TB-DROP: deep learning-based drug resistance prediction of Mycobacterium tuberculosis utilizing whole genome mutations.

The most widely practiced strategy for constructing the deep learning (DL) prediction model for drug resistance of Mycobacterium tuberculosis (MTB) involves the adoption of ready-made and state-of-the-art architectures usually proposed for non-biological problems. However, the ultimate goal is to construct a customized model for predicting the drug resistance of MTB and eventually for the biological phenotypes based on genotypes. Here, we constructed a DL training framework to standardize and modularize each step during the training process using the latest tensorflow 2 API. A systematic and comprehensive evaluation of each module in the three currently representative models, including Convolutional Neural Network, Denoising Autoencoder, and Wide & Deep, which were adopted by CNNGWP, DeepAMR, and WDNN, respectively, was performed in this framework regarding module contributions in order to assemble a novel model with proper dedicated modules. Based on the whole-genome level mutations, a de novo learning method was developed to overcome the intrinsic limitations of previous models that rely on known drug resistance-associated loci. A customized DL model with the multilayer perceptron architecture was constructed and achieved a competitive performance (the mean sensitivity and specificity were 0.90 and 0.87, respectively) compared to previous ones. The new model developed was applied in an end-to-end user-friendly graphical tool named TB-DROP (TuBerculosis Drug Resistance Optimal Prediction: https://github.com/nottwy/TB-DROP ), in which users only provide sequencing data and TB-DROP will complete analysis within several minutes for one sample. Our study contributes to both a new strategy of model construction and clinical application of deep learning-based drug-resistance prediction methods.

Drug resistance prediction and resistance genes identification in Mycobacterium tuberculosis based on a hierarchical attentive neural network utilizing genome-wide variants.

Prediction of antimicrobial resistance based on whole-genome sequencing data has attracted greater attention due to its rapidity and convenience. Numerous machine learning-based studies have used genetic variants to predict drug resistance in Mycobacterium tuberculosis (MTB), assuming that variants are homogeneous, and most of these studies, however, have ignored the essential correlation between variants and corresponding genes when encoding variants, and used a limited number of variants as prediction input. In this study, taking advantage of genome-wide variants for drug-resistance prediction and inspired by natural language processing, we summarize drug resistance prediction into document classification, in which variants are considered as words, mutated genes in an isolate as sentences, and an isolate as a document. We propose a novel hierarchical attentive neural network model (HANN) that helps discover drug resistance-related genes and variants and acquire more interpretable biological results. It captures the interaction among variants in a mutated gene as well as among mutated genes in an isolate. Our results show that for the four first-line drugs of isoniazid (INH), rifampicin (RIF), ethambutol (EMB) and pyrazinamide (PZA), the HANN achieves the optimal area under the ROC curve of 97.90, 99.05, 96.44 and 95.14% and the optimal sensitivity of 94.63, 96.31, 92.56 and 87.05%, respectively. In addition, without any domain knowledge, the model identifies drug resistance-related genes and variants consistent with those confirmed by previous studies, and more importantly, it discovers one more potential drug-resistance-related gene.

Neck circumference as an additional predictor of cardiovascular disease mortality: A multi-center prospective population-based study in northeastern China.

BACKGROUND AND AIMS: This study aimed to assess the potential of neck circumference (NC) and neck-to-height ratio (NHR) as predictors of future cardiovascular disease (CVD) mortality in a general population from Northeastern China. METHODS: A multi-center prospective study was conducted in Northeastern China, involving 18, 796 participants. The associations between NC or NHR and the incidence of overall CVD mortality, stroke mortality, and coronary heart disease (CHD) mortality were examined using multivariate Cox regression models. Hazard ratios (HRs) and the corresponding 95% confidence intervals (CIs) were calculated. Reclassification analyses were conducted to determine the incremental predictive value of NC or NHR. RESULTS: NC was significantly associated with the risk of CVD mortality, independent of other anthropometric measurements for obesity. Individuals in the highest quartile of NC had a 1.83-fold (95% CI 1.29 to 2.61) and a 2.40-fold (95% CI 1.45 to 4.00) higher risk of overall CVD mortality and CHD mortality, respectively. Larger NC was significantly related to a heightened risk of ischemic stroke mortality, although no such association was observed with hemorrhagic stroke mortality. Furthermore, the risk of overall CVD mortality, stroke mortality, and CHD mortality increased by approximately 1.21 to 1.25 times per 1-SD change in NC. Similar findings were observed for NHR. The percentages of correct classification of overall CVD mortality improved by 12.1% and 16.3% after the addition of NC or NHR into established models, respectively. CONCLUSIONS: NC and NHR might be promising predictors of CVD mortality, with higher values indicating greater risk.

Common carotid artery diameter and the risk of cardiovascular disease mortality: a prospective cohort study in northeast China.

BACKGROUND: The association between the common carotid artery (CCA) diameter and cardiovascular disease (CVD) is recognized, but the precise nature of this link remains elusive. This study aimed to investigate the potential relationship between CCA diameter and the risk of CVD mortality in a large population in northeast China. METHODS: The current study included 5668 participants (mean age 58.9 ± 10.1 years) from a population-based study conducted in rural areas of northeast China between September 2017 and May 2018. Information on death was collected from baseline until July 31, 2022. The CCA inter-adventitial diameter was measured using ultrasound. Cox proportional-hazard models were employed to explore the relationship between the common carotid artery diameter and cardiovascular mortality. RESULTS: At baseline, the mean CCA diameter (mm) of subjects was 7.30 ± 0.99 and increased significantly with age, ranging from 6.65 ± 0.71 among people 40-49 years to 7.99 ± 1.04 among people ≥ 80 years. CCA diameter was significantly larger in males compared to females (7.51 ± 1.03 versus vs. 7.16 ± 0.94; P < 0.001). A total of 185 participants died of CVD during a median follow-up of 4.48 years. CCA diameters were divided into quartiles, and the highest quartile of carotid diameter (≥ 8.06 mm) had a 2.29 (95% confidence interval [CI]: 1.24, 4.22) times higher risk of CVD mortality than the lowest quartile (≤ 6.65 mm) (P < 0.01) in the fully adjusted model. Each increase in the diameter of the common carotid artery (per SD) raised the risk of cardiovascular death by 36% (hazard ratio [HR]: 1.36; 95% CI: 1.18, 1.57). The subgroup analysis results demonstrated that a per SD increase was associated with a 42% increased risk of CVD mortality in participants aged ≥ 64 years in the fully adjusted model (HR: 1.42; 95%CI: 1.21, 1.66). CONCLUSIONS: Our study indicates the possible incremental value of CCA diameter in optimizing the risk stratification of cardiovascular disease and provides essential insights into reducing the burden of cardiovascular disease.

Prevalence of prediabetes and risk of CVD mortality in individuals with prediabetes alone or plus hypertension in Northeast China: insight from a population based cohort study.

BACKGROUND: To evaluate the current prevalence of prediabetes in northeast China, and further determine the association between prediabetes alone or coexistent with hypertension and cardiovascular disease (CVD) mortality. METHODS: In the prospective study, 15,557 participants without diabetes among aged ≥40 years in northeast China, were followed for a median of 5.5 years. Following the American Diabetes Association, prediabetes was defined as fasting plasma glucose (FPG) range of 5.6-6.9 mmol/L or glycated hemoglobin (HbA1c) range of 5.7-6.4% in people without diabetes. RESULTS: The prevalence of prediabetes was 44.3% among population aged ≥40 years in northeast China. Prediabetes alone did not promote risk of CVD mortality. However, when the subgroups were stratified by hypertension, the CVD mortality risk in prediabetes plus hypertension subjects increased significantly compared with population without prediabetes and hypertension. Multivariate-adjusted hazard ratios for CVD mortality in prediabetes subgroups plus hypertension were 2.28 (95% CI: 1.50, 3.47) for those diagnosed by FPG < 5.6 mmol/L & HbA1c 5.7-6.4%, 2.18 (95% CI: 1.53, 3.10) for those diagnosed by FPG 5.6-6.0 mmol/L & HbA1c < 6.5% and 2.35 (95% CI: 1.65, 3.35) for those diagnosed by FPG 6.1-6.9 & HbA1c < 6.5% compared with the reference group. Moreover, the percentage of hypertension in prediabetes subjects was high (60.4%), but the awareness, treatment and control rates were far from satisfactory (45.3, 35.1 and 4.8%, respectively). CONCLUSIONS: The prevalence of prediabetes remains high in northeast China, and the CVD mortality was elevated significantly in prediabetes coexistent with hypertension. Considering the high percentage and low control rate of hypertension in prediabetes, strategies focused on HbA1c screening, FPG lowering and blood pressure management should be emphasized in northeast China.

[Medical image segmentation data augmentation method based on channel weight and data-efficient features].

In computer-aided medical diagnosis, obtaining labeled medical image data is expensive, while there is a high demand for model interpretability. However, most deep learning models currently require a large amount of data and lack interpretability. To address these challenges, this paper proposes a novel data augmentation method for medical image segmentation. The uniqueness and advantages of this method lie in the utilization of gradient-weighted class activation mapping to extract data efficient features, which are then fused with the original image. Subsequently, a new channel weight feature extractor is constructed to learn the weights between different channels. This approach achieves non-destructive data augmentation effects, enhancing the model's performance, data efficiency, and interpretability. Applying the method of this paper to the Hyper-Kvasir dataset, the intersection over union (IoU) and Dice of the U-net were improved, respectively; and on the ISIC-Archive dataset, the IoU and Dice of the DeepLabV3+ were also improved respectively. Furthermore, even when the training data is reduced to 70 %, the proposed method can still achieve performance that is 95 % of that achieved with the entire dataset, indicating its good data efficiency. Moreover, the data-efficient features used in the method have interpretable information built-in, which enhances the interpretability of the model. The method has excellent universality, is plug-and-play, applicable to various segmentation methods, and does not require modification of the network structure, thus it is easy to integrate into existing medical image segmentation method, enhancing the convenience of future research and applications.

Lactiplantibacillus plantarum J-15 reduced calcium oxalate kidney stones by regulating intestinal microbiota, metabolism, and inflammation in rats.

The prevention role of Lactiplantibacillus plantarum against the formation of kidney stones has been increasingly recognized; its mechanism, however, has mainly been focused on inhibiting the inflammation in the colon in the gastrointestinal (GI) system, and the intestinal metabolites from microflora have not been revealed fully with regarding to the stone formation. In this study, we investigated the effect of L. plantarum J-15 on kidney stone formation in renal calcium oxalate (CaOx) rats induced by ethylene glycol and monitored the changes of intestinal microflora and their metabolites detected by 16S rRNA sequencing and widely targeted analysis, followed by the evaluation of the intestinal barrier function and inflammation levels in the colon, blood and kidney. The results showed that L. plantarum J-15 effectively reduced renal crystallization and urinary oxalic acid. Ten microbial genera, including anti-inflammatory and SCFAs-related Faecalibaculum, were enriched in the J-15 treatment group. There are 136 metabolites from 11 categories significantly different in the J-15 supplementation group compared with CaOx model rats, most of which were enriched in the amino acid metabolic and secondary bile acid pathways. The expression of intestinal tight junction protein Occludin and the concentration of pro-inflammatory cytokines and prostaglandin were decreased in the intestine, which further reduced the translocated lipopolysaccharide and inflammation levels in the blood upon J-15 treatment. Thus, the inflammation and injury in the kidney might be alleviated by downregulating TLR4/NF-κB/COX-2 signaling pathway. It suggested that L. plantarum J-15 might reduce kidney stone formation by restoring intestinal microflora and metabolic disorder, protecting intestinal barrier function, and alleviating inflammation. This finding provides new insights into the therapies for renal stones.

Genome-wide association analyses of leaf rust resistance in cultivated emmer wheat.

KEY MESSAGE: Fifteen and eleven loci, with most loci being novel, were identified to associate with seedling and adult resistances, respectively, to the durum-specific races of leaf rust pathogen in cultivated emmer. Leaf rust, caused by Puccinia triticina (Pt), constantly threatens durum (Triticum turgidum ssp. durum) and bread wheat (Triticum aestivum) production worldwide. A Pt race BBBQD detected in California in 2009 poses a potential threat to durum production in North America because resistance source to this race is rare in durum germplasm. To find new resistance sources, we assessed a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for seedling resistance to BBBQD and for adult resistance to a mixture of durum-specific races BBBQJ, CCMSS, and MCDSS in the field, and genotyped the panel using genotype-by-sequencing (GBS) and the 9 K SNP (Single Nucleotide Polymorphism) Infinium array. The results showed 24 and nine accessions consistently exhibited seedling and adult resistance, respectively, with two accessions providing resistance at both stages. We performed genome-wide association studies using 46,383 GBS and 4,331 9 K SNP markers and identified 15 quantitative trait loci (QTL) for seedling resistance located mostly on chromosomes 2B and 6B, and 11 QTL for adult resistance on 2B, 3B and 6A. Of these QTL, one might be associated with leaf rust resistance (Lr) gene Lr53, and two with the QTL previously reported in durum or hexaploid wheat. The remaining QTL are potentially associated with new Lr genes. Further linkage analysis and gene cloning are necessary to identify the causal genes underlying these QTL. The emmer accessions with high levels of resistance will be useful for developing mapping populations and adapted durum germplasm and varieties with resistance to the durum-specific races.

Identification of ST1 reveals a selection involving hitchhiking of seed morphology and oil content during soybean domestication.

Seed morphology and quality of cultivated soybean (Glycine max) have changed dramatically during domestication from their wild relatives, but their relationship to selection is poorly understood. Here, we describe a semi-dominant locus, ST1 (Seed Thickness 1), affecting seed thickness and encoding a UDP-D-glucuronate 4-epimerase, which catalyses UDP-galacturonic acid production and promotes pectin biosynthesis. Interestingly, this morphological change concurrently boosted seed oil content, which, along with up-regulation of glycolysis biosynthesis modulated by ST1, enabled soybean to become a staple oil crop. Strikingly, ST1 and an inversion controlling seed coat colour formed part of a single selective sweep. Structural variation analysis of the region surrounding ST1 shows that the critical mutation in ST1 existed in earlier wild relatives of soybean and the region containing ST1 subsequently underwent an inversion, which was followed by successive selection for both traits through hitchhiking during selection for seed coat colour. Together, these results provide direct evidence that simultaneously variation for seed morphology and quality occurred earlier than variation for seed coat colour during soybean domestication. The identification of ST1 thus sheds light on a crucial phase of human empirical selection in soybeans and provides evidence that our ancestors improved soybean based on taste.

Rapid and simultaneous detection of multiple pathogens in the lower reproductive tract during pregnancy based on loop-mediated isothermal amplification-microfluidic chip.

BACKGROUND: Female reproductive tract infection (RTI) is the common source of varied diseases, especially as an important risk factor for pregnancy outcomes, therefore the rapid, accurate and simultaneous detection of multiple pathogens is in urgent need for assisting the diagnosis and treatment of RTI in pregnant women. Streptococcus agalactiae (S. agalactiae), Enterococcus faecalis (E. faecalis), Gardnerella vaginalis (G. vaginalis), Candida albicans (C. albicans) and Chlamydia trachomatis (C. trachomatis) are five main pathogens in lower genital tract with high risk, serious consequences and clinical demands. The combination of loop-mediated isothermal amplification (LAMP) and microfluidic technology was used to develop the LAMP-microfluidic chip for rapid, simple, sensitive and simultaneous detection of the five target pathogens above. RESULTS: Standard strains and clinical isolates were used for the establishment of the novel LAMP method in tube and LAMP-microfluidic chip, followed by the chip detection on 103 clinical samples and PCR verification partially. The sensitivities of LAMP of S. agalactiae, E. faecalis, G. vaginalis, and C. albicans in tube were 22.0, 76.0, 13.2, 1.11 CFU/µL, respectively, and C. trachomatis was 41.3 copies/µL; on LAMP-microfluidic chip they were 260, 154, 3.9 and 7.53 CFU/µL, respectively, and C. trachomatis was 120 copies/µL. The positive coincidence rates of clinical stains in tube and on chip experiments were 100%. Compared with the classic culture method performed in hospitals, the positive coincidence rate of the 103 clinical samples detected by LAMP-microfluidic chip were 100%. For the six inconsistent ones, including four G. vaginalis and two C. albicans positive samples tested by LAMP-microfluidic chip and verified by PCR were negative by culturing method in hospitals, indicating the lack of efficient detection by the classic culturing method. CONCLUSION: Our study suggested that the LAMP-microfluidic chips could simultaneously, efficiently, and accurately detect multiple main pathogens, including S. agalactiae, E. faecalis, G. vaginalis, C. albicans and C. trachomatis, in clinical samples of female RTI to give a great clinical value. Accordingly, this novel method has the potential to provide a valuable reference for female RTI screening and early diagnosis during pregnancy.

Efficacy and Safety of Anti-Interleukin-5 Therapies in Chronic Rhinosinusitis with Nasal Polyps: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

INTRODUCTION: The efficacy and safety of benralizumab in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) remain unresolved, and relevant meta-analyses are lacking. Additionally, mepolizumab has been evaluated in far fewer patients, and the evidence is unclear. We conducted a meta-analysis to identify evidence gaps that will guide future investigation of therapies targeting interleukin (IL)-5 signaling (anti-IL-5Rα or anti-IL-5) for CRSwNP. METHODS: We performed a systematic review and meta-analysis that were registered with PROSPERO (No. CRD42021276867). A comprehensive search was performed in PubMed, Embase, Web of Science, and the Cochrane Library on September 2, 2021. Only randomized controlled trials (RCTs) assessing anti-IL-5 treatments (anti-IL-5Rα or anti-IL-5) in adult patients for CRSwNP were included. RESULTS: Seven RCTs with 799 patients evaluating the efficacy and safety of treatments targeting IL-5 pathway (benralizumab [anti-IL-5Rα], mepolizumab, and reslizumab [anti-IL-5]) were included. The overall pooled meta-analysis showed that anti-IL-5 treatments were associated with a significantly better nasal polyp score (weighted mean difference [WMD]: -0.71; 95% confidence interval [CI]: [-0.87, -0.55]; p < 0.00001). Anti-IL-5 treatments were associated with a significantly better nasal congestion score (WMD: -1.73; 95% CI: [-2.29, -1.16]; p < 0.00001). Anti-IL-5 treatments were associated with a significantly better Sino-Nasal Outcome Test (SNOT-22) score (WMD: -11.30; 95% CI: [-14.77, -7.83]; p < 0.00001). The overall pooled meta-analysis showed that anti-IL-5 treatments were associated with a significantly better University of Pennsylvania Smell Identification Test (UPSIT) score (WMD: 2.09; 95% CI: [0.42, 3.77]; p = 0.01). Anti-IL-5 treatments significantly reduced the loss of smell score in the overall pooled meta-analysis (WMD: -1.38; 95% CI: [-1.97, -0.79]; p < 0.00001). In the overall pooled meta-analysis, anti-IL-5 treatments showed no difference with the placebo in the risk of adverse events (AEs; risk ratio [RR]: 1.01; 95% CI: [-0.93, 1.09]; p = 0.83) and serious AEs (SAEs; RR: 0.73; 95% CI: [0.40, 1.34]; p = 0.32). CONCLUSION: This systematic review and meta-analysis identified that anti-IL-5 treatments significantly improved the size of nasal polyps, health-related quality of life, and sense of smell in moderate to severe CRSwNP, and they were safe and well tolerated.

Probiotic Lactiplantibacillus plantarum N-1 could prevent ethylene glycol-induced kidney stones by regulating gut microbiota and enhancing intestinal barrier function.

Defective permeability barrier is considered to be an incentive of hyperuricemia, however, the link between them has not been proven. Here, we evaluated the potential preventive effects of Lactiplantibacillus plantarum N-1 (LPN1) on gut microbiota and intestinal barrier function in rats with hyperoxaluria-induced kidney stones. Male rats were supplied with 1% ethylene glycol (EG) dissolved in drinking water for 4 weeks to develop hyperoxaluria, and some of them were administered with LPN1 for 4 weeks before EG treatment as a preventive intervention. We found that EG not only resulted hyperoxaluria and kidney stone formation, but also promoted the intestinal inflammation, elevated intestinal permeability, and gut microbiota disorders. Supplementation of LPN1 inhibited the renal crystalline deposits through reducing urinary oxalic acid and renal osteopontin and CD44 expression and improved EG-induced intestinal inflammation and barrier function by decreasing the serum LPS and TLR4/NF-κB signaling and up-regulating tight junction Claudin-2 in the colon, as well as increasing the production of short-chain fatty acid (SCFAs) and the abundance of beneficial SCFAs-producing bacteria, mainly from the families of Lachnospiraceae and Ruminococcaceae. Probiotic LPN1 could prevent EG-induced hyperoxaluria by regulating gut microbiota and enhancing intestinal barrier function.

Gliadin interacted with tea polyphenols: potential application and action mechanism.

The effect of tea polyphenols (TPs) on noodles quality was investigated, and the interaction mechanism between catechins and gliadins was explored. With TPs addition, noodles showed the significant changes in physicochemical and sensory properties. The water absorption, tensile strength and elasticity increased by 1.35%, 4.98%, 28.51% with 0.5% of TPs, and then decreased with the increasing of TPs. According to the determinations of surface hydrophobicity, spatial structure, thermal properties, amidogen and sulfhydryl content, the structure and properties of gliadin were affected by catechins. Esterified catechins tended to disrupt gliadin structures and non-esterified catechins polymerised gliadin molecules. Furthermore, molecular docking results indicated that catechins interacted with gliadin mainly by hydrogen bonds and hydrophobic action. The reactivity of catechins with gliadin was in the sequence as: epigallocatechin gallate > epicatechin gallate > epigallocatechin > epicatechin, which was based on the account of gallate and B-ring hydroxyl number discrepancy. All results suggested that catechins affected greatly on gliadin, and TPs were potentially used to improve the quality of flour products.

The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease.

The relationship of gut microbiota and calcium oxalate stone has been limited investigated, especially with no study of gut microbiota and short chain fatty acids (SCFAs) in nephrolithiasis. We provided Sprague Dawley rats of renal calcium oxalate stones with antibiotics and examined the renal crystals deposition. We also performed a case-control study by analyzing 16S rRNA microbial profiling, shotgun metagenomics and SCFAs in 153 fecal samples from non-kidney stone (NS) controls, patients with occasional renal calcium oxalate stones (OS) and patients with recurrent stones (RS). Antibiotics reduced bacterial load in feces and could promote the formation of renal calcium crystals in model rats. In addition, both OS and RS patients exhibited higher fecal microbial diversity than NS controls. Several SCFAs-producing gut bacteria, as well as metabolic pathways associated with SCFAs production, were considerably lower in the gut microbiota among the kidney stone patients compared with the NS controls. Representation of genes involved in oxalate degradation showed no significance difference among groups. However, fecal acetic acid concentration was the highest in RS patients with high level of urinary oxalate, which was positively correlated with genes involvement in oxalate synthesis. Administration of SCFAs reduced renal crystals. These results shed new light on bacteria and SCFAs, which may promote the development of treatment strategy in nephrolithiasis.

Biochemical and synergistic properties of a novel alpha-amylase from Chinese nong-flavor Daqu.

BACKGROUND: Daqu is the most important fermentation starter for Chinese liquor, with large number of microbes and enzymes being openly enriched in the Daqu system over thousands of years. However, only a few enzymes have been analyzed with crude protein for total liquefying power and saccharifying power of Daqu. Therefore, the complex enzymatic system present in Daqu has not been completely characterized. Moreover, their pivotal and complicated functions in Daqu are completely unknown. RESULTS: In this study, a novel α-amylase NFAmy13B, from GH13_5 subfamily (according to the Carbohydrate-Active enZYmes Database, CAZy) was successfully heterologous expressed by Escherichia coli from Chinese Nong-flavor (NF) Daqu. It exhibited high stability ranging from pH 5.5 to 12.5, and higher specific activity, compared to other GH13_5 fungal α-amylases. Moreover, NFAmy13B did not show activity loss and retained 96% residual activity after pre-incubation at pH 11 for 21 h and pH 12 for 10 h, respectively. Additionally, 1.25 mM Ca2+ significantly improved its thermostability. NFAmy13B showed a synergistic effect on degrading wheat starch with NFAmy13A (GH13_1), another α-amylase from Daqu. Both enzymes could cleave maltotetraose and maltopentaose in same degradation pattern, and only NFAmy13A could efficiently degrade maltotriose. Moreover, NFAmy13B showed higher catalytic efficiency on long-chain starch, while NFAmy13A had higher catalytic efficiency on short-chain maltooligosaccharides. Their different catalytic efficiencies on starch and maltooligosaccharides may be caused by their discrepant substrate-binding region. CONCLUSIONS: This study mined a novel GH13_5 fungal α-amylase (NFAmy13B) with outstanding alkali resistance from Nong-flavor (NF) Daqu. Furthermore, its synergistic effect with NFAmy13A (GH13_1) on hydrolyzing wheat starch was confirmed, and their possible contribution in NF Daqu was also speculated. Thus, we not only provide a candidate α-amylase for industry, but also a useful strategy for further studying the interactions in the complex enzyme system of Daqu.

Genetic dissection of seed appearance quality using recombinant inbred lines in soybean.

Soybean seed appearance quality greatly affects the marketability. The objective of this study was to identify the quantitative trait loci (QTLs) that control the appearance quality of soybean seeds. A total of 256 recombinant inbred lines from Qi Huang No.34 × Ji Dou No.17 were utilized for QTL mapping. We innovatively applied a machine vision system to quantify the seed appearance of each line. As a result of QTL mapping, a total of 145 QTLs for the machine vision parameters were detected across three environments. We integrated QTLs mapped overlapped and obtained 16 QTL hotspots in total. Of these hotspots, hotspot-4-1 was suggested to be a major locus controlling seed size, and hotspot-15 was identified to affect the seed color and texture. The mapping for principal components of the seed appearance also supported it. This study comprehensively dug up the QTLs for seed appearance quality of soybean cultivars while providing an efficient method for phenotyping of seed appearance. These results would contribute to dissecting the genetic bases of seed appearance quality for the improvement of soybean. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01262-9.

Aspergillus fumigatus Induces the Release of IL-8 and MCP-1 by Activating Nuclear Transcription Through Dectin-1 and CR3 Receptors in Alveolar Epithelial Cells.

Invasive pulmonary aspergillosis induced by the pathogenic fungus Aspergillus fumigatus is one of the common fatal complications in immunocompromised patients. Lung epithelial cells play an important role in host immune defense against A. fumigatus. However, the interaction between lung epithelial cells and A. fumigatus conidia is not fully understood. In this study, we used the swollen conidia of A. fumigatus to stimulate the type II lung epithelial A549 cells. Results showed that swollen conidia could significantly increase RNA transcription and protein expression of interleukin 8 (IL-8) and monocyte chemoattractant protein 1 (MCP-1), but not TNF-α in A549 cells in a time-dependent manner. Moreover, serum opsonization was able to improve the release of inflammatory factors induced by swollen conidia. Blocking of the dectin-1 or CR3 receptors, or both simultaneously, in the A549 cells could decrease the release of IL-8 and MCP-1. Additionally, blocking dectin-1 or CR3 could inhibit the transcription of nuclear factor NF-κB that was activated by swollen conidia. Here we reported for the first time that dectin-1 and CR3 receptors in A549 cells mediate the release of pro-inflammatory factors IL-8 and MCP-1 induced by A. fumigatus.

The impact of smoking on annual healthcare cost: an econometric model analysis in China, 2015.

BACKGROUND: Smoking exerts substantial medical burdens on society. Precise estimation of the smoking-attributable medical expenditures (SAME) helps to inform tobacco control policy makers. Based on the epidemiological approach, prior studies in China only focused on a few smoking-related diseases to estimate SAME. In contrast, this study used the econometric approach, which is capable of capturing all of the potential costs. METHODS: Three waves of panel data from the 2011-2015 national China Health and Retirement Longitudinal Study (CHARLS) were used. A total of 34,503 observations aged 45 and above were identified. Estimates from econometric models were combined to predict the smoking-attributable fraction (SAF) and medical expenditures attributable to smoking by sex, registered residency and healthcare service categories. All monetary amounts were adjusted to 2015 dollars. RESULTS: In 2015, the overall smoking-attributable fraction (SAF) of China was 10.97%, ranging from 5.77% for self-medication to 16.87% for inpatient visits. The smoking-attributable medical expenditure (SAME) was about $45.28 billion, accounting for 7.24% of the total health expenditure. The SAME was $226.77 per smoker aged 45 and above. The regression results suggest that being a former smoker has the greatest impact, which decreases over time after quitting however, on the value of medical expenditures. CONCLUSIONS: Smoking-attributable medical expenditures was substantial and placed a heavy burden on Chinese society. Comprehensive tobacco control policies and regulations are still needed to promote progress toward curbing the tobacco related losses.

First Report of Postharvest Fruit Rot Disease of Hardy Kiwifruit Caused by Diaporthe eres in China.

Hardy kiwifruit (Actinidia arguta), as an economically important fruit crop growing in Northeast China with thin, hairless and smooth skin, is susceptible to postharvest decay. In September 2018, infected cultivar Kwilv fruits were obtained from a commercial farm in Liaoning province, northeastern China. The occurring incidence of the rot disease varied from 20% to 90% according to the fruit number in each box during a 7-day-long storage at room temperature, and the initial symptom included a small, soft, chlorosis to light brown lesion and later watery brown lesions. Pure cultures of the same characteristics were obtained from the isolated strains in four rotten fruits on PDA medium. The isolates grew into transparent radial mycelium on PDA in the first two days followed by abundant white, fluffy aerial mycelium. After 14 days, colonies formed white to light brown aerial mycelial mats with gray concentric rings, and they produced gray and embedded pycnidia. Alpha conidia of 4.4 to 8.8 µm × 1.4 to 3.3 µm (n = 50) were abundant in culture, hyaline, aseptate, ellipsoidal to fusiform, while Beta conidia at 20.5 to 28.6 µm × 1.0 to 1.4 µm (n = 50) were hyaline, long, slender, curved to hamate. These morphological characteristics were similar to Diaporthe species (anamorph: Phomopsis spp.) (Udayanga et al. 2014). For identification, DNA was extracted from three single isolates respectively , and the internal transcribed spacer (ITS) region, ß-tubulin (BT), and histone (HIS) H3 gene were amplified by using primers ITS1/ITS4 (White et al. 1990), T1/T22 (O'Donnell et al. 1997) and HIS1F/HISR (Gao et al. 2017), respectively. The three isolates produced identical sequences across all three gene regions, which were submitted to NCBI (Genbank accession numbers MT561361, MT561360 and MT855966). Nucleotide BLAST analysis revealed that the ITS sequence shared 99% homology with those of ex-type Diaporthe eres in NCBI GenBank (MG281047.1 and KJ210529.1), so did the BT sequence that had 98% identity to D. eres (MG281256.1 and KJ420799.1) and the HIS 99% identity to D. eres (MG28431.1 and MG281395.1) (Hosseini et al. 2020, Udayanga et al. 2014). Pathogenicity was tested by wound inoculation on the cv. Kwilv fruits. Five mature and healthy fruits were surface-sterilized with 1% NaClO solution, rinsed in sterile distilled water and dried. Every fruit was wounded by penetrate the peel 1-2 mm with a sterile needle, and inoculated with mycelium plugs (5 mm in diameter) of the isolate on PDA, with five inoculated with sterile PDA plugs as controls. Treated fruits were kept in sterilized transparent plastic cans separately under high humidity (RH 90 to 100%) at 28°C. After five days, the same rot symptoms were observed on all fruits inoculated with mycelium while the control remained symptomless. The fungi was re-isolated from the lesions of inoculated fruits and identified as D. eres by sequencing, thus fulfilling Koch's postulates. The pathogenicity experiment was re-performed using D. eres conidial suspension (107 conidia/ml) in sterile distilled water in October 2019 and the same results were obtained. D. eres was recently reported to cause European pear rot in Italy (Bertetti et al. 2018). To our knowledge, this is the first report of D. eres causing a postharvest rot in hardy kiwifruit in China, leading to severe disease and thus huge economic losses in Northeast China. Accordingly, effective measures should be taken to prevent its spreading to other production regions in China.

Integrated Whole-Genome Sequencing Infrastructure for Outbreak Detection and Source Tracing of Salmonella enterica Serotype Enteritidis.

As an important foodborne pathogen, Salmonella enterica serotype Enteritidis is recognized as one of the most common causes of human salmonellosis globally. Outbreak detection for this highly homogenous serotype, however, has remained challenging. Rapid advances in sequencing technologies have presented whole-genome sequencing (WGS) as a significant advancement for source tracing and molecular typing of foodborne pathogens. A retrospective analysis was conducted using Salmonella Enteritidis isolates (n = 65) from 11 epidemiologically confirmed outbreaks and a collection of contemporaneous sporadic isolates (n = 258) during 2007-2017 to evaluate the performance of WGS in delineating outbreak-associated isolates. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis revealed well-supported clades in concordance with epidemiological evidence and pairwise distances of ≤3 SNPs for all outbreaks. WGS-based framework of outbreak detection was thus proposed and applied prospectively to investigate isolates (n = 66) from nine outbreaks during 2018-2019. We further demonstrated the superior discriminatory power and accuracy of WGS to resolve and delineate outbreaks for pragmatic food source tracing. The proposed integrated WGS framework is the first in China for Salmonella Enteritidis and has the potential to serve as a paradigm for outbreak detection and source tracing of Salmonella throughout the stages of food production, as well as expanded to other foodborne pathogens.