiation. H1339 cells with overexpression CDK4 and negative control group were sequenced by transcriptomic sequencing before and after radiotherapy. Taken together, differential genes were consistently enriched in MAPK pathway. Western blot showed that, compared with the negative control group, overexpression CDK4 group of H1339 and SW1271 cells after radiotherapy all showed significant changes on pERK proteins in the ERK pathway increased significantly (P<0.001).

CONCLUSION

In this study, the overexpression/knockdown CDK4 and negative control group were successfully constructed in H1339 and SW1271 cells, revealing the radiotherapy resistance of CDK4 alterations in vitro and in vivo experiment. And CDK4 alterations was shown to promote radiotherapy resistance through phosphorylation of MAPK/ERK signaling pathway in SCLC.

scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic data

Technological advances have now made it possible to simultaneously profile the changes of epigenomic, transcriptomic and proteomic at the single cell level, allowing a more unified view of cellular phenotypes and heterogeneities. However, current computational tools for single-cell multi-omics data integration are mainly tailored for bi-modality data, so new tools are urgently needed to integrate tri-modality data with complex associations. To this end, we develop scMHNN to integrate single-cell multi-omics data based on hypergraph neural network. After modeling the complex data associations among various modalities, scMHNN performs message passing process on the multi-omics hypergraph, which can capture the high-order data relationships and integrate the multiple heterogeneous features. Followingly, scMHNN learns discriminative cell representation via a dual-contrastive loss in self-supervised manner. Based on the pretrained hypergraph encoder, we further introduce the pre-training and fine-tuning paradigm, which allows more accurate cell-type annotation with only a small number of labeled cells as reference. Benchmarking results on real and simulated single-cell tri-modality datasets indicate that scMHNN outperforms other competing methods on both cell clustering and cell-type annotation tasks. In addition, we also demonstrate scMHNN facilitates various downstream tasks, such as cell marker detection and enrichment analysis.

[Clinical features of non-cirrhotic portal hypertension in patients with common variable immunodeficiency]

We wished to summarize the clinical features of common variable immunodeficiency (CVID) complicated by non-cirrhotic portal hypertension (NCPH) and to deepen our understanding of it. The case data of CVID complicated with NCPH admitted to Peking Union Medical College Hospital from January 1983 to May 2021 were analyzed retrospectively to summarize their clinical characteristics. Six patients with CVID combined with NCPH (three of each sex; 16-45 years) were assessed. Four patients had portal hypertension. All patients had anemia, splenomegaly, a normal serum level of albumin and transaminases, and possibly increased levels of alkaline phosphatase and gamma-glutamyl transpeptidase. Two patients were diagnosed with esophagogastric fundic varices by gastroscopy. Two patients underwent splenectomy (which improved hematologic abnormalities partially). Four patients had autoimmune disease. Two cases were diagnosed with nodular regenerative hyperplasia (NRH) upon liver biopsy. Six patients were administered intravenous immunoglobulin-G (0.4-0.6 g/kg bodyweight) once every 3-4 weeks as basic therapy. Often, CVID complicated with NCPH has: (1) The manifestations of portal hypertension as the primary symptom. (2) Autoimmune-related manifestations. Imaging can provide important diagnostic clues. The etiology may be related to hepatic NRH and splenomegaly due to recurrent infections.

Homeobox transcription factor HbxA influences expression of over one thousand genes in the model fungus Aspergillus nidulans

In fungi, conserved homeobox-domain proteins are transcriptional regulators governing development. In Aspergillus species, several homeobox-domain transcription factor genes have been identified, among them, hbxA/hbx1. For instance, in the opportunistic human pathogen Aspergillus fumigatus, hbxA is involved in conidial production and germination, as well as virulence and secondary metabolism, including production of fumigaclavines, fumiquinazolines, and chaetominine. In the agriculturally important fungus Aspergillus flavus, disruption of hbx1 results in fluffy aconidial colonies unable to produce sclerotia. hbx1 also regulates production of aflatoxins, cyclopiazonic acid and aflatrem. Furthermore, transcriptome studies revealed that hbx1 has a broad effect on the A. flavus genome, including numerous genes involved in secondary metabolism. These studies underline the importance of the HbxA/Hbx1 regulator, not only in developmental processes but also in the biosynthesis of a broad number of fungal natural products, including potential medical drugs and mycotoxins. To gain further insight into the regulatory scope of HbxA in Aspergilli, we studied its role in the model fungus Aspergillus nidulans. Our present study of the A. nidulans hbxA-dependent transcriptome revealed that more than one thousand genes are differentially expressed when this regulator was not transcribed at wild-type levels, among them numerous transcription factors, including those involved in development as well as in secondary metabolism regulation. Furthermore, our metabolomics analyses revealed that production of several secondary metabolites, some of them associated with A. nidulans hbxA-dependent gene clusters, was also altered in deletion and overexpression hbxA strains compared to the wild type, including synthesis of nidulanins A, B and D, versicolorin A, sterigmatocystin, austinol, dehydroaustinol, and three unknown novel compounds.

dbCAN3: automated carbohydrate-active enzyme and substrate annotation

Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server for automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) was further developed in 2018 as a meta server to combine multiple tools for improved CAZyme annotation. dbCAN2 also included CGC-Finder, a tool for identifying CAZyme gene clusters (CGCs) in (meta-)genomes. We have updated the meta server to dbCAN3 with the following new functions and components: (i) dbCAN-sub as a profile Hidden Markov Model database (HMMdb) for substrate prediction at the CAZyme subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) with known glycan substates of the dbCAN-PUL database for substrate prediction at the CGC level; (iii) a majority voting method to consider all CAZymes with substrate predicted from dbCAN-sub for substrate prediction at the CGC level; (iv) improved data browsing and visualization of substrate prediction results on the website. In summary, dbCAN3 not only inherits all the functions of dbCAN2, but also integrates three new methods for glycan substrate prediction.

Predictive value of DEEPVESSEL-fractional flow reserve and quantitative plaque analysis based on coronary CT angiography for major adverse cardiac events

AIM

To investigate the predictive value of the combination of DEEPVESSEL-fractional flow reserve (DVFFR) and quantitative plaque analysis using coronary computed tomographic angiography (CCTA) for major adverse cardiac events (MACE).

METHOD

In this retrospective study, data from 69 vessels from 58 consecutive patients were collected. These patients who underwent coronary angiography (CAG) with DVFFR were divided into MACE-positive and MACE-negative groups. DVFFR measurements were obtained from CCTA images acquired before CAG, and an FFR or DVFFR value ≤ 0.80 was considered haemodynamically significant. CCTA images were analysed quantitatively using automated software to obtain the following indices: total plaque volume (TPV) and burden (TPB), calcified plaque volume (CPV) and burden (CPB), non-calcified plaque volume (NCPV) and burden (NCPB), low-attenuation plaque (LAP), minimum lumen area (MLA), stenosis grade (SG) and lesion length (LL). Univariate and multivariate logistic regression, correlation, and receiver operating characteristic (ROC) analyses were used for statistical analysis.

RESULTS

DVFFR was highly correlated with invasive FFR (R=0.728), and the Bland-Altman plot showed good agreement between DVFFR and FFR (95% CI: -0.109-0.087) on a per-vessel level. DVFFR showed a high diagnostic performance in identifying abnormal haemodynamic vessels, with an area under the ROC curve (AUC) of 0.984. In multivariate analysis, the following biomarkers were predictors of MACE: DVFFR ≤ 0.8, SG, TPB, NCPB, and LL values. The combination of the above independent risk factors yielded the most valuable prediction for MACE (AUC:0.888).

CONCLUSIONS

DVFFR was highly correlated with FFR with satisfactory diagnostic accuracy. DVFFR, together with plaque analysis indices, yielded valuable predictions for MACE.

[Progress in research of relationship between metal or metalloid and persistent organic pollutants exposures and cardiovascular disease]

Cardiovascular disease (CVD) is the leading cause of mortality and healthy life expectancy loss, ranking first in causing the global burden of disease. In addition to the traditional CVD risk factors, such as hypertension and diabetes, environmental chemical pollutants may also play a role in the development of CVD. This paper summarizes the evidence regarding the relation of exposures to metal or metalloid and persistent organic pollutants with risk for CVD and introduces the research progress in the relation between the exposures to two environmental chemical pollutants and CVD risk. The study aims to provide scientific evidence for the effective prevention of CVD through the management of chemical pollutants in environment.

Genome mining for anti-CRISPR operons using machine learning

MOTIVATION

Encoded by (pro-)viruses, anti-CRISPR (Acr) proteins inhibit the CRISPR-Cas immune system of their prokaryotic hosts. As a result, Acr proteins can be employed to develop more controllable CRISPR-Cas genome editing tools. Recent studies revealed that known acr genes often coexist with other acr genes and with phage structural genes within the same operon. For example, we found that 47 of 98 known acr genes (or their homologs) co-exist in the same operons. None of the current Acr prediction tools have considered this important genomic context feature. We have developed a new software tool AOminer to facilitate the improved discovery of new Acrs by fully exploiting the genomic context of known acr genes and their homologs.

RESULTS

AOminer is the first machine learning based tool focused on the discovery of Acr operons (AOs). A two-state HMM (hidden Markov model) was trained to learn the conserved genomic context of operons that contain known acr genes or their homologs, and the learnt features could distinguish AOs and non-AOs. AOminer allows automated mining for potential AOs from query genomes or operons. AOminer outperformed all existing Acr prediction tools with an accuracy = 0.85. AOminer will facilitate the discovery of novel anti-CRISPR operons.

AVAILABILITY AND IMPLEMENTATION

The webserver is available at: http://aca.unl.edu/AOminer/AOminer_APP/. The python program is at: https://github.com/boweny920/AOminer.

Two interacting basic helix-loop-helix transcription factors control flowering time in rice

Flowering time is one of the most important agronomic traits affecting the adaptation and yield of rice (Oryza sativa). Heading date 1 (Hd1) is a key factor in the photoperiodic control of flowering time. In this study, two basic helix-loop-helix (bHLH) transcription factors, Hd1 Binding Protein 1 (HBP1) and Partner of HBP1 (POH1) were identified as transcriptional regulators of Hd1. We generated knockout mutants of HBP1 and ectopically expressed transgenic lines of the two bHLH transcription factors and used these lines to investigate the roles of these two factors in regulating flowering time. HBP1 physically associated with POH1 forming homo- or heterodimers to perform their functions. Both HBP1 and POH1 bound directly to the cis-acting elements located in the promoter of Hd1 to activate its expression. CRISPR/Cas9-generated knockout mutations of HBP1, but not POH1 mutations, promoted earlier flowering time; conversely, HBP1 and POH1 overexpression delayed flowering time in rice under long-day and short-day conditions by activating the expression of Hd1 and suppressing the expression of Early heading date 1 (Ehd1), Heading date 3a (Hd3a), and Rice Flowering locus T 1 (RFT1), thus controlling flowering time in rice. Our findings revealed a mechanism for flowering time control through transcriptional regulation of Hd1 and laid theoretical and practical foundations for improving the growth period, adaptation, and yield of rice.

BOS1 is a basic helix-loop-helix transcription factor involved in regulating panicle development in rice

Panicle development is crucial to increase the grain yield of rice (Oryza sativa). The molecular mechanisms of the control of panicle development in rice remain unclear. In this study, we identified a mutant with abnormal panicles, termed branch one seed 1-1 (bos1-1). The bos1-1 mutant showed pleiotropic defects in panicle development, such as the abortion of lateral spikelets and the decreased number of primary panicle branches and secondary panicle branches. A combined map-based cloning and MutMap approach was used to clone BOS1 gene. The bos1-1 mutation was located in chromosome 1. A T-to-A mutation in BOS1 was identified, which changed the codon from TAC to AAC, resulting in the amino acid change from tyrosine to asparagine. BOS1 gene encoded a grass-specific basic helix-loop-helix transcription factor, which is a novel allele of the previously cloned LAX PANICLE 1 (LAX1) gene. Spatial and temporal expression profile analyses showed that BOS1 was expressed in young panicles and was induced by phytohormones. BOS1 protein was mainly localized in the nucleus. The expression of panicle development-related genes, such as OsPIN2, OsPIN3, APO1, and FZP, was changed by bos1-1 mutation, suggesting that the genes may be the direct or indirect targets of BOS1 to regulate panicle development. The analysis of BOS1 genomic variation, haplotype, and haplotype network showed that BOS1 gene had several genomic variations and haplotypes. These results laid the foundation for us to further dissect the functions of BOS1.

[Thinking about development of multi-channel surveillance and multi-dimensional early warning system of emerging respiratory communicable diseases]

The world has paid a heavy price for the pandemic of the emerging respiratory communicable disease, so more concern about communicable disease surveillance and early warning has been aroused. This paper briefly reviews the establishment of the surveillance and early warning system of respiratory communicable diseases in China, discusses its future development and introduces the novel surveillance methods and early warning models for the purpose of establishment of a multi-channel surveillance and multi-dimensional early warning system of communicable diseases in the future and the improvement of the prevention and control of emerging respiratory communicable diseases in China.

Braille recognition by E-skin system based on binary memristive neural network

Braille system is widely used worldwide for communication by visually impaired people. However, there are still some visually impaired people who are unable to learn Braille system due to various factors, such as the age (too young or too old), brain damage, etc. A wearable and low-cost Braille recognition system may substantially help these people recognize Braille or assist them in Braille learning. In this work, we fabricated polydimethylsiloxane (PDMS)-based flexible pressure sensors to construct an electronic skin (E-skin) for the application of Braille recognition. The E-skin mimics human touch sensing function for collecting Braille information. Braille recognition is realized with a neural network based on memristors. We utilize a binary neural network algorithm with only two bias layers and three fully connected layers. Such neural network design remarkably reduces the calculation burden and, thus, the system cost. Experiments show that the system can achieve a recognition accuracy of up to 91.25%. This work demonstrates the possibility of realizing a wearable and low-cost Braille recognition system and a Braille learning-assistance system.

Root cell wall remodeling: A way for exopolysaccharides to mitigate cadmium toxicity in rice seedling

Exopolysaccharides (EPS) are macromolecules with environment beneficial properties. Currently, numerous studies focus on the absorption of heavy metals by EPS, but less attention has been paid to the effects of EPS on the plants. This study explored the effects of EPS from Lactobacillus plantarum LPC-1 on the structure and function of cell walls in rice seedling roots under cadmium (Cd) stress. The results showed that EPS could regulate the remodeling process of the cell walls of rice roots. EPS affects the synthesis efficiency and the content of the substances that made up the cell wall, and thus plays an essential role in limiting the uptake and transport of Cd in rice root. Furthermore, EPS could induce plant resistance to heavy metals by regulating the lignin biosynthesis pathway in rice roots. Finally, the cell wall remodeling induced by EPS likely contributes to plant stress responses by activating the reactive oxygen species (ROS) signaling.

Analysis of the Safety and Pregnancy Outcomes of Fertility-sparing Surgery in Ovarian Malignant Sex Cord-stromal Tumours: A Multicentre Retrospective Study

AIMS

To assess the difference in survival between fertility-sparing surgery (FSS) and radical surgery and explore pregnancy outcomes after FSS in stage I malignant sex cord-stromal tumours (MSCSTs).

MATERIALS AND METHODS

We carried out a multicentre retrospective cohort study on patients who were diagnosed with MSCSTs and the tumour was confined to one ovary. The patients were divided into FSS and radical surgery groups. Inverse probability of treatment weighting (IPTW) was used to balance variables between the two groups. Kaplan-Meier analysis was used to compare the difference in disease-free survival (DFS). Univariate and multivariate Cox regression analysis was used to find risk factors of DFS. Univariate logistic regression analysis was used to assess risk factors of pregnancy.

RESULTS

In total, 107 patients were included, of whom 54 (50.5%) women underwent FSS and 53 (49.5%) received radical surgery. After IPTW, a pseudo-population of 208 was determined and all of the covariates were well balanced. After a median follow-up time of 50 months (range 7-156 months), 10 patients experienced recurrence and two died. There was no significant difference in DFS between the two groups, both in unweighted (P = 0.969) or weighted cohorts (P = 0.792). In the weighted cohort, stage IC (P = 0.014), tumour diameter >8 cm (P = 0.003), incomplete staging surgery (P = 0.003) and no adjuvant chemotherapy (P < 0.001) were the four high-risk factors associated with a shorter DFS. Among 14 patients who had pregnancy desire, 11 (78.6%) women conceived successfully; the live birth rate was 76.9%. In univariate analysis, only adjuvant chemotherapy (P = 0.009) was associated with infertility.

CONCLUSIONS

On the premise of complete staging surgery, FSS is safe and feasible in early stage MSCSTs with satisfactory reproductive outcomes.

Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution

The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of Zygnema circumcarinatum and one strain of Z. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model system Z. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.

Application of Poly(ether sulfone)-Based Membranes in Clean Energy Technology

Poly(ether sulfone) (PES) is a kind of polymer materials with excellent electrical insulation and acid/alkali stability. PES can be operated at high temperature continuously for a long time and still maintain excellent property stability in the environments with rapidly changed temperature, namely, great thermostability. Moreover, PES has low molding shrinkage, good dimensional stability and excellent film-forming characteristics. Compared with inorganic membranes, PES-based membranes have lower cost, which have received more attention and wide recognition in the field of clean energy technologies in recent years, such as flow batteries, fuel cells, water treatment, and gas separation. Therefore, this review summarizes the research status and prospect of the utilization of PES-based membranes in clean energy fields, in order to further promote their development and application.

Aging-induced down-regulation of Pka/Bkca pathway in rat cerebral arteries

The incidence of cerebrovascular diseases increases significantly with aging. This study aimed to test the hypothesis that aging may influence the protein kinase A (PKA)-dependent vasodilation via RyR/BKCa pathway in the middle cerebral arteries (MCA). Male Sprague-Dawley rats were randomly divided into control (4-6 month-old) and aged (24-month-old) groups. The functions of MCA and ion channel activities in smooth muscle cells were examined using myograph system and patch-clamp. Aging decreased the isoproterenol/forskolin-induced relaxation in the MCA. Large-conductance Ca2+-activated-K+ (BKCa) channel inhibitor, iberiotoxin, significantly attenuated the forskolin-induced vasodilatation and hyperpolarization in the young group, but not in the aged group. The amplitude and frequency of spontaneous transient outward currents (STOCs) were significantly decreased in the aged group. Single channel recording revealed that the mean open time of BKCa channels were decreased, while an increased mean closed time of BKCa channels were found in the aged group. The Ca2+/voltage sensitivity of the channels was decreased accompanied by reduced BKCa α and β1-subunit, the expression of RyR2, PKA-Cα and PKA-Cβ subunits were also declined in the aged group. Aging induced down-regulation of PKA/BKCa pathway in cerebral artery in rats. The results provides new information on further understanding in cerebrovascular diseases resulted from age-related cerebral vascular dysfunction.

Critical assessment of pan-genomic analysis of metagenome-assembled genomes

Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.

dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes

Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.