The Making of a Flight Feather: Bio-architectural Principles and Adaptation.

The evolution of flight in feathered dinosaurs and early birds over millions of years required flight feathers whose architecture features hierarchical branches. While barb-based feather forms were investigated, feather shafts and vanes are understudied. Here, we take a multi-disciplinary approach to study their molecular control and bio-architectural organizations. In rachidial ridges, epidermal progenitors generate cortex and medullary keratinocytes, guided by Bmp and transforming growth factor ß (TGF-ß) signaling that convert rachides into adaptable bilayer composite beams. In barb ridges, epidermal progenitors generate cylindrical, plate-, or hooklet-shaped barbule cells that form fluffy branches or pennaceous vanes, mediated by asymmetric cell junction and keratin expression. Transcriptome analyses and functional studies show anterior-posterior Wnt2b signaling within the dermal papilla controls barbule cell fates with spatiotemporal collinearity. Quantitative bio-physical analyses of feathers from birds with different flight characteristics and feathers in Burmese amber reveal how multi-dimensional functionality can be achieved and may inspire future composite material designs. VIDEO ABSTRACT.

Innovative super-resolution in spatial transcriptomics: a transformer model exploiting histology images and spatial gene expression.

Spatial transcriptomics technologies have shed light on the complexities of tissue structures by accurately mapping spatial microenvironments. Nonetheless, a myriad of methods, especially those utilized in platforms like Visium, often relinquish spatial details owing to intrinsic resolution limitations. In response, we introduce TransformerST, an innovative, unsupervised model anchored in the Transformer architecture, which operates independently of references, thereby ensuring cost-efficiency by circumventing the need for single-cell RNA sequencing. TransformerST not only elevates Visium data from a multicellular level to a single-cell granularity but also showcases adaptability across diverse spatial transcriptomics platforms. By employing a vision transformer-based encoder, it discerns latent image-gene expression co-representations and is further enhanced by spatial correlations, derived from an adaptive graph Transformer module. The sophisticated cross-scale graph network, utilized in super-resolution, significantly boosts the model's accuracy, unveiling complex structure-functional relationships within histology images. Empirical evaluations validate its adeptness in revealing tissue subtleties at the single-cell scale. Crucially, TransformerST adeptly navigates through image-gene co-representation, maximizing the synergistic utility of gene expression and histology images, thereby emerging as a pioneering tool in spatial transcriptomics. It not only enhances resolution to a single-cell level but also introduces a novel approach that optimally utilizes histology images alongside gene expression, providing a refined lens for investigating spatial transcriptomics.

METTL3 protects METTL14 from STUB1-mediated degradation to maintain m6 A homeostasis.

N6 -Methyladenosine (m6 A) is an important RNA modification catalyzed by methyltransferase-like 3 (METTL3) and METTL14. m6 A homeostasis mediated by the methyltransferase (MTase) complex plays key roles in various biological processes. However, the mechanism underlying METTL14 protein stability and its role in m6 A homeostasis remain elusive. Here, we show that METTL14 stability is regulated by the competitive interaction of METTL3 with the E3 ligase STUB1. STUB1 directly interacts with METTL14 to mediate its ubiquitination at lysine residues K148, K156, and K162 for subsequent degradation, resulting in a significant decrease in total m6 A levels. The amino acid regions 450-454 and 464-480 of METTL3 are essential to promote METTL14 stabilization. Changes in STUB1 expression affect METTL14 protein levels, m6 A modification and tumorigenesis. Collectively, our findings uncover an ubiquitination mechanism controlling METTL14 protein levels to fine-tune m6 A homeostasis. Finally, we present evidence that modulating STUB1 expression to degrade METTL14 could represent a promising therapeutic strategy against cancer.

Mutant VPS35-D620N induces motor dysfunction and impairs DAT-mediated dopamine recycling pathway.

The D620N mutation in vacuolar protein sorting protein 35 (VPS35) gene has been identified to be linked to late onset familial Parkinson disease (PD). However, the pathophysiological roles of VPS35-D620N in PD remain unclear. Here, we generated the transgenic Caenorhabditis elegans overexpressing either human wild type or PD-linked mutant VPS35-D620N in neurons. C. elegans expressing VPS35-D620N, compared with non-transgenic controls, showed movement disorders and dopaminergic neuron loss. VPS35-D620N worms displayed more swimming induced paralysis but showed no defects in BSR assays, thus indicating the disruption of dopamine (DA) recycling back inside neurons. Moreover, VPS35 formed a protein interaction complex with DA transporter (DAT), RAB5, RAB11 and FAM21. In contrast, the VPS35-D620N mutant destabilized these interactions, thus disrupting DAT transport from early endosomes to recycling endosomes, and decreasing DAT at the cell surface. These effects together increased DA in synaptic clefts, and led to dopaminergic neuron degeneration and motor dysfunction. Treatment with reserpine significantly decreased the swimming induced paralysis in VPS35-D620N worms, as compared with vehicle treated VPS35-D620N worms. Our studies not only provide novel insights into the mechanisms of VPS35-D620N-induced dopaminergic neuron degeneration and motor dysfunction via disruption of DAT function and the DA signaling pathway but also indicate a potential strategy to treat VPS35-D620N-related PD and other disorders.

Obtaining Lower Query Complexities Through Lightweight Zeroth-Order Proximal Gradient Algorithms.

Zeroth-order (ZO) optimization is one key technique for machine learning problems where gradient calculation is expensive or impossible. Several variance, reduced ZO proximal algorithms have been proposed to speed up ZO optimization for nonsmooth problems, and all of them opted for the coordinated ZO estimator against the random ZO estimator when approximating the true gradient, since the former is more accurate. While the random ZO estimator introduces a larger error and makes convergence analysis more challenging compared to coordinated ZO estimator, it requires only O(1) computation, which is significantly less than O(d) computation of the coordinated ZO estimator, with d being dimension of the problem space. To take advantage of the computationally efficient nature of the random ZO estimator, we first propose a ZO objective decrease (ZOOD) property that can incorporate two different types of errors in the upper bound of convergence rate. Next, we propose two generic reduction frameworks for ZO optimization, which can automatically derive the convergence results for convex and nonconvex problems, respectively, as long as the convergence rate for the inner solver satisfies the ZOOD property. With the application of two reduction frameworks on our proposed ZOR-ProxSVRG and ZOR-ProxSAGA, two variance-reduced ZO proximal algorithms with fully random ZO estimators, we improve the state-of-the-art function query complexities from Omindn1/2ε2,dε3 to O˜n+dε2 under d>n12 for nonconvex problems, and from Odε2 to O˜nlog1ε+dε for convex problems. Finally, we conduct experiments to verify the superiority of our proposed methods.

Variability of ecosystem carbon source from microbial respiration is controlled by rainfall dynamics.

Soil heterotrophic respiration (Rh) represents an important component of the terrestrial carbon cycle that affects whether ecosystems function as carbon sources or sinks. Due to the complex interactions between biological and physical factors controlling microbial growth, Rh is uncertain and difficult to predict, limiting our ability to anticipate future climate trajectories. Here we analyze the global FLUXNET 2015 database aided by a probabilistic model of microbial growth to examine the ecosystem-scale dynamics of Rh and identify primary predictors of its variability. We find that the temporal variability in Rh is consistently distributed according to a Gamma distribution, with shape and scale parameters controlled only by rainfall characteristics and vegetation productivity. This distribution originates from the propagation of fast hydrologic fluctuations on the slower biological dynamics of microbial growth and is independent of biome, soil type, and microbial physiology. This finding allows us to readily provide accurate estimates of the mean Rh and its variance, as confirmed by a comparison with an independent global dataset. Our results suggest that future changes in rainfall regime and net primary productivity will significantly alter the dynamics of Rh and the global carbon budget. In regions that are becoming wetter, Rh may increase faster than net primary productivity, thereby reducing the carbon storage capacity of terrestrial ecosystems.

Clinical evaluation of tooth angle and peripheral bone thickness considering sex and age for implant placement in the maxillary anterior region.

STATEMENT OF PROBLEM: Consideration of the thickness of alveolar bone on both the palatal and labial sides and the inclination angle of teeth is important for immediate implant placement in the maxillary anterior region. However, comprehensive research exploring how sex and age influence the thickness of bone and tooth angle in the maxillary anterior region is lacking. PURPOSE: The purpose of this clinical study was to investigate the effect of sex and age on the thickness of labial and palatal bone and on the tooth inclination angle of maxillary central and lateral incisors using cone beam computed tomography (CBCT) images in an Asian population. MATERIAL AND METHODS: The labial and palatal bone thickness and the inclination angle of maxillary central and lateral incisors were measured from the CBCT images of 149 participants aged between 20 and 65 years. The correlation between the angles of the maxillary central and lateral incisors and sex and age on the tooth angles and thicknesses of labial and palatal bone was determined statistically. RESULTS: A high correlation (R=0.73) was found between the angle of maxillary central and lateral incisors. Men had higher angles of the maxillary central and lateral incisors and thicker palatal bone at the middle and root of the teeth compared with women. In both sexes, the angle and palatal bone thickness of maxillary central incisors were significantly higher than those of maxillary lateral incisors. The angle of both maxillary central and lateral incisors decreased gradually with age, with a difference in angle of over 10 degrees. CONCLUSIONS: The study revealed that women exhibited relatively thinner palatal bone compared with men. Additionally, participants aged between 40 and 65 years exhibited significantly thicker palatal bone compared with younger age groups, potentially providing a larger site for implant placement. Furthermore, tooth angle gradually decreases with age in the maxillary anterior region.

Metformin attenuates chronic lung allograft dysfunction: evidence in rat models.

BACKGROUND: Chronic lung allograft dysfunction (CLAD) directly causes an abysmal long-term prognosis after lung transplantation (LTx), but effective and safe drugs are not available. Metformin exhibits high therapeutic potential due to its antifibrotic and immunomodulatory effects; however, it is unclear whether metformin exerts a therapeutic effect in CLAD. We sought to investigate the effect of metformin on CLAD based on rat models. METHODS: Allogeneic LTx rats were treated with Cyclosporin A (CsA) in the first week, followed by metformin, CsA, or vehicle treatment. Syngeneic LTx rats received only vehicles. All rats were sacrificed on post-transplant week 4. Pathology of lung graft, spleen, and thymus, extent of lung fibrosis, activity of profibrotic cytokines and signaling pathway, adaptive immunity, and AMPK activity were then studied. RESULTS: Allogeneic recipients without maintenance CsA treatment manifested CLAD pathological characteristics, but these changes were not observed in rats treated with metformin. For the antifibrotic effect, metformin suppressed the fibrosis extent and profibrotic cytokine expression in lung grafts. Regarding immunomodulatory effect, metformin reduced T- and B-cell infiltration in lung grafts, spleen and thymus weights, the T- and B-cell zone areas in the spleen, and the thymic medullary area. In addition, metformin activated AMPK in lung allografts and in α-SMA+ cells and T cells in the lung grafts. CONCLUSIONS: Metformin attenuates CLAD in rat models, which could be attributed to the antifibrotic and immunomodulatory effects. AMPK activation suggests the potential molecular mechanism. Our study provides an experimental rationale for further clinical trials.

Pararespiratory and paradigestive lymph node metastases in esophageal squamous cell carcinoma: predicting survival and refining the N staging system.

BACKGROUND: The site of lymph node metastasis (LNM) may affect the prognosis of patients with esophageal squamous cell carcinoma (ESCC). To investigate the prognoses of pararespiratory and paradigestive LNM and to propose a novel N (nN) staging system that integrates both the LNM site and count. METHODS: This study was a multicenter, large-sample, retrospective cohort study that included ESCC patients with LNM between January 2014 and December 2019 from three Chinese institutes. Patients were set into training (two institutes) and external validation (one institute) cohorts. The primary outcomes were survival differences in LNM site and the development of novel nodal staging system. The overall survival (OS) of patients with pararespiratory LNM only (Group A), paradigestive LNM only (Group B), and both sites (Group C) was evaluated by Kaplan-Meier. Cox proportional hazards models were used to identify the independent prognostic factors. An nN staging system considering both the LNM site and count was developed and evaluated by the area under the receiver operating characteristic curve (AUC). RESULTS: In total, 1313 patients were included and split into training (n = 1033) and external validation (n = 280) cohorts. There were 342 (26.0%), 568 (43.3%) and 403 (30.7%) patients in groups A, B and C, respectively. The OS of patients with pararespiratory and patients with paradigestive LNM presented significant differences in the training and validation cohorts (P < 0.050). In the training cohort, LNM site was an independent prognostic factor (hazard ratio: 1.58, 95% confidence intervals: 1.41-1.77, P < 0.001). The nN staging definition: nN1 (1-2 positive pararespiratory/paradigestive LNs), nN2 (3-6 pararespiratory LNs or 1 pararespiratory with 1paradigestive LN), nN3 (3-6 LNs with ≥ 1 paradigestive LN), nN4 (≥ 7 LNs). Subsets of patients with different nN stages showed significant differences in OS (P < 0.050). The prognostic model of the nN staging system presented higher performance in the training and validation cohorts at 3-year OS (AUC, 0.725 and 0.751, respectively) and 5-year OS (AUC, 0.740 and 0.793, respectively) than the current N staging systems. CONCLUSIONS: Compared to pararespiratory LNM, the presence of paradigestive LNM is associated with worse OS. The nN staging system revealed superior prognostic ability than current N staging systems.

Integrating structure annotation and machine learning approaches to develop graphene toxicity models.

Modern nanotechnology provides efficient and cost-effective nanomaterials (NMs). The increasing usage of NMs arises great concerns regarding nanotoxicity in humans. Traditional animal testing of nanotoxicity is expensive and time-consuming. Modeling studies using machine learning (ML) approaches are promising alternatives to direct evaluation of nanotoxicity based on nanostructure features. However, NMs, including two-dimensional nanomaterials (2DNMs) such as graphenes, have complex structures making them difficult to annotate and quantify the nanostructures for modeling purposes. To address this issue, we constructed a virtual graphenes library using nanostructure annotation techniques. The irregular graphene structures were generated by modifying virtual nanosheets. The nanostructures were digitalized from the annotated graphenes. Based on the annotated nanostructures, geometrical nanodescriptors were computed using Delaunay tessellation approach for ML modeling. The partial least square regression (PLSR) models for the graphenes were built and validated using a leave-one-out cross-validation (LOOCV) procedure. The resulted models showed good predictivity in four toxicity-related endpoints with the coefficient of determination (R2) ranging from 0.558 to 0.822. This study provides a novel nanostructure annotation strategy that can be applied to generate high-quality nanodescriptors for ML model developments, which can be widely applied to nanoinformatics studies of graphenes and other NMs.

Ovarian cyst torsion in Prader-Willi Syndrome.

BACKGROUND: Prader-Willi syndrome (PWS) is a genetic disorder involving multiple systems, with an incidence of about 1/10000-25000. Ovarian torsion (OT) is not commonly found in children. Ovarian cyst acts as one of the primary factors resulting in OT. While ovarian cyst torsion with Prader-Willi Syndrome has not been reported before. CASE PRESENTATION: A 12-years old female was admitted to Emergency Department of our hospital with the chief complaint of abdominal pain. The outcomes of physical examination revealed the height of 150 cm, weight of 103 kg, BMI of 45.77 kg/m2. The patient manifested the special facial features, an obese body, with the abdomen distended into a spherical shape. The fat accumulation in the abdomen significantly embarrassed the palpation. The abdominal CT scan indicated a huge cystic mass in the abdominal cavity, sized about 138 mm × 118 mm. According to medical history, the patient was born with low crying and hypotonia, who has developed the uncontrollable eating behavior since 3-years old. These abnormalities led to a speculation of PWS syndrome, so a genetic test was performed and finally confirmed it, concluding a torsion of ovarian cyst with PWS. With the multidisciplinary consultation, a careful treatment strategy containing the control of blood pressure and blood sugar, coenzyme Q10 was administrated to nourish the myocardium and the application of Growth Hormone was developed. All the above preoperative treatments have brought great benefits to patients. Thus promising the successful completion of operation. The postoperative follow-up till now indicated that the abdominal incision was well healed, without operative complications. CONCLUSIONS: This may be the first case report. In the treatment of ovarian cyst torsion, PWS syndrome requires fully consideration, as the latter can lead to multisystem abnormalities, especially the relation to perioperative management, and even fatalities. Genetic testing should be conducted early when PWS was suspected, accompanied with adequate preparation for the perioperative period, the follow-ups of patients should be maintained for a long time after surgery.

Interindividual Variability in Self-Monitoring of Blood Pressure Using Consumer-Purchased Wireless Devices.

BACKGROUND: Engagement with self-monitoring of blood pressure (BP) declines, on average, over time but may vary substantially by individual. OBJECTIVES: We aimed to describe different 1-year patterns (groups) of self-monitoring of BP behaviors, identify predictors of those groups, and examine the association of self-monitoring of BP groups with BP levels over time. METHODS: We analyzed device-recorded BP measurements collected by the Health eHeart Study-an ongoing prospective eCohort study-from participants with a wireless consumer-purchased device that transmitted date- and time-stamped BP data to the study through a full 12 months of observation starting from the first day they used the device. Participants received no instruction on device use. We applied clustering analysis to identify 1-year self-monitoring, of BP patterns. RESULTS: Participants had a mean age of 52 years and were male and White. Using clustering algorithms, we found that a model with three groups fit the data well: persistent daily use (9.1% of participants), persistent weekly use (21.2%), and sporadic use only (69.7%). Persistent daily use was more common among older participants who had higher Week 1 self-monitoring of BP frequency and was associated with lower BP levels than the persistent weekly use or sporadic use groups throughout the year. CONCLUSION: We identified three distinct self-monitoring of BP groups, with nearly 10% sustaining a daily use pattern associated with lower BP levels.

Double-lung versus heart-lung transplantation for end-stage cardiopulmonary disease: a systematic review and meta-analysis.

We compared posttransplant outcomes following double-lung transplantation (DLTx) and heart-lung transplantation (HLTx), based on a search of PubMed, Cochrane Library, and Embase, from inception to March 8, 2022, for studies that report outcomes of these procedures. We then performed a meta-analysis of baseline characteristics and posttransplant outcomes. Subgroup analyses were implemented according to indication, publication year, and center. This study was registered on PROSPERO (number CRD42020223493). Ten studies were included in this meta-analysis, involving 1230 DLTx patients and 1022 HLTx patients. The DLTx group was characterized by older donors (P = 0.04) and a longer allograft ischemia time (P < 0.001) than the HLTx group. The two groups had comparable 1-year, 3-year, 5-year, 10-year survival rates (all P > 0.05), with similar results identified in subgroup analyses. We found no significant differences in 1-year, 5-year, and 10-year chronic lung allograft dysfunction (CLAD)-free survival, length of intensive care unit stay and hospital stay, length of postoperative ventilation, in-hospital mortality, or surgical complications between the groups (all P > 0.05). Thus, DLTx provides similar posttransplant survival to HLTx for end-stage cardiopulmonary disease. These two procedures have a comparable risk of CLAD and other posttransplant outcomes.

Functional and Anatomical Outcomes of Anti-Vascular Endothelial Growth Factor Treatment for Exudative Age-Related Macular Degeneration with or without Obstructive Sleep Apnea.

(1) To investigate the functional and anatomical outcomes of anti-vascular endothelial growth factor (anti-VEGF) treatment in patients with exudative age-related macular degeneration (AMD) with or without obstructive sleep apnea (OSA); (2) In total, 65 patients with AMD with or without OSA who received three consecutive doses of intravitreal anti-VEGF injections were enrolled. The primary outcomes-best-corrected visual acuity (BCVA) and central macular thickness (CMT)-were assessed at 1 and 3 months. Moreover, morphological changes observed through optical coherence tomography were analyzed; (3) In total, 15 of the 65 patients had OSA and were included in the OSA group; the remaining 50 patients were included in the non-OSA (control) group. At 1 and 3 months after treatment, BCVA and CMT had improved but did not differ significantly between the groups. More patients in the OSA group demonstrated subretinal fluid (SRF) resorption at 3 months after treatment than in the non-OSA group (p = 0.009). Changes in other imaging biomarkers, such as intraretinal cysts, retinal pigment epithelium detachment, hyperreflective dots, and ellipsoid zone disruptions, did not differ significantly between the groups; (4) Our results suggest that the BCVA and CMT outcomes 3 months after anti-VEGF treatment are similar between patients with and without OSA. Moreover, patients with OSA may exhibit superior SRF resorption. A large-scale prospective study is mandatory to evaluate the association between SRF resorption and visual outcomes in AMD patients with OSA.

Retrospective Analysis of Surgical Outcomes on Axial Length Elongation in Eyes with Posterior and Combined Persistent Fetal Vasculature.

This study aims to investigate the outcomes and risk factors associated with poor vision (vision less than counting fingers, 2.0 logMAR, Snellen vision 20/2000) in patients with posterior or combined persistent fetal vasculature (PFV), with or without surgery. We retrospectively reviewed the medical records of patients who were diagnosed with PFV from January 2008 to April 2021. We included 51 eyes of 44 patients who presented with PFV, of which 38 eyes underwent surgical correction (pars plicata/plana vitrectomy, with or without lensectomy, and intraocular lens implantation) at the median age of 6.0 months (range: 0.7 to 82.0). The mean follow-up was 68.8 months ± 38.0 months. The axial length change in the eyes undergoing surgery was significantly higher than the eyes without surgery (p = 0.025). Initial anterior chamber collapse and retinal detachment were associated with poor vision (p = 0.006 and p = 0.002, respectively). In addition, 37% of eyes with posterior or combined PFV had vision better than counting fingers. Surgery for eyes with PFV could result in better eye growth. Visual outcomes remained poor and were associated with the level of macular abnormality. Initial anterior chamber collapse and retinal detachment at presentation were the risk factors for poor visual outcomes. Vitrectomy for selected PFV eyes is valuable and associated with a better cosmetic outcome (better eye growth).

New classification for bone type at dental implant sites: a dental computed tomography study.

OBJECTIVE: This study proposed a new classification method of bone quantity and quality at the dental implant site using cone-beam computed tomography (CBCT) image analysis, classifying cortical and cancellous bones separately and using CBCT for quantitative analysis. METHODS: Preoperative CBCT images were obtained from 128 implant patients (315 sites). First, measure the crestal cortical bone thickness (in mm) and the cancellous bone density [in grayscale values (GV) and bone mineral density (g/cm3)] at the implant sites. The new classification for bone quality at the implant site proposed in this study is a "nine-square division" bone classification system, where the cortical bone thickness is classified into A: > 1.1 mm, B:0.7-1.1 mm, and C: < 0.7 mm, and the cancellous bone density is classified into 1: > 600 GV (= 420 g/cm3), 2:300-600 GV (= 160 g/cm3-420 g/cm3), and 3: < 300 GV (= 160 g/cm3). RESULTS: The results of the nine bone type proportions based on the new jawbone classification were as follows: A1 (8.57%,27/315), A2 (13.02%), A3 (4.13%), B1 (17.78%), B2 (20.63%), B3 (8.57%) C1 (4.44%), C2 (14.29%), and C3 (8.57%). CONCLUSIONS: The proposed classification can complement the parts overlooked in previous bone classification methods (bone types A3 and C1). TRIAL REGISTRATION: The retrospective registration of this study was approved by the Institutional Review Board of China Medical University Hospital, No. CMUH 108-REC2-181.

Predicting Prenatal Developmental Toxicity Based On the Combination of Chemical Structures and Biological Data.

For hazard identification, classification, and labeling purposes, animal testing guidelines are required by law to evaluate the developmental toxicity potential of new and existing chemical products. However, guideline developmental toxicity studies are costly, time-consuming, and require many laboratory animals. Computational modeling has emerged as a promising, animal-sparing, and cost-effective method for evaluating the developmental toxicity potential of chemicals, such as endocrine disruptors, without the use of animals. We aimed to develop a predictive and explainable computational model for developmental toxicants. To this end, a comprehensive dataset of 1244 chemicals with developmental toxicity classifications was curated from public repositories and literature sources. Data from 2140 toxicological high-throughput screening assays were extracted from PubChem and the ToxCast program for this dataset and combined with information about 834 chemical fragments to group assays based on their chemical-mechanistic relationships. This effort revealed two assay clusters containing 83 and 76 assays, respectively, with high positive predictive rates for developmental toxicants identified with animal testing guidelines (PPV = 72.4 and 77.3% during cross-validation). These two assay clusters can be used as developmental toxicity models and were applied to predict new chemicals for external validation. This study provides a new strategy for constructing alternative chemical developmental toxicity evaluations that can be replicated for other toxicity modeling studies.

Cymbopogom Citratus Essential Oils: A Promising Source of Antifungals Against Panax Notoginseng-Associated Pathogenic Fungi.

Due to the great threat of chemical pesticides to the ecosystem environment, it is a long-term goal to find environmentally friendly green pesticides. Essential oils (EOs) are considered weapons in plant chemical defense and are important sources of green pesticides. Therefore, the antifungal effects and action mechanisms of Cymbopogom citratus (C. citratus) EOs against seven kinds of Panax notoginseng (P. notoginseng) pathogenic fungi were investigated. Oxford Cup results showed that C. citratus EOs had an excellent detraction effects against seven fungi of P. notoginseng. Gas chromatography-mass spectrometry (GC-MS) was used to construct the chemical profiles of C. citratus EOs, disclosed that the main categories are terpenes and oxygenated terpenes. In addition, compared with the hymexazol, the minimum inhibitory concentration (MIC) showed that EOs and their main components had strong antifungal activities. Besides, EOs had a synergistic effect with hymexazol (a chemical pesticide). The antifungal mechanism of C. citratus EOs was studied by using Fusarium oxysporum (F. oxysporum) as the dominant pathogen. C. citratus EOs may affect the metabolism of fungi and induce mycotoxins to destroy the cell wall to achieve antifungal effects. Finally, EOs were found to significantly retard P. notoginseng infection by F. oxysporum. According to our research, C. citratus EOs are potential green antifungal agent that can be used in the cultivation of P. notoginseng.

BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data.

Droplet-based single cell transcriptome sequencing (scRNA-seq) technology, largely represented by the 10× Genomics Chromium system, is able to measure the gene expression from tens of thousands of single cells simultaneously. More recently, coupled with the cutting-edge Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), the droplet-based system has allowed for immunophenotyping of single cells based on cell surface expression of specific proteins together with simultaneous transcriptome profiling in the same cell. Despite the rapid advances in technologies, novel statistical methods and computational tools for analyzing multi-modal CITE-Seq data are lacking. In this study, we developed BREM-SC, a novel Bayesian Random Effects Mixture model that jointly clusters paired single cell transcriptomic and proteomic data. Through simulation studies and analysis of public and in-house real data sets, we successfully demonstrated the validity and advantages of this method in fully utilizing both types of data to accurately identify cell clusters. In addition, as a probabilistic model-based approach, BREM-SC is able to quantify the clustering uncertainty for each single cell. This new method will greatly facilitate researchers to jointly study transcriptome and surface proteins at the single cell level to make new biological discoveries, particularly in the area of immunology.

Control of pathogenic fungi on Panax notoginseng by volatile oils from the food ingredients Allium sativum and Foeniculum vulgare.

To screen natural drugs with strong inhibitory effects against pathogenic fungi related to P. notoginseng, the antifungal activities of garlic and fennel EOs were studied by targeting P. notoginseng disease-associated fungi, and the possible action mechanisms of garlic and fennel EOs as plant fungicides were preliminarily discussed. At present, the antifungal mechanism of EOs has not been fully established. Therefore, understanding the antifungal mechanism of plant EOs is helpful to address P. notoginseng diseases continuous cropping disease-related obstacles and other agricultural cultivation problems. First, the Oxford cup method and chessboard were used to confirm that the EOs and oxamyl had a significant inhibitory effect on the growth of Fusarium oxysporum. F. oxysporum is the main pathogen causing root rot of P. notoginseng and the preliminary study on the antifungal mechanisms of the EOs against F. oxysporum showed that the inhibition of EOs mainly affects cell membrane permeability and cell processes and affects the enzyme activities of micro-organism, to achieve antifungal effects. Finally, an in vivo model verified that both two EOs could significantly inhibit the occurrence of root rot caused by F. oxysporum.