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Chinese jujube (Ziziphus jujuba Mill.), an economically significant species in the Rhamnaceae family, is a popular fruit tree in Asia. The sugar and acid concentrations in jujube are considerably higher than those in other plants. Due to the low kernel rate, it is extremely difficult to establish hybrid populations. Little is known about jujube evolution and domestication, particularly with regard to the role of the sugar and acid components of jujube. Therefore, we used cover net control as a hybridization technique for the cross-breeding of Ziziphus jujuba Mill and ‘JMS2’ and (Z. acido jujuba) ‘Xing16’ to obtain an F1 population (179 hybrid progeny). The sugar and acid levels in the F1 and parent fruit were determined by HPLC. The coefficient of variation ranged from 28.4 to 93.9%. The sucrose and quinic acid levels in the progeny were higher than those in the parents. The population showed continuous distributions with transgressive segregation on both sides. Analysis by the mixed major gene and polygene inheritance model was performed. It was found that glucose is controlled by one additive-dominant major gene and polygenes, malic acid is controlled by two additive-dominant major genes and polygenes, and oxalic acid and quinic acid are controlled by two additive-dominant-epistatic major genes and polygenes. The results of this study provide insights into the genetic predisposition and molecular mechanisms underlying the role of sugar acids in jujube fruit.

It is known that chlorphoxim is a broad‐spectrum and high‐effective pesticide. With the wide use in agricultural practice, chlorphoxim residue is also frequently detected in water, but its potential toxicity to aquatic life is still unclear. In this study, zebrafish is used as a model to detect the toxicity of chlorphoxim. Our results showed that exposure of high concentration of chlorphoxim at 96 h post‐fertilization (hpf) resulted in a high mortality and pericardium edema rate, a low hatchability rate and heart rate. The nervous system damage, swimming behavior alteration and acetylcholinesterase (AChE) inhibition were measured in zebrafish embryos after a 6 days post‐fertilization (dpf) of chlorphoxim exposure. The expression of neural‐related genes is abnormal in zebrafish embryos. Chlorphoxim exposure significantly increases oxidative stress in zebrafish embryos by inhibiting antioxidant enzyme (SOD and CAT) and activating reactive oxygen species (ROS). As expected, chlorphoxim exposure induces apoptosis by enhancing the expression of apoptotic genes (Bax, Bcl2, and p53). Astaxanthin (ATX), an effective antioxidant, was found to be able to rescue the neurotoxicity of chlorphoxim through relieving oxidative stress and apoptosis. Altogether, the results showed that chlorphoxim exposure led to severe neurotoxicity to zebrafish embryos, which was contributed to a more comprehensive understanding of the safety use of the organophosphorus pesticide. [ABSTRACT FROM AUTHOR]

Hydroponic and aquaponic farming is becoming increasingly popular as a solution to address global food security. Plants in hydroponic systems are grown hydroponically under controlled environments and are considered to have fewer food safety concerns than traditional field farming. However, hydroponics and aquaponics might have very different sources of microbial food safety risks that remain under-examined. In this study, we investigated the microbiomes, microbial hazards, and potential bacterial transmission routes inside two commercial hydroponic and aquaponic farming systems using 16S-ITS-23S rRNA sequencing and a hydroponic food safety practice survey. The hydroponic farming system microbiome was analyzed from the fresh produce, nutrient solution, tools, and farmworkers. Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes were the main components of hydroponic/aquaponic farming systems, with Pseudomonas being the most abundant genus in fresh produce samples. We further identified the presence of multiple spoilage bacteria and potential human, plant, and fish pathogens at the subspecies level. Spoilage Pseudomonas spp. and spoilage Clostridium spp. were abundant in the hydroponic microgreen farm and aquaponic lettuce farm, respectively. Moreover, we demonstrated the mapping of Escherichia coli 16s-ITS-23s rRNA sequence reads (∼2,500 bp) to small or large subunit rRNA databases and whole-genome databases to confirm pathogenicity and showed the potential of using 16s-ITS-23s rRNA sequencing for pathogen identification. With the SourceTracker and overlapping amplicon sequence variants, we predicted the bidirectional transmission route between plants and the surrounding environment and constructed the bacteria transmission map, which can be implemented in future food safety risk control plans. [ABSTRACT FROM AUTHOR]

Rationale and Objectives: We assess the performance of a model combining a deep convolutional neural network and a hand-crafted radiomics signature for predicting KRAS status in patients with colorectal cancer (CRC).Materials and Methods: The primary cohort consisted of 279 patients with clinicopathologically confirmed CRC between April 2011 and April 2015. Portal venous phase computed tomographic images were analyzed to extract traditional hand-crafted radiomics features as well as deep learning features. A Wilcoxon rank sum test, the minimum redundancy maximum relevance algorithm, and multivariable logistic regression analysis were used to select features and build a radiomics signature. A combined model was then developed using multivariable logistic regression analysis. An independent validation cohort of 119 patients from May 2015 to April 2016 was used to confirm the combined model's predictive performance.Results: The C-index of hand-crafted radiomics signature's discriminative ability was 0.719 (95% confidence interval, CI: 0.658-0.776) for the primary cohort and 0.720 (95% CI: 0.625-0.813) for the validation cohort. The C-index of the deep radiomics signature's discriminative ability was 0.754 (95% CI: 0.696-0.813) for the primary cohort and 0.786 (95% CI: 0.702-0.863) for the validation cohort. The combined model, which merged the hand-crafted radiomics features and deep radiomics features, achieve a C-index of 0.815 (95% CI: 0.766-0.868) for the primary cohort and 0.832 (95% CI: 0.762-0.905) for the validation cohort.Conclusion: This study presents a model that incorporates the hand-crafted and deep radiomics signature, which can be used for individualized preoperative prediction of KRAS mutations in patients with CRC. [ABSTRACT FROM AUTHOR]

The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15 342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major β-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control. [ABSTRACT FROM AUTHOR]

Abstract: Queen bee larvae (QBL), by‐products of royal jelly processing, was enzymatically hydrolyzed to produce bioactive peptides. Five enzymes were firstly used to obtain hydrolysates which were evaluated for their antioxidative performances. QBL hydrolyzed by pepsin, showing the highest antioxidant resistance, were prepared and isolated by ultrafiltration using different molecular weight cutoffs of <1, 1–5, 5–10, and >10 kDa. Then, hydrolysate III (MW 1–5 kDa) with the highest activity was purified through continuous chromatography. Antioxidant capacities of active peak 3 (P3) to DPPH, hydroxyl, superoxide, ABTS, oxygen radical absorbance capacity radicals assay were 74.31%, 82.44%, 74.53%, 78.81%, and 1,074 μM TE/g, respectively. Finally, the most potent antioxidant hydrolysate was determined through a high‐speed amino acid analyzer. The results of the QBLH for in vitro antioxidant assays have indicated that P3 is a good antioxidative peptide due to its high percentage of hydrophobic amino acids and has vast prospects for future development and application. Practical applications: QBL has been used as a traditional medicine for several millennia in China due to its rich nutrition and potent effect in improving human immunity, however, the utilization of QBL resources industry is rather low. This article evaluated the antioxidant activities of queen bee larvae using DPPH, hydroxyl, superoxide, ABTS, ORAC radicals assay, respectively. This article indicates that high antioxidant amino acid residues can be obtained from QBL through simple processing methods (enzymatic hydrolyzing and membrane isolating). Our study could arouse a great interest among researchers to develop a new series of QBL products with high efficient antioxidant properties. [ABSTRACT FROM AUTHOR]

Sun-drying is a low-cost, low-technology fish preservation method frequently employed in developing areas. However, the process promotes lipid oxidation and its associated undesired flavours and odours. This study investigated low-technology solutions for impact on lipid oxidation and sensory attributes of oven-dried omena fish ( Rastrineobola argentea). Two oven-drying conditions and four doses of clove water extract 'dip' pretreatments were studied in a complete factorial design. Lipid oxidation in dried fish was assessed by TBARS, peroxide value and fatty acid analysis by GC- FID. Results showed that soaking in 10 g L−1 clove water extract for 1 h and oven-drying at 150 °C × 30 min significantly reduced TBARS and peroxide values in omena fish by 77% and 79%, respectively, and polyene index showed improved retention of long-chain polyunsaturated fats, compared to original drying condition. Lastly, panellists of a triangle test were able to discriminate between biscuits made with the modified and original dried fish. [ABSTRACT FROM AUTHOR]

Sprouts and microgreens present unique food safety risks. This study aimed to enhance microbial food safety of sprouts and microgreens via seed sanitation and antimicrobial spray. Radish, broccoli, and kale seeds inoculated with Escherichia coli O157:H7 were sanitized by a high acoustic power density (APD) ultrasound and mild heat (55 °C water) combined treatment for 5 min (US-5) or 10 min (US-10) that was compared with the FDA-recommended 20 min, 20,000 mg/L chlorine treatment. E. coli O157:H7 populations of the seeds and sprouts/microgreens were enumerated immediately after seed sanitation, on day-4 of germination, and after 4 more days in storage, or at the time of harvesting (day 7) for microgreens. Sanitated seeds were planted into germination mix and sprayed with water, 0.1% or 0.2% of calcium oxide (CaO) solution three times a day for 7 days. The US-5 treatment achieved a comparable E. coli O157:H7 reduction and sprout yield as the 20,000 mg/L chlorine treatment. The US-10 treatment exhibited a significantly higher E. coli O157: H7 reduction in all three seed types than the chlorine treatment but with a lower germination rate (p < 0.05). The 0.1% CaO spray effectively inhibited E. coli O157:H7 growth in kale microgreens while maintaining the yield and germination rate. For the same varieties of seeds regardless of treatment, microgreens harvested without roots showed much lower microbial loads (3.0–3.9 log CFU/g) than sprouts (6.0–7.0 log CFU/g) with roots. Overall, the US-5 treatment can be an adequate and environmentally friendly alternative to the traditional chlorine treatment. This study provided a practical solution to ensure microbial safety of the sprouts and presented evidence that microgreens are generally safer than sprouts. • High acoustic power density (APD) ultrasound is effective for surface sanitation. • High APD ultrasound +55 °C water seed sanitation can replace the 20,000-ppm chlorine method. • Seed sanitation efficiency is negatively correlated with seed surface roughness. • Microgreens have lower E. coli concentration in edible parts than sprouts. • Broccoli seed skin was damaged the most during pre-germination treatments. [ABSTRACT FROM AUTHOR]

This study was conducted to determine the prevalence of integrons and associated gene cassettes in Escherichia coli (E. coli) isolates from waterfowls in Hainan, China. The antimicrobial resistance profile of the isolates was examined by using disc diffusion test. In addition, PCR, RFLP, plasmid replicon typing and DNA sequencing analyses were used for the characterization of integrase genes (class 1, 2 and 3) and associated gene cassettes. Approximatively, 90% of the isolates were positive for the integrase genes by PCR. Specifically, class 1 and class 2 integrons were found in 252 (81%) and 7 (2.3%) strains, respectively. While 21 (6.7%) isolates were positive for both class 1 and class 2 integrons. However, none of the isolate was positive for the class 3 integrons. In addition, 5 various cassette arrays, dfrA1-orfC, aadA2, aadA1, dfrA1-aadA1, and dfrA1-orfC- aadA1, were found within the variable regions (VRs) of class 1 integron isolates. While only single cassette array, dfrA1-sat2- aadA1, was identified within VRs of class 2 integron isolates. We identified incF plasmid as the most common plasmid type, which was detected in 81 of 243 VRs containing isolates. This study is the first report showing the baseline characteristics of integrons in E. coli isolates from waterfowls in Hainan, China. Our results provide evidence of the waterfowl birds as a reservoir of class 1 and class 2 integrons carrying antibiotic resistance gene cassettes. Therefore, strict preventive measures should be taken to avoid the spread of mobile genetic resistance elements in waterfowls in China. Image 1 • Prevalence of class 1, class 2 and class 3 integrons were studied in waterfowl farms. • The waterfowl birds are possible reservoirs of AMRg and integrons. • AMRg were found in various gene cassettes harboring IncF plasmids. • The significant correlations among AMR phenotypes and integrons were detected. [ABSTRACT FROM AUTHOR]

Although vaccines play a major role in the prevention of infectious bronchitis (IB), Anti-IB drugs still have great potential in poultry production. Radix Isatidis polysaccharide (RIP) is a crude extract of Banlangen with antioxidant, antibacterial, antiviral, and multiple immunomodulatory functions. The aim of this study was to explore the innate immune mechanisms responsible for RIP-mediated alleviation of infectious bronchitis virus (IBV)-induced kidney lesions in chickens. Specific-pathogen-free (SPF) chicken and chicken embryo kidney (CEK) cells cultures were pretreated with RIP and then infected with the QX-type IBV strain, Sczy3. Morbidity, mortality, and tissue mean lesion scores were calculated for IBV-infected chickens, and the viral loads, inflammatory factor gene mRNA expression levels, and innate immune pathway gene mRNA expression levels in infected chickens and CEK cell cultures were determined. The results show that RIP could alleviate IBV-induced kidney damage, decrease CEK cells susceptibility to IBV infection, and reduce viral loads. Additionally, RIP reduced the mRNA expression levels of the inflammatory factors IL-6, IL-8, and IL-1β by decreasing the mRNA expression level of NF-κB. Conversely, the expression levels of MDA5, TLR3, STING, Myd88, IRF7, and IFN-β were increased, indicating that RIP conferred resistance to QX-type IBV infection via the MDA5, TLR3, IRF7 signaling pathway. These results provide a reference for both further research into the antiviral mechanisms of RIP and the development of preventative and therapeutic drugs for IB. [ABSTRACT FROM AUTHOR]

Contaminated leafy vegetables have been associated with high-profile outbreaks causing severe illnesses. A good understanding of the interactions between human pathogen and produce is important for developing improved food safety control strategies. Currently, the role played by produce surface physiochemical characteristics in such interactions is not well-understood. This work was performed to examine the effects of produce physiochemical characteristics, including surface roughness, epicuticular wax composition, and produce and bacteria surface hydrophobicity on attachment and removal of vegetative bacteria. Escherichia coli K12 was used as a model microorganism to evaluate attachment to and removal from five leafy green vegetables after washing with selected sanitizers. A detailed epicuticular wax component analysis was conducted and the changes of wax composition after sanitation were also evaluated. The results showed that E. coli K12 removal is positively correlated with alkanes, ketones, and total wax content on leaf surfaces. Vegetables with high surface wax content had less rough leaf surfaces and more bacterial removal than the low wax produce. Produce surface roughness positively correlated to E. coli K12 adhesion and negatively correlated to removal. The cells preferentially attached to cut vegetable surfaces, with up to 1.49 times more attachment than on leaf adaxial surfaces. • E. coli K-12 attachment and removal are mediated by physiochemical properties of leaf surfaces. • Bacterial removal is positively correlated with alkanes, ketones, and total wax content on leaf surfaces. • High surface wax vegetables have less rough leaf surfaces and more bacterial removal than the low wax produce. • Produce surface roughness positively correlates to bacterial adhesion and negatively correlates to removal. • E. coli K-12 cells preferentially attach to cut surfaces, with up to 1.49 times more attachment than to leaf adaxial surfaces. [ABSTRACT FROM AUTHOR]

Limited data are published regarding changes in the physicochemical properties of rice flours from germinated de-hulled rice treated by ultrasound. This work was undertaken to evaluate the effect of ultrasound treatment (25 kHz, 16 W/L, 5 min) on starch hydrolysis and functional properties of rice flours produced from ultrasound-treated red rice and brown rice germinated for up to 36 h. Environmental Scanning Electron Microscopy (ESEM) microimages showed that the ultrasound treatment altered the surface microstructure of rice, which helped to improve moisture transfer during steam-cooking. The flours from sonicated germinated de-hulled rice exhibited significantly ( p  < .05) enhanced starch hydrolysis, increased the glucose content, and decreased falling number values and viscosities determined by a Rapid Visco Analyzer. The amylase activity of the germinating red rice and brown rice displayed different sensitivity to ultrasonic treatment. The ultrasonic pre-treatment resulted in a significant reduction in energy use during germination with a potential to further reduce energy use in germinated rice cooking process. The present study indicated that ultrasound could be a low-power consumption method to modify the rheological behavior of germinated rice flour, as well as an efficient approach to improve the texture, flavor, and nutrient properties of steam-cooked germinated rice. [ABSTRACT FROM AUTHOR]

Objectives: To develop and validate a radiomics nomogram for preoperative prediction of tumor histologic grade in gastric adenocarcinoma (GA)., Methods: This retrospective study enrolled 592 patients with clinicopathologically confirmed GA (low-grade: n=154; high-grade: n=438) from January 2008 to March 2018 who were divided into training (n=450) and validation (n=142) sets according to the time of computed tomography (CT) examination. Radiomic features were extracted from the portal venous phase CT images. The Mann-Whitney U test and the least absolute shrinkage and selection operator (LASSO) regression model were used for feature selection, data dimension reduction and radiomics signature construction. Multivariable logistic regression analysis was applied to develop the prediction model. The radiomics signature and independent clinicopathologic risk factors were incorporated and presented as a radiomics nomogram. The performance of the nomogram was assessed with respect to its calibration and discrimination., Results: A radiomics signature containing 12 selected features was significantly associated with the histologic grade of GA (P<0.001 for both training and validation sets). A nomogram including the radiomics signature and tumor location as predictors was developed. The model showed both good calibration and good discrimination, in which C-index in the training set, 0.752 [95% confidence interval (95% CI): 0.701-0.803]; C-index in the validation set, 0.793 (95% CI: 0.711-0.874)., Conclusions: This study developed a radiomics nomogram that incorporates tumor location and radiomics signatures, which can be useful in facilitating preoperative individualized prediction of histologic grade of GA., (Copyright © 2021 Chinese Journal of Cancer Research. All rights reserved.)

Objective: To develop and validate a computed tomography (CT)-based radiomics nomogram for predicting human epidermal growth factor receptor 2 (HER2) status in patients with gastric cancer., Methods: This retrospective study included 134 patients with gastric cancer (HER2-negative: n=87; HER2-positive: n=47) from April 2013 to March 2018, who were then randomly divided into training (n=94) and validation (n=40) cohorts. Radiomics features were obtained from the CT images showing gastric cancer. Least absolute shrinkage and selection operator (LASSO) regression analysis was utilized for building the radiomics signature. A multivariable logistic regression method was applied to develop a prediction model incorporating the radiomics signature and independent clinicopathologic risk predictors, which were then visualized as a radiomics nomogram. The predictive performance of the nomogram was assessed in the training and validation cohorts., Results: The radiomics signature was significantly associated with HER2 status in both training (P<0.001) and validation (P=0.023) cohorts. The prediction model that incorporated the radiomics signature and carcinoembryonic antigen (CEA) level demonstrated good discriminative performance for HER2 status prediction, with an area under the curve (AUC) of 0.799 [95% confidence interval (95% CI): 0.704-0.894] in the training cohort and 0.771 (95% CI: 0.607-0.934) in the validation cohort. The calibration curve of the radiomics nomogram also showed good calibration. Decision curve analysis showed that the radiomics nomogram was useful., Conclusions: We built and validated a radiomics nomogram with good performance for HER2 status prediction in gastric cancer. This radiomics nomogram could serve as a non-invasive tool to predict HER2 status and guide clinical treatment., (Copyright © 2020 Chinese Journal of Cancer Research. All rights reserved.)

Biofortification of staple grains with high contents of essential micronutrients is an important strategy to overcome micronutrient malnutrition. However, few attempts have targeted at γ-aminobutyric acid (GABA), a functional nutrient for aging populations. In this study, two rice cultivars, Heinuo and Xianhui 207, were used to investigate changes in GABA and other nutritional compounds of dehulled rice after germination under normoxic and hypoxic conditions. Forty-one metabolites were identified in both cultivars treated by normoxic germination, whereas the germinated dehulled rice of Heinuo and Xianhui 207 under hypoxic treatment had 43 and 41 metabolites identified, respectively. GABA increased in dehulled rice after germination, especially under hypoxia. Meanwhile, a number of other health-beneficial and/or flavor-related compounds such as lysine and d-mannose increased after the hypoxic treatment. The accumulation of GABA exhibited genotype-specific modes in both normoxic and hypoxic treatments. With regard to GABA production, Xianhui 207 was more responsive to the germination process than Heinuo, whereas Heinuo was more responsive to hypoxia than Xianhui 207. This study provides a promising approach to biofortify dehulled rice with increased GABA and other nutrients through metabolomic-based regulation.