WTV2.0: A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode

Volatilomics is essential for understanding the biological functions and fragrance contributions of plant volatiles. However, the annotation coverage of current untargeted and widely-targeted methods has been limited by low sensitivity and/or low acquisition coverage. Here, we introduce WTV 2.0. It enables the construction of a high-coverage library containing 2111 plant volatiles; the development of a comprehensive-selective ion monitoring (cSIM) acquisition method that contains the fewest but sufficient ions for most plant volatiles, including the selection of characteristic qualitative ions with minimal ions number for each compound and the optimized segmentation of acquisition method; and finally, the automatic qualitative and semi-quantitative analysis of cSIM data. Furthermore, the library and acquisition method can be self-expanded by incorporating compounds not present in the library, utilizing the obtained cSIM data. WTV 2.0 increased the median signal-to-noise ratio by 7.6-fold compared to the untargeted method, doubled the annotation coverage compared to the untargeted and WTV 1.0 methods in tomato fruit, and leading to the discovery of menthofuran as a novel flavor compound in passion fruit. WTV 2.0 is a Python library with a user-friendly interface, and is applicable to volatiles and primary metabolites profiling in any species.

Association between infarct location and haemorrhagic transformation of acute ischaemic stroke after intravenous thrombolysis

AIM

To evaluate the association between computed tomography (CT)-based imaging variables at the time of admission and haemorrhagic transformation (HT) after intravenous thrombolysis (IVT).

MATERIALS AND METHODS

One hundred and eight patients who were treated with IVT for acute ischaemic stroke (AIS) during January 2021 to July 2023 were analysed retrospectively. The infarct location was classified as cortical or subcortical in accordance with the Alberta Stroke Program Early CT Score (ASPECTS) system. Logistic regression and receiver operating characteristic curve analyses were performed to determine the relationship between ischaemic variables and HT.

RESULTS

Of the total, 18 (16.7%) patients had HT and seven (6.5%) had symptomatic intracerebral haemorrhage (sICH). Multivariate analysis revealed that cortical ASPECTS was independently associated with HT (odds ratio [OR], 0.197; 95% confidence interval [CI], 0.076-0.511; p=0.001) and cortical ASPECTS was independently associated with sICH (OR, 0.066; 95% CI, 0.009-0.510; p=0.009). To predict HT and sICH, cortical ASPECTS (HT area under the curve [AUC] = 0.881, sICH AUC = 0.971) provided a higher AUC compared with ASPECTS (HT AUC = 0.850, sICH AUC = 0.918).

CONCLUSION

Cortical ASPECTS seen on CT at the time of admission is associated with HT and sICH after IVT.

An optimal de Quervain's tenosynovitis splint with ergonomic thumb support and evenly distributed pressure

Splinting is a conventional treatment for de Quervain's tenosynovitis (dQt). However, existing splints have problems such as excessive thermal discomfort and poor fit, which have been pointed out in previous studies. This study proposes a new functional splint consisting of both hard and soft materials with the aim of providing wear comfort with a good fit and sufficient stability of the injured hand. Thumb support of the splint is an important component that controls and protects the affected thumb. To develop an ergonomically shaped thumb support, 16 participants with dQt were recruited for three-dimensional (3D) scanning of their hands. The angles of the wrist and the curvature of the thumb were measured using computer software, and the results were used as a reference for the design of the prototype supports. Excessive pressure on particular regions, such as bony areas, may cause discomfort or pain. To ensure the wear comfort of the proposed splint, a finite element model (FEM) was built to simulate the wear process of the splint and hence to predict the pressure distribution exerted from the splint onto the hand of the wearer. The simulated results show that the pressure is evenly distributed over the hand, indicating that patients are likely to wear the proposed splint comfortably during their treatment period.

[Effectiveness of the central government-funded echinococcosis control programme in Tianzhu Tibetan Autonomous County, Gansu Province from 2007 to 2022]

OBJECTIVE

To evaluate the effectiveness of the central government-funded echinococcosis control programme in Tianzhu Tibetan Autonomous County, Gansu Province from 2007 to 2022, so as to provide insights into echinococcosis control.

METHODS

Administrative villages were sampled using a multi-stage cluster random sampling method from Tianzhu Tibetan Autonomous County, Gansu Province from 2007 to 2022, and all residents at ages of 12 years and older in the sampled villages were screened for echinococcosis, and schools were sampled using a cluster sampling method, and all children at ages of 12 years and older in the sampled schools were screened for echinococcosis. Domestic dogs were sampled using a systematic random sampling method, and one domestic dog stool sample was collected from each household. Stray dog stool samples were collected outside the villages, and Echinococcus coproantigens were detected using enzyme-linked immunosorbent assay in domestic and stray dogs. In addition, echinococcosis was screened in sheep and cattle in designated slaughterhouses in Tianzhu Tibetan Autonomous County. The trends in the prevalence of echinococcosis in humans and livestock and the positive rate of Echinococcus coproantigens in dogs were examined with the Cochran-Armitage trend test. In addition, individuals screened for echinococcosis were randomly sampled from 2007 to 2022 for survey on the awareness of echinococcosis control knowledge.

RESULTS

A total of 290 356 person-times were screened for echinococcosis among residents at ages of 12 years and older in Tianzhu Tibetan Autonomous County, Gansu Province from 2007 to 2022, with 1 094 residents detected with cystic echinococcosis, and the detection of echinococcosis appeared a tendency towards a gradual decline over years (χ2 = 358.602, P < 0.001). A total of 32 931 person-times were screened for echinococcosis among children at ages of 12 years and older in Tianzhu Tibetan Autonomous County, Gansu Province from 2007 to 2022, with 296 children detected with echinococcosis, and the detection of echinococcosis appeared a tendency towards a gradual decline over years (χ2 = 267.673, P < 0.001). A total of 33 230 domestic dog stool samples were tested for Echinococcus coproantigens in Tianzhu Tibetan Autonomous County, Gansu Province from 2007 to 2022, with 1 777 Echinococcus coproantigens-positive samples tested, and the positive rate of Echinococcus coproantigens appeared a tendency towards a decline in domestic dogs over years (χ2 = 2 210.428, P < 0.001), while the positive rate of Echinococcus coproantigens showed a tendency towards a rise in domestic animals from 2016 to 2022 (χ2 = 37.745, P < 0.001). The positive rate of Echinococcus coproantigens remained relatively stable in stray dogs in Tianzhu Tibetan Autonomous County, Gansu Province from 2019 to 2022 (χ2 = 0.315, P = 0.575). A total of 10 973 sheep were screened for echinococcosis in Tianzhu Tibetan Autonomous County from 2007 to 2022, with 334 sheep detected with echinococcosis, and the detection of echinococcosis appeared a tendency towards a decline in sheep over years (χ2 = 53.579, P < 0.001); however, there was no significant change in the detection of echinococcosis during the period from 2015 through 2022 (χ2 = 1.520, P = 0.218). A total of 2 400 cattle were screened for echinococcosis in Tianzhu Tibetan Autonomous County from 2017 to 2022, with 231 cattle detected with echinococcosis, and the detection of echinococcosis showed a tendency towards a decline over years (χ2 = 5.579, P < 0.05). The awareness of echinococcosis control knowledge increased from 44.37% in 2007 to 94.00% in 2022 among residents at ages of 12 years and older and from 52.50% in 2007 to 92.50% in 2022 among children at ages of 12 years and older in Tianzhu Tibetan Autonomous County, respectively.

CONCLUSIONS

There has been a reduction in the detection of echinococcosis in humans and domestic animals and the positive rate of Echinococcus coproantigens in dogs and a rise in the awareness of the echinococcosis control knowledge following the implementation of the central government-funded echinococcosis control programme in Tianzhu Tibetan Autonomous County, Gansu Province; however, integrated echinococcosis control measures are still required for further control of the prevalence of echinococcosis.

OsDWARF10, transcriptionally repressed by OsSPL3, regulates the nutritional metabolism of polished rice

Strigolactone (SL) plays essential roles in plant development and the metabolism of rice leaves. However, the impact of SL on the accumulation of nutritional metabolites in polished rice, as well as the transcription factors directly involved in SL synthesis, remains elusive. In this study, we performed a metabolome analysis on polished rice samples from mutants of an SL biosynthetic gene, OsDWARF10 (OsD10). Compared with those in the wild type plants, primary and secondary metabolites exhibited a series of alterations in the d10 mutants. Notably, the d10 mutants showed a substantial increase in the amino acids and vitamins content. Through a yeast one-hybridization screening assay, we identified OsSPL3 as a transcription factor that binds to the OsD10 promoter, thereby inhibiting OsD10 transcription in vivo and in vitro. Furthermore, we conducted a metabolic profiling analysis in polished rice from plants that overexpressed OsSPL3 and observed enhanced levels of amino acids and vitamins. This study identified a novel transcriptional repressor of the SL biosynthetic gene and elucidated the regulatory roles of OsSPL3 and OsD10 on the accumulation of nutritional metabolites in polished rice.

Genome-wide association study for charcoal rot resistance in soybean harvested in Kazakhstan

Charcoal rot (CR) caused by the fungal pathogen Macrophomina phaseolina is a devastating disease affecting soybean (Glycine max (L.) Merrill.) worldwide. Identifying the genetic factors associated with resistance to charcoal rot is crucial for developing disease-resistant soybean cultivars. In this research, we conducted a genome-wide association study (GWAS) using different models and genotypic data to unravel the genetic determinants underlying soybean resistance to сharcoal rot. The study relied on a panel of 252 soybean accessions, comprising commercial cultivars and breeding lines, to capture genetic variations associated with resistance. The phenotypic evaluation was performed under natural conditions during the 2021-2022 period. Disease severity and survival rates were recorded to quantify the resistance levels in the accessions. Genotypic data consisted of two sets: the results of genotyping using the Illumina iSelect 6K SNP (single-nucleotide polymorphism) array and the results of whole-genome resequencing. The GWAS was conducted using four different models (MLM, MLMM, FarmCPU, and BLINK) based on the GAPIT platform. As a result, SNP markers of 11 quantitative trait loci associated with CR resistance were identified. Candidate genes within the identified genomic regions were explored for their functional annotations and potential roles in plant defense responses. The findings from this study may further contribute to the development of molecular breeding strategies for enhancing CR resistance in soybean cultivars. Marker-assisted selection can be efficiently employed to accelerate the breeding process, enabling the development of cultivars with improved resistance to сharcoal rot. Ultimately, deploying resistant cultivars may significantly reduce yield losses and enhance the sustainability of soybean production, benefiting farmers and ensuring a stable supply of this valuable crop.

Comparative Metabolomic Analysis Reveals the Role of OsHPL1 in the Cold-Induced Metabolic Changes in Rice

Cytochrome P450 (CYP74) family members participate in the generation of oxylipins and play essential roles in plant adaptation. However, the metabolic reprogramming mediated by CYP74s under cold stress remains largely unexplored. Herein, we report how cold-triggered OsHPL1, a member of the CYP74 family, modulates rice metabolism. Cold stress significantly induced the expression of OsHPL1 and the accumulation of OPDA (12-oxo-phytodienoic acid) and jasmonates in the wild-type (WT) plants. The absence of OsHPL1 attenuates OPDA accumulation to a low temperature. Then, we performed a widely targeted metabolomics study covering 597 structurally annotated compounds. In the WT and hpl1 plants, cold stress remodeled the metabolism of lipids and amino acids. Although the WT and hpl1 mutants shared over one hundred cold-affected differentially accumulated metabolites (DAMs), some displayed distinct cold-responding patterns. Furthermore, we identified 114 and 56 cold-responding DAMs, specifically in the WT and hpl1 mutants. In conclusion, our work characterized cold-triggered metabolic rewiring and the metabolic role of OsHPL1 in rice.

Nondestructive 3D phenotyping method of passion fruit based on X-ray micro-computed tomography and deep learning

Passion fruit is a tropical liana of the Passiflora family that is commonly planted throughout the world due to its abundance of nutrients and industrial value. Researchers are committed to exploring the relationship between phenotype and genotype to promote the improvement of passion fruit varieties. However, the traditional manual phenotyping methods have shortcomings in accuracy, objectivity, and measurement efficiency when obtaining large quantities of personal data on passion fruit, especially internal organization data. This study selected samples of passion fruit from three widely grown cultivars, which differed significantly in fruit shape, size, and other morphological traits. A Micro-CT system was developed to perform fully automated nondestructive imaging of the samples to obtain 3D models of passion fruit. A designed label generation method and segmentation method based on U-Net model were used to distinguish different tissues in the samples. Finally, fourteen traits, including fruit volume, surface area, length and width, sarcocarp volume, pericarp thickness, and traits of fruit type, were automatically calculated. The experimental results show that the segmentation accuracy of the deep learning model reaches more than 0.95. Compared with the manual measurements, the mean absolute percentage error of the fruit width and length measurements by the Micro-CT system was 1.94% and 2.89%, respectively, and the squares of the correlation coefficients were 0.96 and 0.93. It shows that the measurement accuracy of external traits of passion fruit is comparable to manual operations, and the measurement of internal traits is more reliable because of the nondestructive characteristics of our method. According to the statistical data of the whole samples, the Pearson analysis method was used, and the results indicated specific correlations among fourteen phenotypic traits of passion fruit. At the same time, the results of the principal component analysis illustrated that the comprehensive quality of passion fruit could be scored using this method, which will help to screen for high-quality passion fruit samples with large sizes and high sarcocarp content. The results of this study will firstly provide a nondestructive method for more accurate and efficient automatic acquisition of comprehensive phenotypic traits of passion fruit and have the potential to be extended to more fruit crops. The preliminary study of the correlation between the characteristics of passion fruit can also provide a particular reference value for molecular breeding and comprehensive quality evaluation.

A Case Series of Bosworth Fracture-Dislocations and Review of 129 Reported Cases

Introduction

Bosworth fracture dislocations of the ankle are rare injuries of the ankle caused by extreme external rotation of the supinated foot where the proximal fibula fracture fragment is posteriorly dislocated and entrapped behind the posterior-lateral ridge of the tibia. This case series aims to document three such cases treated in our institution over a nine year period. We also provide a review of 129 cases in the existing literature.

Materials and methods

Medical records and relevant radiographs for each patient were analysed and collected from the time of presentation till the point of latest follow-up. During each clinic visit, all physical exam findings as well as all complications were recorded. The American Foot and Ankle Society (AOFAS) Hindfoot score was also tabulated for each patient at the point of latest review.

Results

Closed reduction was unsuccessful in all three patients, and all required open reduction. One patient had an uncomplicated recovery whilst the remaining two suffered significant soft tissue complications. One patient suffered severe soft tissue swelling preventing primary closure at the time of surgery, whilst another suffered post-operative wound dehiscence and infection. Eventually all fractures healed, and all three patients obtained satisfactory AOFAS scores.

Conclusion

The diagnosis of Bosworth fracture dislocations of the ankle is often delayed or missed, due to its rare occurrence. Closed reduction is often unsuccessful, and early open reduction is required to avoid poor clinical outcomes due to severe soft tissue damage or even compartment syndrome.

Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice

Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation. However, the role of rhythmicity in altering the global aspects of metabolism is poorly characterized. Here, we subjected four rice (Oryza sativa) varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism. More than 40% of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions. Compared with the metabolome, the transcriptome was more strongly regulated by rhythm; however, the rhythm of metabolites had an obvious opposite trend between day and night. Through association analysis, the time delay of rhythmic transmission from the transcript to the metabolite level was ∼4 h under long-day conditions, although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism. The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network, whereas the correlation of some rhythmic metabolites, such as branched-chain amino acids (BCAAs), was significantly different intervariety. We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn. Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity.

Integrative Analysis of Metabolome and Transcriptome Reveals the Role of Strigolactones in Wounding-Induced Rice Metabolic Re-Programming

Plants have evolved mechanisms to adapt to wounding, a threat occurring separately or concomitantly with other stresses. During the last decades, many efforts have been made to elucidate the wounding signaling transduction. However, we know little about the metabolic re-programming under wounding, let alone whether and how strigolactones (SLs) participate in this progress. Here, we reported a metabolomic and transcriptomic analysis of SLs synthetic and signal mutants in rice before and after wounding. A series of metabolites differentially responded to wounding in the SLs mutants and wild-type rice, among which flavones were enriched. Besides, the SLs mutants accumulated more jasmonic acid (JA) and jasmonyl isoleucine (JA-lle) than the wild-type rice after wounding, suggesting an interplay of SLs and JAs during responding to wounding. Further transcriptome data showed that cell wall, ethylene, and flavones pathways might be affected by wounding and SLs. In addition, we identified candidate genes regulated by SLs and responding to wounding. In conclusion, our work provides new insights into wounding-induced metabolic re-programming and the SLs’ function.

A clinical investigation into the usefulness of fractional exhaled nitric oxide in guiding glucocorticoid therapy in children with bronchial asthma

The present study aims to investigate the value of fractional exhaled nitric oxide (FeNO) combined with pulmonary function in guiding the dose adjustment of inhaled glucocorticosteroids (ICSs) in children with asthma. A total of 133 children aged 6-12 years with newly diagnosed asthma were enrolled as the study subjects and randomly divided into the experimental group (n=68) and the control group (n=65). After three months of ICS treatment, in the experimental group, the dose of ICSs was adjusted based on the control status of the children and the results of the pulmonary function tests and FeNO assays, and in the control group, the dose was adjusted based on the control status of the children and the results of the pulmonary function tests. After another three months of treatment, the number of acute asthma attacks and the Childhood Asthma Control Test (C-ACT) scores were compared between the two groups, and the outcome of pulmonary function tests and FeNO assays during treatment were analyzed. When examining pulmonary function and FeNO levels, when compared with before treatment, there were no statistically significant differences in either group or between the groups after three months of ICS treatment (P>0.05). After dose adjustment and another three months of treatment, when compared with the control group, the improvement in pulmonary function in the experimental group was greater, the reduction in FeNO levels was greater, the incidence of acute asthma attacks was lower, and the C-ACT score was higher (P<0.05). We concluded that the combination of FeNO assays and pulmonary function tests to guide the ICS dose adjustment in children with asthma could improve asthma control and reduce the risk of acute asthma attacks.

[Metagenomic data-analysis reveals enrichment of lipopolysaccharide synthesis in the gut microbiota of atrial fibrillation patients]

Objective: To investigate the functional changes of key gut microbiota (GM) that produce lipopolysaccharide (LPS) in atrial fibrillation (AF) patients and to explore their potential role in the pathogenesis of AF. Methods: This was a prospective cross-sectional study. Patients with AF admitted to Beijing Chaoyang Hospital of Capital Medical University were enrolled from March 2016 to December 2018. Subjects with matched genetic backgrounds undergoing physical examination during the same period were selected as controls. Clinical baseline data and fecal samples were collected. Bacterial DNA was extracted and metagenomic sequencing was performed by using Illumina Novaseq. Based on metagenomic data, the relative abundances of KEGG Orthology (KO), enzymatic genes and species that harbored enzymatic genes were acquired. The key features were selected via the least absolute shrinkage and selection operator (LASSO) analysis. The role of GM-derived LPS biosynthetic feature in the development of AF was assessed by receiver operating characteristic (ROC) curve, partial least squares structural equation modeling (PLS-SEM) and logistic regression analysis. Results: Fifty nonvalvular AF patients (mean age: 66.0 (57.0, 71.3), 32 males(64%)) were enrolled as AF group. Fifty individuals (mean age 55.0 (50.5, 57.5), 41 males(82%)) were recruited as controls. Compared with the controls, AF patients showed a marked difference in the GM genes underlying LPS-biosynthesis, including 20 potential LPS-synthesis KO, 7 LPS-biosynthesis enzymatic genes and 89 species that were assigned as taxa harbored nine LPS-enzymatic genes. LASSO regression analysis showed that 5 KO, 3 enzymatic genes and 9 species could be selected to construct the KO, enzyme and species scoring system. Genes enriched in AF group included 2 KO (K02851 and K00972), 3 enzymatic genes (LpxH, LpxC and LpxK) and 7 species (Intestinibacter bartlettii、Ruminococcus sp. JC304、Coprococcus catus、uncultured Eubacterium sp.、Eubacterium sp. CAG:251、Anaerostipes hadrus、Dorea longicatena). ROC curve analysis revealed the predictive capacity of differential GM-derived LPS signatures to distinguish AF patients in terms of above KO, enzymatic and species scores: area under curve (AUC)=0.957, 95%CI: 0.918-0.995, AUC=0.940, 95%CI 0.889-0.991, AUC=0.972, 95%CI 0.948-0.997. PLS-SEM showed that changes in lipopolysaccharide-producing bacteria could be involved in the pathogenesis of AF. The key KO mediated 35.17% of the total effect of key bacteria on AF. After incorporating the clinical factors of AF, the KO score was positively associated with the significantly increased risk of AF (OR<0.001, 95%CI:<0.001-0.021, P<0.001). Conclusion: Microbes involved in LPS synthesis are enriched in the gut of AF patients, accompanied with up-regulated LPS synthesis function by encoding the LPS-enzymatic biosynthesis gene.

Development of a widely targeted volatilomics method for profiling volatilomes in plants

Volatile organic compounds play essential roles in plant environment interactions as well as determining the fragrance of plants. Although gas chromatography-mass spectrometry-based untargeted metabolomics is commonly used to assess plant volatiles, it suffers from high spectral convolution, low detection sensitivity, a limited number of annotated metabolites, and relatively poor reproducibility. Here, we report a widely targeted volatilomics (WTV) method that involves using a "targeted spectra extraction" algorithm to address spectral convolution, constructing a high-coverage MS² spectral tag library to expand volatile annotation, adapting a multiple reaction monitoring mode to improve sensitivity, and using regression models to adjust for signal drift. The newly developed method was used to profile the volatilome of rice grains. Compared with the untargeted method, the newly developed WTV method shows higher sensitivity (for example, the signal-to-noise ratio of guaicol increased from 4.1 to 18.8), high annotation coverage (the number of annotated volatiles increased from 43 to 132), and better reproducibility (the number of volatiles in quality control samples with relative standard deviation value below 30.0% increased from 14 to 92 after normalization). Using the WTV method, we studied the metabolic responses of tomato to environmental stimuli and profiled the volatilomes of different rice accessions. The results identified benzothiazole as a potential airborne signal priming tomato plants for enhanced defense and 2-nonanone and 2-heptanone as novel aromatic compounds contributing to rice fragrance. These case studies suggest that the widely targeted volatilomics method is more efficient than those currently used and may considerably promote plant volatilomics studies.

Buntanetap, a Novel Translational Inhibitor of Multiple Neurotoxic Proteins, Proves to Be Safe and Promising in Both Alzheimer's and Parkinson's Patients

BACKGROUND

Previously we reported the clinical safety and pharmacological activity of buntanetap (known as Posiphen or ANVS401) in healthy volunteers and mild cognitive impaired (MCI) patients (21). The data supported continued clinical evaluation of buntanetap for treating Alzheimer's Disease (AD). Neurodegenerative diseases such as AD and Parkinson's disease (PD) share several pathological manifestations, including increased levels of multiple neurotoxic protein aggregates. Therefore, a treatment strategy that targets toxic species common to both disorders can potentially provide better clinical outcomes than attacking one neurotoxic protein alone. To test this hypothesis, we recently completed a clinical study in early AD and early PD participants and report the data here.

OBJECTIVES

We evaluated safety, pharmacokinetics, biomarkers, and efficacy of buntanetap in treating early AD and PD patients.

DESIGN

Double-blind, placebo-controlled, multi-center study.

SETTING

13 sites in the US participated in this clinical trial. The registration number is NCT04524351 at ClinicalTrials.gov.

PARTICIPANTS

14 early AD patients and 54 early PD patients.

INTERVENTION

AD patients were given either 80mg buntanetap or placebo QD. PD patients were given 5mg, 10mg, 20mg, 40mg, 80mg buntanetap or placebo QD.

MEASUREMENTS

Primary endpoint is safety and tolerability; secondary endpoint is pharmacokinetics of buntanetap in plasma; exploratory endpoints are 1) biomarkers in cerebrospinal fluid (CSF) in both AD and PD patients 2) psychometric tests specific for AD (ADAS-Cogs and WAIS coding test) or PD (MDS-UPDRS and WAIS coding test).

RESULTS

Buntanetap was safe and well tolerated. Biomarker data indicated a trend in lowering levels of neurotoxic proteins and inflammatory factors and improving axonal integrity and synaptic function in both AD and PD cohorts. Psychometric tests showed statistically significant improvements in ADAS-Cog11 and WAIS coding in AD patients and MDS-UPDRS and WAIS coding in PD patients.

CONCLUSIONS

Buntanetap is well tolerated and safe at doses up to 80mg QD in both AD and PD patients. Cmax and AUC increase with dose without evidence for a plateau up to 80mg QD. The drug shows promising evidence in exploratory biomarker and efficacy measures. Further evaluation of buntanetap in larger, longer-term clinical trials for the treatment of AD and PD are warranted.

Viscoelasticity of 3D actin networks dictated by the mechanochemical characteristics of cross-linkers

In this study, we report a computational investigation on how the mechanochemical characteristics of crosslinking molecules influence the viscoelasticity of three dimensional F-actin networks, an issue of key interest in analyzing the behavior of living cells and biological gels. In particular, it was found that the continuous breakage and rebinding of cross-linkers result in a locally peaked loss modulus in the rheology spectrum of the network, reflecting the fact that maximum energy dissipation is achieved when the driving frequency of the applied oscillating shear becomes comparable to the dissociation/association rate of crosslinking molecules. In addition, we showed that when subjected to constant rate of shear, an actin network can exhibit either strain hardening or softening depending on the ratio between the loading rate and unbinding speed of cross-linkers. A criterion for predicting the transition from softening to hardening was also obtained, in agreement with recent experiments. Finally, significant structural evolution was found to occur in random networks undergoing mechanical "training" (i.e. under a constant applied shear stress over a period of time), eventually leading to a pronounced anisotropic response of the network afterward which again is consistent with experimental observations.

Sustainable bio-bricks prepared with synthetic urine enabled by biomineralization reactions

In this study, mineralization during brick preparation was performed with ureolytic bacterium, Lysinibacillus fusiformis that use urine as a substrate, omitting the heat that is normally required. Artificial urine for reasons of standardization was used to grow the bacterium for bio-bricks made of clay and cement, but their mineralization was enabled by biological activity instead of by heat. Scanning electron microscopy and energy dispersion X-ray spectroscopy were conducted to analyse the microstructures formed by L. fusiformis that precipitated various minerals in synthetic urine. The brick specimens were tested for compressive strength that was 59% more than control ones, whereas porosity of bio-bricks was 13% compared to 22% of control specimens. The minerals formed in the bio-bricks confirmed as struvite, apatite and calcite by Fourier-transform infrared spectroscopy and X-ray diffraction spectra, were responsible for improved strength and reduced porosity. The research provided evidence in utilizing ureolytic bacteria as a mode to mineralize clay in brick production with the use of (artificial) urine as a substrate.

Geolocation Inference of Forensic Individual Origin by Soil Metagenomic Analysis

Abstract

Objective To preliminarily discuss the feasibility of geolocation inference of forensic individual origin by soil metagenomic analysis. Methods The 33 soil samples from Heilongjiang, Qinghai and Tibet were collected, total bacterial DNA in the samples were extracted, and universal primers were used to amplify the V3 and V4 hypervariable region of bacterial 16S rDNA. The region was sequenced by high-throughput sequencing （HTS） with the MiSeq sequencer. Bioinformatics analysis such as species composition and sample comparison was performed on sequencing data. The richness index and diversity index were calculated based on operational taxonomic unit （OTU） results. Results A total of 2 720 149 sequences were generated by sequencing. Those sequences were clustered into 114 848 OTUs. The Chao1 indexes of soil microorganisms in Heilongjiang, Qinghai, and Tibet were 797.45, 745.11 and 535.98, respectively, and Shannon indexes were 6.46, 6.36 and 6.25, respectively. The number of bacterial species and the community diversity in the soil from high to low were Heilongjiang > Qinghai > Tibet. The composition of soil bacteria in three provinces at various classification levels were obtained, the dominant genuses in Heilongjiang were Chthoniobacteraceae DA101 and an unannotated genus of Thermogemmatisporaceae; the dominant genuses in Qinghai were an unannotated genus of Cytophagaceae and an unannotated genus of Nocardioidaceae; the dominant genuses in Tibet were an unannotated genus of Comamonadaceae and Verrucomicrobiaceae Luteolibacter. The results of principal co-ordinates analysis demonstrated that, according to the weighted UniFrac analysis, the three principle components represented 56.36% of the total variable, and according to the unweighted UniFrac analysis, the three principle components represented 34.81% of the total variable. The samples from the same province could be clustered together, and the species and content of soil microorganisms from different provinces were significantly different. Conclusion Based on the metagenomic analysis method, soil samples from different regions can be effectively distinguished, which has potential application value in geolocation inference of forensic individual origin in the future.

Safety and efficacy of irreversible electroporation treatment in hepatobiliary and pancreatic tumours: a single-centre experience

AIM

To report initial experience with irreversible electroporation (IRE) in a single tertiary oncology centre and to describe its role in the management of liver and pancreatic tumours.

MATERIALS AND METHODS

The present study was a retrospective review of the technical success rate, complications, and treatment efficacy of patients who had undergone IRE treatment for hepatobiliary and pancreatic tumours between February 2014 to January 2020. The patients were divided into two cohorts: first 30 patients (cohort A) and subsequent 70 patients (cohort B) after a change in protocol.

RESULTS

One hundred IRE procedures (n=69 liver lesions; n=28 pancreatic lesions, n=3 nodal disease) were reviewed. The overall technical success rate was 99%. Early and immediate complications were 4% and 3%, respectively. In cohort A, the complete tumour ablation rate was 65% (13/20) for hepatic tumours, 20% (1/5) for locally advanced pancreatic adenocarcinoma, 50% (2/4) for pancreatic neuroendocrine tumours, and 0% (0/1) for nodal metastasis. For cohort B, the rate improved to 87.76% (43/49) for hepatic tumours, 28.57% (4/14) for locally advanced pancreatic adenocarcinoma, 80% (4/5) for pancreatic neuroendocrine, and 50% (1/2) for nodal metastasis. After the initial cohort A, cohort B showed a significant increase in the initial complete ablation rate in hepatic tumours (p=0.028).

CONCLUSION

IRE is a complex technique with a steep learning curve. It is safe, effective, and is valuable in the treatment of liver tumours that are unsuitable or considered high risk for conventional thermal ablation. Its role in the management of pancreatic tumours is less clear and requires larger studies.

A Novel Method to Construct Binary CRISPR Vectors for Plant Transformation by Single Round of PCR Amplification

CRISPR/Cas9 is an established and flexible tool for genome editing. However, most methods used to generate expression clones for the CRISPR/Cas9 are time-consuming. Hence, we have developed a one-step protocol to introduce sgRNA expression cassette(s) directly into binary vectors ( Liu et al., 2020 ). In this approach, we have optimized the multiplex PCR to produce an overlapping PCR product in a single reaction to generate the sgRNA expression cassette. We also amplified two sgRNA expression cassettes through a single round of PCR. Then, the sgRNA expression cassette(s) is cloned into the binary vectors in a Gateway LR or Golden gate reaction. The system reported here provides a much more efficient and simpler procedure to construct expression clones for CRISPR/Cas9-mediated genome editing. In this protocol, we describe the detailed step-by-step instructions for using this system.

Cross-Species Comparison of Metabolomics to Decipher the Metabolic Diversity in Ten Fruits

Fruits provide humans with multiple kinds of nutrients and protect humans against worldwide nutritional deficiency. Therefore, it is essential to understand the nutrient composition of various fruits in depth. In this study, we performed LC-MS-based non-targeted metabolomic analyses with ten kinds of fruit, including passion fruit, mango, starfruit, mangosteen, guava, mandarin orange, grape, apple, blueberry, and strawberry. In total, we detected over 2500 compounds and identified more than 300 nutrients. Although the ten fruits shared 909 common-detected compounds, each species accumulated a variety of species-specific metabolites. Additionally, metabolic profiling analyses revealed a constant variation in each metabolite’s content across the ten fruits. Moreover, we constructed a neighbor-joining tree using metabolomic data, which resembles the single-copy protein-based phylogenetic tree. This indicates that metabolome data could reflect the genetic relationship between different species. In conclusion, our work enriches knowledge on the metabolomics of fruits, and provides metabolic evidence for the genetic relationships among these fruits.

Intestinal epithelium-derived BATF3 promotes colitis-associated colon cancer through facilitating CXCL5-mediated neutrophils recruitment

Inflammation is a critical player in the development and progression of colon cancer. Basic leucine zipper transcription factor ATF-like 3 (BATF3) plays an important role in infection and tumor immunity through regulating the development of conventional type 1 dendritic cells (cDC1s). However, the function of BATF3 in colitis and colitis-associated colon cancer (CAC) remains unclear. Here, BATF3 wild-type and knockout mice were used to construct an AOM/DSS-induced CAC model. In addition, DSS-induced chronic colitis, bone marrow cross-transfusion (BMT), neutrophil knockout, and other animal models were used for in-depth research. We found that BATF3 deficiency in intestinal epithelial cells rather than in cDC1s inhibited CAC, which was depended on inflammatory stimulation. Mechanistically, BATF3 directly promoted transcription of CXCL5 by forming a heterodimer with JunD, and accelerated the recruitment of neutrophils through the CXCL5-CXCR2 axis, ultimately increasing the occurrence and development of CAC. Tissue microarray and TCGA data also indicated that high expression of BATF3 was positively correlated with poor prognosis of colorectal cancer and other inflammation-related tumors. In summary, our results demonstrate that intestinal epithelial-derived BATF3 relies on inflammatory stimulation to promote CAC, and BATF3 is expected to be a novel diagnostic indicator for colitis and CAC.

Benefiting others and self: Production of vitamins in plants

Vitamins maintain growth and development in humans, animals, and plants. Because plants serve as essential producers of vitamins, increasing the vitamin contents in plants has become a goal of crop breeding worldwide. Here, we begin with a summary of the functions of vitamins. We then review the achievements to date in elucidating the molecular mechanisms underlying how vitamins are synthesized, transported, and regulated in plants. We also stress the exploration of variation in vitamins by the use of forward genetic approaches, such as quantitative trait locus mapping and genome-wide association studies. Overall, we conclude that exploring the diversity of vitamins could provide new insights into plant metabolism and crop breeding.

Predictors of plaque erosion in current smokers and non-current smokers presented with ST-segment elevation myocardial infarction: an optical coherence tomography study

Background

Plaque erosion with subsequent coronary thrombosis is considered as an important cause of ST-segment elevation myocardial infarction (STEMI). Smoking is a major risk factor for acute coronary thrombosis. However, the relationship between current smoking status and plaque erosion has not been systematically investigated.

Purpose

The present study aimed to investigate predictors of plaque erosion in current smokers and non-current smokers with STEMI by using optical coherence tomography (OCT).

Methods

Between January 2015 to December 2017, a total of 1313 STEMI patients underwent pre-intervention OCT of culprit lesion were enrolled and divided into two groups based on current smoking status: current smoking group (n=713) and non-current smoking group (n=600). Using established criteria, quantitative and qualitative underlying plaque characteristics were assessed by OCT. Clinical, angiographic and OCT characteristics of all enrolled patients were recorded. Univariable and multivariable logistic regression analyses were used to identify predictors of plaque erosion in two groups.

Results

Plaque erosion were found in 30.9% (220/713) culprit lesions in current smoking group and 20.8% (125/600) of those in non-current smoking group detected by OCT. In multivariate regression analysis, the predictors that strongly related to plaque erosion in the current smoking group were nearby bifurcation (OR: 4.84; 95% CI:2.38–9.87; p&lt;0.001); the minimum fiber cap thickness (FCT, OR:1.05; 95% CI:1.03–1.08; p&lt;0.001); thin-cap fibroatheroma (TCFA, OR: 0.22; 95% CI: 0.07–0.67; p=0.007) and lipid core length (OR: 0.91; 95% CI: 0.84–0.97; p=0.007). The predictors in the non-current smoking group were nearby bifurcation (OR: 4.84; 95% CI: 2.38–9.87; p=0.006); the minimal FCT (OR: 1.09; 95% CI: 1.06–1.13; p&lt;0.001); multi-vessel disease (MVD, OR: 0.43; 95% CI: 0.19–0.97; p=0.042) and dyslipidemia (OR: 0.34; 95% CI: 0.14–0.84; p=0.020).

Conclusions

Predictors of plaque erosion causing STEMI onset are different between current smokers and non-current smoker, with nearby bifurcation and thicker minimal FCT both predicting plaque erosion in two groups of patients.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): National Key Research and Development Program of China, National Natural Science Foundation of China.

Coronary plaque characteristics associated with reduced thrombolysis in myocardial infarction flow in st-segment elevation myocardial infarction patients with plaque erosion

Background

It has been reported that the lumen factors of the culprit lesions are related to Thrombolysis in Myocardial Infarction (TIMI) flow grade in ST-Segment–Elevation Myocardial Infarction (STEMI) patients, but the factors of reduced TIMI flow in plaque erosion have not been studied.

Methods

329 STEMI patients with plaque erosion who underwent pre-intervention optical coherence tomography after thrombectomy were included and divided into 2 groups according to preprocedural TIMI flow grade [TIMI 0–1 (n=219) and TIMI 2–3 (n=110)].

Results

The patients with older age (55.7±11.1yrs vs. 51.8±10.6yrs, P=0.003) and diabetes patients (18.3% vs. 8.2%, P=0.015) had poorer TIMI flow, and the patients with reduced TIMI flow grade have lower initial cTnI (1.2ng/mL vs. 2.1ng/mL, P=0.023). The lesion in the LAD had better blood flow than the lesion in RCA (P=0.003), and the patients in TIMI 0–1 grade had more lipid plaques (53.9% vs. 41.8%, P=0.039), more macrophage (59.8% vs. 41.8%, P=0.002), and more calcification (34.2% vs. 21.8%, P=0.020). There was no statistically significant difference in the descriptive indicators of lipid or lumen between the two groups. And In a multivariate logistic regression model, the independent correlation factors of reduced TIMI flow grade in erosion patients were age, diabetes mellitus, lesion vessel, and macrophage.

Conclusions

In STEMI patients with plaque erosion non-lumen factors greatly affect flow, which suggests that systemic treatment is as important as local treatment for plaque erosion.

Flow Chart

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): National Natural Science Foundation of China (81827806, 81801861), National Key R&D Program of China (2016YFC1301100)

Morphological characteristics of plaque erosion with noncritical coronary stenosis: an optical coherence tomography study

Background

Plaque erosion is a frequent and important mechanism of acute coronary thrombosis only secondary to plaque rupture. Recent studies suggested plaque erosion with noncritical stenosis could be treated conservatively that distinct from those with critical stenosis. However, characteristics of plaque erosions with different coronary stenosis remain unknown.

Purpose

The present study aimed to investigate morphological features of plaque erosions with different coronary stenosis using optical coherence tomography (OCT).

Methods

Consecutive ST-segment elevated myocardial infarction (STEMI) patients with OCT images of culprit lesion between August 2014 and December 2017 were enrolled and 348 cases presented with plaque erosion identified by OCT. Based on the severity of lumen area stenosis [calculated by (1-minimal lumen area/reference lumen area) * 100%], all culprit plaque erosions were divided into three groups: Group A (area stenosis&lt;50%, n=50, 14.4%); Group B (50%≤area stenosis&lt;75%, n=146, 42.0%); Group C (area stenosis≥75%, n=152, 43.7%). Clinical characteristics, lesion features detected by coronary angiography and OCT were compared among three groups.

Results

Of all 348 STEMI patients with plaque erosions, patients in Group A were youngest (p=0.008) and had the lowest frequency of hypertension (p=0.029) as compared with those in Group B and C. Angiographic analysis showed 72.0% of plaque erosions in Group A located in LAD, while 67.8% in Group B and 53.9% in Group C (p=0.039). OCT findings (Figure 1-A) showed the prevalence of fibrous plaque was significantly highest in Group A than those in Group B and C (82.0% vs. 54.8% vs. 34.9%, p&lt;0.001), whereas lipid rich plaque was most frequent in Group C (16.0% vs. 43.8% vs. 62.5%, p&lt;0.001). The prevalence of macrophage (p&lt;0.001), microvessel (p=0.009) and cholesterol crystals (p&lt;0.001) increased gradually from plaque erosion with lumen area stenosis &lt;50% to 50–75% to ≥75%. Notably, compared with Group B and C, nearby bifurcation was most common in Group A (72.0% vs. 67.1% vs. 55.3%, p=0.036). Multivariable regression analyses (Figure 1-B) showed fibrous plaque and nearby bifurcation were independently associated with plaque erosion with noncritical stenosis (area stenosis&lt;75%).

Conclusion

56.3% plaque erosion in STEMI patients presented with noncritical stenosis, having distinct morphological features from erosion with critical stenosis. Fibrous plaque and nearby bifurcation were independently associated with the presence of noncritically stenotic plaque erosion, remaining a desire to tailor treatment therapy to individual patients.

Figure 1

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): National Key R&D Program of China

Relation of microchannel identified by optical coherence tomography to clinical, angiography and other plaque morphological characteristics in ST-segment Elevation myocardial infarction patients

Background

Previous studies have suggested that Microchannel (MC) is associated with plaque progression and vulnerability. Optical coherence tomography (OCT) could provide a chance to directly visualize plaque neovascularization in vivo.

Methods

1268 STEMI patients who underwent OCT examination of culprit lesion were included and divided into MC group (the culprit plaque with MC, n=560) and no-MC group (the culprit plaque without MC, n=708). MC was defined as a no-signal tubuloluminal structure on the cross-sectional optical coherence tomographic image. Clinical, angiography and other plaque morphological characteristics were compared between the two groups. Logistic regression analysis was used to identify independent predictors of MC in overall. In addition, the difference of predictors on MC was found in plaque rupture (PR) and plaque erosion (PE).

Results

Significant differences between MC group and no-MC group were found in the frequency of thin-cap fibroatheroma (74.6% vs 64.4%, p&lt;0.001), lipid plaque (91.8% vs 82.9%, p&lt;0.001), lipid core length (13.7±6.5mm vs 12.6±6.3mm, p=0.006) and the minimal lumen area (MLA, 1.95±0.98mm2 vs 2.10±1.58mm2, p=0.046). In MC group, the other vulnerable plaque morphological characteristics, such as macrophage (88.8% vs 75.1%, p&lt;0.001), cholesterol crystal (39.6% vs 32.9%, p=0.013), spotty calcification (38.6% vs 29.5%, p&lt;0.001) were more frequent. And compared with MLA the more locations of the culprit lesion in MC group was proximal (proximal, 47.3% vs 38.1%, at MLA, 38.2% vs 44.2%, distal, 14.5% vs 17.7%, p=0.004).The difference of Hemoglobin (Hb, 147.5±16.9g/L vs 144.1±18.2g/L, p&lt;0.001), lipidemia (TC, 188.7±43.6mmol/L vs 180.8±40.0mmol/L, p&lt;0.001, LDL-C, 121.5±37.4mmol/L vs 115.7±36.8mmol/L, p=0.005, and TC/HDL, 4.0±1.6 vs 3.8±1.0, p&lt;0.001), and hypertension (50.7% vs 44.2%, p=0.021) between 2 groups was statistically significant. Multivariable logistic regression models showed 7 independent parameters associated with MC in culprit plaque of overall: hypertension, Hb, TC, MLA, lesion location (compared with MLA), lipid core length, macrophage, spotty calcification. In addition, Hb, TC and MLA were common predictors of MC in PR and PE, however, the predictive effect of MLA on MC was opposite in PR [OR (95% CI)=1.266 (1.095–1.463), p=0.001] and PE [OR (95% CI)=0.742 (0.597–0.922), p=0.007].

Conclusions

MC in culprit plaque is associated with more lipid (especially cholesterol), higher Hb, hypertension, lesion location (compared with MLA) and the other vulnerable plaque morphological characteristics. The predictors of MC were different in plaque rupture and plaque erosion.

Flow chart

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): National Natural Science Foundation of China (81827806, 81801861); National Key R&D Program of China (2016YFC1301100)

Prevalence of hypoxia and correlation with glycolytic metabolism and angiogenic biomarkers in metastatic colorectal carcinoma

PURPOSE

Hypoxia is associated with aggressive tumour behaviour and can influence response to systemic therapy and radiotherapy. The prevalence of hypoxia in metastatic colorectal cancer is poorly understood, and the relationship of hypoxia to patient outcomes has not been clearly established. The aims of the study were to evaluate hypoxia in metastatic colorectal cancer with [¹⁸F]Fluoromisonidazole ([¹⁸F]FMISO PET) and correlate these findings with glycolytic metabolism ([¹⁸F]FDG PET) and angiogenic blood biomarkers and patient outcomes.

METHODS

Patients with metastatic colorectal cancer received routine staging investigations and both [¹⁸F] FMISO PET and [¹⁸F] FDG PET scans. Correlative blood specimens were also obtained at the time of the [¹⁸F] FMISO PET scan. Patient follow-up was performed to establish progression-free survival.

RESULTS

A total of 40 patients were recruited into the trial. [¹⁸F]FMISO and [¹⁸F]FDG PET scans showed a significant correlation of SUV_max (p = 0.003). A significant correlation of progression-free survival and [¹⁸F] FMISO TNR (p = 0.02) and overall survival with [¹⁸F]FMISO TNR (p = 0.003) and [¹⁸F]FDG TGV (p = 0.02) was observed. Serum levels of osteopontin, but not VEGF, correlated with [¹⁸F] FMISO and [¹⁸F]FDG PET scan parameters.

CONCLUSION

[¹⁸F]FMISO PET uptake in metastatic colorectal cancer significantly correlates with glycolytic metabolism and is predictive of progression-free and overall survival. These findings have implications for the assessment and treatment of metastatic colorectal cancer patients with novel therapies which affect tumour angiogenesis and hypoxia.

Integrative Metabolomic and Transcriptomic Analyses Reveal Metabolic Changes and Its Molecular Basis in Rice Mutants of the Strigolactone Pathway

Plants have evolved many metabolites to meet the demands of growth and adaptation. Although strigolactones (SLs) play vital roles in controlling plant architecture, their function in regulating plant metabolism remains elusive. Here we report the integrative metabolomic and transcriptomic analyses of two rice SL mutants, d10 (a biosynthesis mutant) and d14 (a perception mutant). Both mutants displayed a series of metabolic and transcriptional alterations, especially in the lipid, flavonoid, and terpenoid pathways. Levels of several diterpenoid phytoalexins were substantially increased in d10 and d14, together with the induction of terpenoid gene cluster and the corresponding upstream transcription factor WRKY45, an established determinant of plant immunity. The fact that WRKY45 is a target of IPA1, which acted as a downstream transcription factor of SL signaling, suggests that SLs contribute to plant defense through WRKY45 and phytoalexins. Moreover, our data indicated that SLs may modulate rice metabolism through a vast number of clustered or tandemly duplicated genes. Our work revealed a central role of SLs in rice metabolism. Meanwhile, integrative analysis of the metabolome and transcriptome also suggested that SLs may contribute to metabolite-associated growth and defense.

Extent of pulmonary thromboembolic disease in patients with COVID-19 on CT: relationship with pulmonary parenchymal disease

AIM

To report the severity and extent of pulmonary thromboembolic disease (PTD) in COVID-19 patients undergoing computed tomography pulmonary angiography (CTPA) in a tertiary centre.

MATERIALS AND METHODS

This is a retrospective analysis of COVID-19 patients undergoing CTPA over a period of 27 days. The presence, extent, and severity of PTD were documented. Two observers scored the pattern and extent of lung parenchymal disease including potential fibrotic features, as well as lymph node enlargement and pleural effusions. Consensus was achieved via a third observer. Interobserver agreement was assessed using kappa statistics. Student's t-test, chi-squared, and Mann-Whitney U-tests were used to compare imaging features between PTD and non-PTD sub-groups.

RESULTS

During the study period, 100 patients with confirmed COVID-19 underwent CTPA imaging. Ninety-three studies were analysed, excluding indeterminate CTPA examinations. Overall incidence of PTD was 41/93 (44%) with 28/93 patients showing small vessel PTD (30%). D-dimer was elevated in 90/93 (96.8%) cases. A high Wells' score did not differentiate between PTD and non-PTD groups (p=0.801). The interobserver agreement was fair (kappa=0.659) for parenchymal patterns and excellent (kappa=0.816) for severity. Thirty-four of the 93 cases (36.6%) had lymph node enlargement; 29/34 (85.3%) showed no additional source of infection. Sixteen of the 93 (17.2%) cases had potential fibrotic features.

CONCLUSION

There is a high incidence of PTD in COVID-19 patients undergoing CTPA and lack of a risk stratification tool. The present data indicates a higher suspicion of PTD is needed in severe COVID-19 patients. The concomitant presence of possible fibrotic features on CT indicates the need for follow-up.

Ultrasound-based liver elastography in the assessment of fibrosis

Ultrasound-based elastography has rapidly replaced the need for liver biopsy in most patients with chronic liver disease in recent years. The technique is now widely supported by many manufacturers. This review will introduce various current ultrasound-based elastography techniques, review the physics and scanning techniques, discuss potential cofounding factors as well as summarising the evidence for its use in staging liver fibrosis using shear-wave elastography among different disease aetiologies. Future challenges and directions will be also be discussed.

A simple and efficient cloning system for CRISPR/Cas9-mediated genome editing in rice

Rapidly growing genetics and bioinformatics studies provide us with an opportunity to obtain a global view of the genetic basis of traits, but also give a challenge to the function validation of candidate genes. CRISPR/Cas9 is an emerging and efficient tool for genome editing. To construct expression clones for the CRISPR/Cas9, most current methods depend on traditional cloning using Gateway reaction or specific type IIS restriction enzymes and DNA ligation, based on multiple steps of PCR. We developed a system for introducing sgRNA expression cassette(s) directly into plant binary vectors in one step. In this system, one sgRNA expression cassette(s) is generated by an optimized multiplex PCR, in which an overlapping PCR took place. Whilst, two sgRNA expression cassettes were amplified in a single round of PCR. Subsequently, an LR or Golden gate reaction was set up with unpurified PCR product and befitting destination vector. We are able to construct expression clones within 36 h, which greatly improves efficiency and saves cost. Furthermore, the efficiency of this system was verified by an agrobacterium-mediated genetic transformation in rice. The system reported here provides a much more efficient and simpler procedure to construct expression clones for CRISPR/Cas9-mediated genome editing.

Comparative analysis of metabolome of rice seeds at three developmental stages using a recombinant inbred line population

Plants are considered an important food and nutrition source for humans. Despite advances in plant seed metabolomics, knowledge about the genetic and molecular bases of rice seed metabolomes at different developmental stages is still limited. Here, using Zhenshan 97 (ZS97) and Minghui 63 (MH63), we performed a widely targeted metabolic profiling in seeds during grain filling, mature seeds and germinating seeds. The diversity between MH63 and ZS97 was characterized in terms of the content of metabolites and the metabolic shifting across developmental stages. Taking advantage of the ultra-high-density genetic map of a population of 210 recombinant inbred lines (RILs) derived from a cross between ZS97 and MH63, we identified 4681 putative metabolic quantitative trait loci (mQTLs) in seeds across the three stages. Further analysis of the mQTLs for the codetected metabolites across the three stages revealed that the genetic regulation of metabolite accumulation was closely related to developmental stage. Using in silico analyses, we characterized 35 candidate genes responsible for 30 structurally identified or annotated compounds, among which LOC_Os07g04970 and LOC_Os06g03990 were identified to be responsible for feruloylserotonin and l-asparagine content variation across populations, respectively. Metabolite-agronomic trait association and colocation between mQTLs and phenotypic quantitative trait loci (pQTLs) revealed the complexity of the metabolite-agronomic trait relationship and the corresponding genetic basis.

YAP-Induced Endothelial-Mesenchymal Transition in Oral Submucous Fibrosis

Oral submucous fibrosis (OSF) is a potentially malignant disorder. Current studies have shown that chewing areca nut is considered the main cause of OSF, and endothelial-mesenchymal transformation (EndMT) participates in the occurrence and development of the fibrotic lesion. However, the specific molecular mechanisms and treatments remain unclear. Here, we report the mechanism of arecoline-induced EndMT and the importance of this mechanism in OSF, and we also identify potential therapeutics for decreasing OSF incidence. We demonstrate the overexpression of Yes-associated protein (YAP) in human samples and that it was significantly associated with OSF pathologic stage. Arecoline activated YAP by increasing reactive oxygen species levels and inducing the PERK pathway (eukaryotic translation initiation factor 2 alpha kinase 3), resulting in the initiation of EndMT and leading to OSF. Verteporfin, a YAP–TEA domain pathway inhibitor, suppressed EndMT and decreased collagen accumulation, resulting in the alleviation of OSF in mice. These data indicate that arecoline regulates the activity of YAP and highlight an alternative method for treating OSF.

An audit of mammographic screen detected lesions of uncertain malignant potential (B3) diagnosed on initial image guided needle biopsy: how has our practice changed over 10 years?

AIM

To review all cases of B3 lesion diagnosed at initial image-guided needle biopsy over two 5-year cohorts to identify upgrade rates to malignancy and the effect of changing guidance on the management of such lesions.

MATERIALS AND METHODS

Data was collected retrospectively. Mammographic features, biopsy type and management were recorded for each lesion. Upgrade rates for each B3 histological category were quantified. Statistical analysis was performed using SPSS.

RESULTS

There were 224 cases in 2005-2010 and 240 cases in 2010-2015. Mammographically 211 lesions were microcalcifications, 182 masses, 65 distortions and six asymmetric densities with no difference in the mammographic features in the two cohorts. Two hundred and eight 14 G core biopsies and 256 initial vacuum-assisted biopsies were performed. There was a statistically significant reduction in benign surgical biopsies and an increase in second-line vacuum biopsy/excision in the latter cohort, with no significant change in the upgrade rate. There was an overall 6% upgrade to invasive malignancy and 13% upgrade to ductal carcinoma in situ (DCIS). The upgrade rates for the following histological categories were atypical intraductal epithelial proliferation (AIDEP) 33.2% (21/63); classical (not pleomorphic) in situ lobular neoplasia (ISLN) 18.2% (6/33); flat epithelial hyperplasia (FEA) 21.7% (20/92); papilloma with atypia 53.8% (7/13), without atypia 12.1% (8/66); and radial scar/complex sclerosing lesion with atypia 16.7% (2/12), and without atypia 7.9% (6/76).

CONCLUSION

Upgrade rates remain high for some histological categories even with first-line use of vacuum biopsy. Management of borderline lesions should be considered carefully in a multidisciplinary meeting. In many cases, the need for diagnostic surgical excision has been replaced by image-guided vacuum sampling.

Dirac nodal surfaces and nodal lines in ZrSiS

Topological semimetals are characterized by symmetry-protected band crossings, which can be preserved in different dimensions in momentum space, forming zero-dimensional nodal points, one-dimensional nodal lines, or even two-dimensional nodal surfaces. Materials harboring nodal points and nodal lines have been experimentally verified, whereas experimental evidence of nodal surfaces is still lacking. Here, using angle-resolved photoemission spectroscopy (ARPES), we reveal the coexistence of Dirac nodal surfaces and nodal lines in the bulk electronic structures of ZrSiS. As compared with previous ARPES studies on ZrSiS, we obtained pure bulk states, which enable us to extract unambiguously intrinsic information of the bulk nodal surfaces and nodal lines. Our results show that the nodal lines are the only feature near the Fermi level and constitute the whole Fermi surfaces. We not only prove that the low-energy quasiparticles in ZrSiS are contributed entirely by Dirac fermions but also experimentally realize the nodal surface in topological semimetals.