Publications by authors named "Tao Zhou"

1,245 Publications

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The complete chloroplast genome of common walnut ().

Mitochondrial DNA B Resour 2016 Mar 24;1(1):189-190. Epub 2016 Mar 24.

Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.

Common walnut ( L.) is cultivated in temperate regions worldwide for its wood and nuts. The complete chloroplast genome of was sequenced using the Illumina MiSeq platform. This is the first complete chloroplast sequence for the Juglandaceae, a family that includes numerous species of economic importance. The chloroplast genome of was 160 367 bp in length, with 36.11% GC content. It contains a pair of inverted repeats (26 035 bp) which were separated by a large single copy (89 872 bp) and a small single copy region (18 425 bp). A total of 137 genes were annotated, which included 86 protein-coding genes, three pseudogenes (two and one ), 40 tRNA genes and eight rRNA genes. The neighbour-joining phylogenetic analysis with the reported chloroplast genomes showed that common walnut chloroplasts are most closely related to those of the Fagaceae family.
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http://dx.doi.org/10.1080/23802359.2015.1137804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7871657PMC
March 2016

Partial splenic embolization combined with endoscopic therapies and NSBB decreases the variceal rebleeding rate in cirrhosis patients with hypersplenism: a multicenter randomized controlled trial.

Hepatol Int 2021 Feb 27. Epub 2021 Feb 27.

Department of Gastroenterology, Qilu Hospital of Shandong University, Wenhua Xi Road, 107, Jinan City, 250012, Shandong Province, People's Republic of China.

Background: Global research on endoscopic therapies in combination with partial splenic embolization (PSE) for variceal hemorrhage (VH) is limited. Therefore, we aimed to evaluate the efficacy and safety of endoscopy plus PSE (EP) treatment in comparison to endoscopic (E) treatment for the secondary prophylaxis of VH in cirrhosis patients with hypersplenism.

Methods: Cirrhosis patients with hypersplenism (platelet count < 100, 000/µL) and those who had recovered from an episode of VH were enrolled in a multicenter randomized controlled trial. The participants were randomly assigned into EP and E groups in a 1:1 ratio. The primary endpoint was variceal rebleeding, and the secondary endpoints were severe variceal recurrence and mortality during the 2-year follow-up. Hematological indices, serum biochemical parameters, and the Child-Pugh score were measured at each time point.

Results: From June 2016 to December 2019, 108 patients were enrolled in the study, among which 102 patients completed the protocol (51 in EP and 51 in E group). The rebleeding rate of the varices was significantly reduced in the EP group compared to that in the E group during the 2 years (16% vs. 31%, p < 0.001). The EP group showed a significantly lower variceal recurrence rate than the E group (22% vs. 67%, p < 0.001). The COX proportional hazard models revealed that grouping was an independent predictor for variceal rebleeding (H = 0.122, 95% CI 0.055-0.270, p < 0.001) and variceal recurrence (hazard ratio, H = 0.160, 95% CI 0.077-0.332, p < 0.001). The peripheral blood cell count, Child-Pugh class/score, albumin concentration, and coagulation function in the EP group improved significantly compared to the values observed in the E group at any time point (p < 0.05).

Conclusions: The EP treatment was more effective in preventing variceal rebleeding and variceal recurrence than the conventional E treatment during the secondary prophylaxis of VH in cirrhosis patients with hypersplenism. Furthermore, the EP treatment could significantly increase the peripheral blood cell count and albumin concentration and also improved the coagulation function and the Child-Pugh score.

Clinical Trials Registration: Trial registration number ClincialTrials.gov: NCT02778425. The URL of the clinical trial: https://clinicaltrials.gov/.
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http://dx.doi.org/10.1007/s12072-021-10155-0DOI Listing
February 2021

Nobiletin downregulates the SKP2-p21/p27-CDK2 axis to inhibit tumor progression and shows synergistic effects with palbociclib on renal cell carcinoma.

Cancer Biol Med 2021 Feb;18(1):227-244

Department of Urology, Xinqiao Hospital of Army Medical University, Chongqing 400037, China.

Objective: Natural extracts, including nobiletin, have been reported to enhance the efficacy and sensitivity of chemotherapeutic drugs. However, whether and how nobiletin affects tumor growth and progression in renal cell carcinoma (RCC) are still unclear.

Methods: Cell proliferation, cell cycle and apoptosis analyses, colony-formation assays, immunoblotting analysis, and qRT-PCR analysis were performed to investigate how nobiletin affected RCC cell proliferation . The nude mouse model was used to test the efficacy of nobiletin alone or in combination with palbociclib.

Results: Nobiletin inhibited cell proliferation by inducing G1 cell cycle arrest and cell apoptosis in RCC cells. Mechanistically, nobiletin decreased SKP2 protein expression by reducing its transcriptional level. The downregulated SKP2 caused accumulation of its substrates, p27 and p21, which further inhibited the activity of the G1 phase-related protein, CDK2, leading to inhibition of cell proliferation and tumor formation. A higher SKP2 protein level indicated less sensitivity to the CDK4/6 inhibitor, palbociclib. A combination of nobiletin and palbociclib showed a synergistic tumor inhibition and in an model.

Conclusions: Nobiletin downregulated the SKP2-p21/p27-CDK2 axis to inhibit tumor progression and showed synergistic tumor inhibition effects with the CDK4/6 inhibitor, palbociclib, on RCC, which indicates a potential new therapeutic strategy.
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http://dx.doi.org/10.20892/j.issn.2095-3941.2020.0186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7877181PMC
February 2021

Chromosome-level genome of Poropuntius huangchuchieni provides a diploid progenitor-like reference genome for the allotetraploid Cyprinus carpio.

Mol Ecol Resour 2021 Feb 23. Epub 2021 Feb 23.

State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.

The diploid Poropuntius huangchuchieni in the cyprinid family, which is widely distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp, which was generated by merging of two diploid genomes during evolution. Therefore, the P. huangchuchieni genome is essential for polyploid evolution studies in Cyprinidae. Here, we report a high-quality chromosome-level genome assembly of P. huangchuchieni by integrating Oxford Nanopore and Hi-C technologies. The assembled genome size was 1021.38 Mb, 895.66 Mb of which was anchored onto 25 chromosomes with a N50 of 32.93 Mb. The genome contained 486.28 Mb repetitive elements and 24,099 protein-coding genes. Approximately 95.9% of the complete BUSCOs were detected, suggesting a high completeness of the genome. Evolutionary analysis revealed that P. huangchuchieni diverged from Cyprinus carpio at approximately 12 Mya. Genome comparison between P. huangchuchieni and the B subgenome of C. carpio provided insights into chromosomal rearrangements during the allotetraploid speciation. With the complete gene set, 17,474 orthologous genes were identified between P. huangchuchieni and C. carpio, providing a broad view of the gene component in the allotetraploid genome, which is critical for future genetic analyses. The high-quality genomic dataset created for P. huangchuchieni provides a diploid progenitor-like reference for the evolution and adaptation of allotetraploid carps.
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http://dx.doi.org/10.1111/1755-0998.13365DOI Listing
February 2021

Prognostic value of neutrophil- lymphocyte count ratio (NLCR) among adult ICU patients in comparison to APACHE II score and conventional inflammatory markers: a multi center retrospective cohort study.

BMC Emerg Med 2021 Feb 23;21(1):24. Epub 2021 Feb 23.

Department of Critical Care Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.

Background: Neutrophil-lymphocyte count ratio (NLCR) has been reported as better indicator of bacteremia than procalcitonin (PCT), and more precise predictor of mortality than C-reactive protein (CRP) under various medical conditions. However, large controversy remains upon this topic. To address the discrepancy, our group has compared the efficiency of NLCR with conventional inflammatory markers in predicting the prognosis of critical illness.

Methods: We performed a multi-center retrospective cohort study involving 536 ICU patients with outcomes of survival, 28- and 7-day mortality. NLCR was compared with conventional inflammatory markers such as PCT, CRP, serum lactate (LAC), white blood cell, neutrophil and severity score APACHE II (Acute Physiology and Chronic Health Evaluation II) to evaluate the potential outcomes of critical illness. Then, receiver operating characteristics (ROC) curves were constructed to assess and compare each marker's sensitivity and specificity respectively.

Results: NLCR values were not different between survival and mortality groups. Meanwhile, remarkable differences were observed upon APACHE II score, CRP, PCT and LAC levels between survival and death groups. ROC analysis revealed that NLCR was not competent to predict prognosis of critical illness. The AUROCs of conventional markers such as CRP, PCT, LAC and APACHE II score were more effective in predicting 28- and 7-day mortality.

Conclusions: NLCR is less reliable than conventional markers CRP, PCT, LAC and APACHE II score in assessing severity and in predicting outcomes of critical illness.
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http://dx.doi.org/10.1186/s12873-021-00418-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7903782PMC
February 2021

Outcome of Liver Transplantation for Neonatal-onset Citrullinemia Type I.

Transplantation 2021 Mar;105(3):569-576

Department of Liver Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Background: We evaluated the outcome of liver transplantation (LT) in neonatal-onset citrullinemia type I patients, especially its impact on neurological deficits and developmental retardation.

Methods: From October 2006 to October 2019, 5 of the 2003 children who received LT at Ren Ji Hospital had been diagnosed with citrullinemia type I. The primary indication for transplantation was repeated metabolic compensation and developmental retardation in 4 patients and prophylactic transplantation in the other. Among them, 3 patients received living donor LT and 2 received orthotopic LT.

Results: All recipients had successfully recovered within the median follow-up period of 32 months (range, 6-54 mo). Transplantation restored citrulline metabolism and liver function. Plasma ammonia and citrulline concentration decreased to normal levels with no further hyperammonemic episodes being reported, even after normal diet intake began. Meanwhile, uracil-2 and orotic acid were not detected in urinary excretion. Strikingly, patients suffered developmental retardation before LT showed improved psychomotor ability and significant catch-up growth during the follow-up period. Cognitive ability, including language skills and academic performance, also greatly improved. Three patients had sustained brain injuries and exhibited severe neurological deficits before transplantation, especially repeated generalized tonic-clonic seizures. LT halted neurological deterioration and controlled seizure episodes, which further facilitated the intellectual development and improvement of life quality.

Conclusions: LT is an effective treatment for neonatal-onset citrullinemia type I patients, which reverses metabolism decompensation and improves quality of life. For patients who have suffered severe hyperammonemic insults, LT should be conducted at an early age to avoid further neurological or developmental deficits.
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http://dx.doi.org/10.1097/TP.0000000000003261DOI Listing
March 2021

Spatial Genetic Structure and Demographic History of the Dominant Forest Oak Hance in Subtropical China.

Front Plant Sci 2020 4;11:583284. Epub 2021 Feb 4.

Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China.

Oak trees ( L.) are important models for estimating abiotic impacts on the population structure and demography of long life span tree species. In this study, we generated genetic data for 17 nuclear microsatellite loci in 29 natural populations of to estimate the population genetic structure. We also integrated approximate Bayesian computation (ABC) and ecological niche analysis to infer the population differentiation processes and demographic history of this oak species. The genetic analyses indicated two genetic clusters across the 29 populations collected, where most approximately corresponded to the intraspecific differentiation among populations from western and eastern China, whereas admixed populations were mainly found in central mountains of China. The best model obtained from hierarchical ABC simulations suggested that the initial intraspecific divergence of potentially occurred during the late Pliocene ( 3.99 Ma) to form the two genetic clusters, and the admixed population group might have been generated by genetic admixture of the two differentiated groups at 53.76 ka. Ecological analyses demonstrated clear differentiation among the population structures, and association estimations also indicated significant correlations between geography and climate with the genetic variation in this oak species. Our results suggest abiotic influences, including past climatic changes and ecological factors, might have affected the genetic differentiation and demographic history of in subtropical China.
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http://dx.doi.org/10.3389/fpls.2020.583284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889815PMC
February 2021

Genome-Wide Association Analysis Reveals the Genetic Architecture of Parasite (Cryptocaryon irritans) Resistance in Large Yellow Croaker (Larimichthys crocea).

Mar Biotechnol (NY) 2021 Feb 20. Epub 2021 Feb 20.

State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.

Large yellow croaker is an important marine culture species in China. Recently, the large yellow croaker industry is threatened by various disease problems, especially for the white spot disease, which is caused by parasite Cryptocaryon irritans. In the current study, we conducted a genome-wide association study (GWAS) for C. irritans resistance in two large yellow croaker populations (n = 264 and n = 480, respectively). We identified 15 QTL with explained genetic variance ranging from 1 to 8% in the two populations. One QTL on chromosome 23 was shared by the two populations, and three QTL had been reported in the previous study. We identified a lot of biological pathways associated with C. irritans resistance, such as hormone transport, response to bacterium, apoptotic process, acute inflammatory response to antigenic stimulus, and NF-kappa B signaling pathway. The genes casp8 and traf6 involved in regulatory network for apoptosis and inflammation were identified to be candidate genes for C. irritans resistance. Our results showed the complex polygenic architecture of resistance of large yellow croaker against C. irritans. These results would be helpful for the researches of the molecular mechanism of C. irritans resistance and genome-assisted breeding of large yellow croaker.
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http://dx.doi.org/10.1007/s10126-021-10019-6DOI Listing
February 2021

Purification, structural characterization, and biological activities of degraded polysaccharides from Porphyra yezoensis.

J Food Biochem 2021 Feb 17:e13661. Epub 2021 Feb 17.

School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, P.R. China.

The degraded polysaccharides from Porphyra yezoensis (DPPY) prepared using the H O -Vc method under optimized conditions were isolated and purified by DEAE Cellulose-52, and Sephadex G-100, providing four pure components, namely, DPPY-0, DPPY-0.1, DPPY-0.3, and DPPY-0.5. Their relative molecular weights were measured to be 10.8, 10.7, 18.7, and 35.5 kDa, respectively. GC-MS analysis revealed that all the four fractions were mainly composed of galactose, together with a small portion of glucose, mannose, xylose, and rhamnose. Structural analysis revealed that the purified polysaccharides mainly possess a backbone of (1 → 3)-β-D-galactose (1 → 4)-3,6-anhydro-α-L-galactopyranose (G-A) units and (1 → 3)-β-D-galactose (1 → 4)-α-L-galactose-6-sulfate (G-L6S) units. They were found to promote the proliferation of RAW264.7 macrophages and enhance phagocytosis of the RAW264.7 cells. Antioxidant assays indicated that DPPY-0.5 possessed the most potent reducing power and free radical scavenging ability among the four purified polysaccharides. High sulfate content and proper molecular weight of these fractions are favorable to their immunomodulatory and antioxidant activities. PRACTICAL APPLICATIONS: Porphyra yezoensis, common economic red algae widely distributed in East Asian countries, contains a high content of polysaccharides with a variety of biological activities. However, P. yezoensis polysaccharide (PPY) has not been well utilized due to the relatively low biological activities and lack of understanding of its structure-activity relationship. Thus, it is necessary to improve the bioactivities and elucidate the structure-activity relationship of this polysaccharide for its practical use. In the present work, four purified fractions (DPPY-0, DPPY-0.1, DPPY-0.3, and DPPY-0.5) were isolated from the degraded P. yezoensis polysaccharide, and were investigated for their antioxidant and immunoregulatory activities. The results of the present work will lay a foundation for the application of the degraded P. yezoensis polysaccharide in the food industry as a functional food ingredient.
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http://dx.doi.org/10.1111/jfbc.13661DOI Listing
February 2021

Transcriptomic and Functional Analyses Indicate Novel Anti-viral Mode of Actions on Tobacco Mosaic Virus of a Microbial Natural Product ε-Poly-l-lysine.

J Agric Food Chem 2021 Feb 15;69(7):2076-2086. Epub 2021 Feb 15.

College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China.

Novel anti-viral natural product ε-poly-l-lysine (ε-PL) produced by is a homopolymer of l-lysine, of which the underlying molecular mode of action remains to be further elucidated. In this study, ε-PL induced significant fragmentation of tobacco mosaic virus (TMV) virions and delayed the systemic infection of TMV-GFP as well as wild-type TMV in plants. ε-PL treatment also markedly inhibited RNA accumulation of TMV in tobacco BY-2 protoplasts. The results of RNA-seq indicated that the agent induced significantly differential expression of genes that are associated with defense response, stress response, autophagy, and ubiquitination. Among them, 15 critical differential expressed genes were selected for real-time quantitative PCR validation. We further demonstrated that ε-PL can induce host defense responses by assessing the activity of several defense-related enzymes in plants. Our results provided valuable insights into molecular anti-viral mode of action for ε-PL, which is expected to be applied as a novel microbial natural product against plant virus diseases.
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http://dx.doi.org/10.1021/acs.jafc.0c07357DOI Listing
February 2021

Evaluating the effect of Chinese control measures on COVID-19 via temporal reproduction number estimation.

PLoS One 2021 11;16(2):e0246715. Epub 2021 Feb 11.

Big Data Research Center, University of Electronic Science and Technology of China, Chengdu, Peoples' Republic of China.

Control measures are necessary to contain the spread of serious infectious diseases such as COVID-19, especially in its early stage. We propose to use temporal reproduction number an extension of effective reproduction number, to evaluate the efficacy of control measures, and establish a Monte-Carlo method to estimate the temporal reproduction number without complete information about symptom onsets. The province-level analysis indicates that the effective reproduction numbers of the majority of provinces in mainland China got down to < 1 just by one week from the setting of control measures, and the temporal reproduction number of the week [15 Feb, 21 Feb] is only about 0.18. It is therefore likely that Chinese control measures on COVID-19 are effective and efficient, though more research needs to be performed.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0246715PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7877593PMC
February 2021

Improving EEG Decoding via Clustering-Based Multitask Feature Learning.

IEEE Trans Neural Netw Learn Syst 2021 Feb 8;PP. Epub 2021 Feb 8.

Accurate electroencephalogram (EEG) pattern decoding for specific mental tasks is one of the key steps for the development of brain-computer interface (BCI), which is quite challenging due to the considerably low signal-to-noise ratio of EEG collected at the brain scalp. Machine learning provides a promising technique to optimize EEG patterns toward better decoding accuracy. However, existing algorithms do not effectively explore the underlying data structure capturing the true EEG sample distribution and, hence, can only yield a suboptimal decoding accuracy. To uncover the intrinsic distribution structure of EEG data, we propose a clustering-based multitask feature learning algorithm for improved EEG pattern decoding. Specifically, we perform affinity propagation-based clustering to explore the subclasses (i.e., clusters) in each of the original classes and then assign each subclass a unique label based on a one-versus-all encoding strategy. With the encoded label matrix, we devise a novel multitask learning algorithm by exploiting the subclass relationship to jointly optimize the EEG pattern features from the uncovered subclasses. We then train a linear support vector machine with the optimized features for EEG pattern decoding. Extensive experimental studies are conducted on three EEG data sets to validate the effectiveness of our algorithm in comparison with other state-of-the-art approaches. The improved experimental results demonstrate the outstanding superiority of our algorithm, suggesting its prominent performance for EEG pattern decoding in BCI applications.
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http://dx.doi.org/10.1109/TNNLS.2021.3053576DOI Listing
February 2021

High-silica CHA Zeolite Membrane with Ultra-high Selectivity and Irradiation Stability for Krypton/Xenon Separation.

Angew Chem Int Ed Engl 2021 Feb 2. Epub 2021 Feb 2.

Delft University of Technology, NETHERLANDS.

Capture and storage of the long-lived 85Kr is an efficient approach to mitigate the emission of volatile radionuclides from the spent nuclear fuel reprocessing facilities. However, it is challenging to separate krypton (Kr) from xenon (Xe) because of the chemical inertness and similar physical properties. Herein we prepared high-silica CHA zeolite membranes with ultra-high selectivity and irradiation stability for Kr/Xe separation. The suitable aperture size and rigid framework endures the membrane a strong size-exclusion effect. The ultrahigh selectivity of 51-152 together with the permeance of 0.7-1.3×10-8 mol m-2 s-1 Pa-1 of high-silica CHA zeolite membranes far surpass the state-of-the-art polymeric membranes. The membrane is among the most stable polycrystalline membranes for separation of humid Kr/Xe mixtures. Together with the excellent irradiation stability, high-silica CHA zeolite membranes pave the way to separate radioactive Kr from Xe for a notable reduction of the volatile nuclear waste storage volume.
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http://dx.doi.org/10.1002/anie.202100172DOI Listing
February 2021

Joint exposure to various ambient air pollutants and incident heart failure: a prospective analysis in UK Biobank.

Eur Heart J 2021 Feb 2. Epub 2021 Feb 2.

Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 1724, New Orleans, LA 70112, USA.

Aims : Little is known about the relation between the long-term joint exposure to various ambient air pollutants and the incidence of heart failure (HF). We aimed to assess the joint association of various air pollutants with HF risk and examine the modification effect of the genetic susceptibility.

Methods And Results : This study included 432 530 participants free of HF, atrial fibrillation, or coronary heart disease in the UK Biobank study. All participants were enrolled from 2006 to 2010 and followed up to 2018. The information on particulate matter (PM) with diameters ≤2.5 µm (PM2.5), ≤10 µm (PM10), and between 2.5 and 10 µm (PM2.5-10) as well as nitrogen oxides (NO2 and NOx) was collected. We newly proposed an air pollution score to assess the joint exposure to the five air pollutants through summing each pollutant concentration weighted by the regression coefficients with HF from single-pollutant models. We also calculated the weighted genetic risk score of HF. During a median of 10.1 years (4 346 642 person-years) of follow-up, we documented 4201 incident HF. The hazard ratios (HRs) [95% confidence interval (CI)] of HF for a 10 µg/m3 increase in PM2.5, PM10, PM2.5-10, NO2, and NOx were 1.85 (1.34-2.55), 1.61 (1.30-2.00), 1.13 (0.80-1.59), 1.10 (1.04-1.15), and 1.04 (1.02-1.06), respectively. We found that the air pollution score was associated with an increased risk of incident HF in a dose-response fashion. The HRs (95% CI) of HF were 1.16 (1.05-1.28), 1.19 (1.08-1.32), 1.21 (1.09-1.35), and 1.31 (1.17-1.48) in higher quintile groups compared with the lowest quintile of the air pollution score (P trend <0.001). In addition, we observed that the elevated risk of HF associated with a higher air pollution score was strengthened by the genetic susceptibility to HF.

Conclusion : Our results indicate that the long-term joint exposure to various air pollutants including PM2.5, PM10, PM2.5-10, NO2, and NOx is associated with an elevated risk of incident HF in an additive manner. Our findings highlight the importance to comprehensively assess various air pollutants in relation to the HF risk.
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http://dx.doi.org/10.1093/eurheartj/ehaa1031DOI Listing
February 2021

Momentum contrastive learning for few-shot COVID-19 diagnosis from chest CT images.

Pattern Recognit 2021 May 16;113:107826. Epub 2021 Jan 16.

Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA.

The current pandemic, caused by the outbreak of a novel coronavirus (COVID-19) in December 2019, has led to a global emergency that has significantly impacted economies, healthcare systems and personal wellbeing all around the world. Controlling the rapidly evolving disease requires highly sensitive and specific diagnostics. While RT-PCR is the most commonly used, it can take up to eight hours, and requires significant effort from healthcare professionals. As such, there is a critical need for a quick and automatic diagnostic system. Diagnosis from chest CT images is a promising direction. However, current studies are limited by the lack of sufficient training samples, as acquiring annotated CT images is time-consuming. To this end, we propose a new deep learning algorithm for the automated diagnosis of COVID-19, which only requires a few samples for training. Specifically, we use contrastive learning to train an encoder which can capture expressive feature representations on large and publicly available lung datasets and adopt the prototypical network for classification. We validate the efficacy of the proposed model in comparison with other competing methods on two publicly available and annotated COVID-19 CT datasets. Our results demonstrate the superior performance of our model for the accurate diagnosis of COVID-19 based on chest CT images.
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http://dx.doi.org/10.1016/j.patcog.2021.107826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7833525PMC
May 2021

Habitual use of vitamin D supplements and risk of coronavirus disease 2019 (COVID-19) infection: a prospective study in UK Biobank.

Am J Clin Nutr 2021 Jan 29. Epub 2021 Jan 29.

Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA.

Background: Previous studies have related vitamin D supplementation to a lower risk of acute respiratory tract infection. Emerging evidence suggests that vitamin D insufficiency is related to a higher risk of coronavirus disease 2019 (COVID-19) infection.

Objectives: We aimed to investigate the prospective association between habitual use of vitamin D supplements and risk of COVID-19 infection, and assess whether such an association differed according to the different levels of circulating and genetically predicted vitamin D.

Methods: This study included 8297 adults who have records of COVID-19 test results from UK Biobank (from 16 March 2020 to 29 June 2020). The use of vitamin D supplements, circulating vitamin D levels, and main covariates were measured at baseline (2006-2010). Genetically predicted vitamin D levels were evaluated by genetic risk score.

Results: After adjustment for covariates, the habitual use of vitamin D supplements was significantly associated with a 34% lower risk of COVID-19 infection (OR, 0.66; 95% CI, 0.45-0.97; P = 0.034). Circulating vitamin D levels at baseline or genetically predicted vitamin D levels were not associated with the risk of COVID-19 infection. The association between the use of vitamin D supplements and the risk of COVID-19 infection did not vary according to the different levels of circulating or genetically predicted vitamin D (P-interactions = 0.75 and 0.74, respectively).

Conclusions: Our findings suggest that habitual use of vitamin D supplements is related to a lower risk of COVID-19 infection, although we cannot rule out the possibility that the inverse association is due to residual confounding or selection bias. Further clinical trials are needed to verify these results.
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http://dx.doi.org/10.1093/ajcn/nqaa381DOI Listing
January 2021

LPA signaling acts as a cell-extrinsic mechanism to initiate cilia disassembly and promote neurogenesis.

Nat Commun 2021 01 28;12(1):662. Epub 2021 Jan 28.

State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.

Dynamic assembly and disassembly of primary cilia controls embryonic development and tissue homeostasis. Dysregulation of ciliogenesis causes human developmental diseases termed ciliopathies. Cell-intrinsic regulatory mechanisms of cilia disassembly have been well-studied. The extracellular cues controlling cilia disassembly remain elusive, however. Here, we show that lysophosphatidic acid (LPA), a multifunctional bioactive phospholipid, acts as a physiological extracellular factor to initiate cilia disassembly and promote neurogenesis. Through systematic analysis of serum components, we identify a small molecular-LPA as the major driver of cilia disassembly. Genetic inactivation and pharmacological inhibition of LPA receptor 1 (LPAR1) abrogate cilia disassembly triggered by serum. The LPA-LPAR-G-protein pathway promotes the transcription and phosphorylation of cilia disassembly factors-Aurora A, through activating the transcription coactivators YAP/TAZ and calcium/CaM pathway, respectively. Deletion of Lpar1 in mice causes abnormally elongated cilia and decreased proliferation in neural progenitor cells, thereby resulting in defective neurogenesis. Collectively, our findings establish LPA as a physiological initiator of cilia disassembly and suggest targeting the metabolism of LPA and the LPA pathway as potential therapies for diseases with dysfunctional ciliogenesis.
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http://dx.doi.org/10.1038/s41467-021-20986-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7843646PMC
January 2021

Effect of CYP2C9 genetic polymorphism and breviscapine on losartan pharmacokinetics in healthy subjects.

Xenobiotica 2021 Feb 3:1-16. Epub 2021 Feb 3.

Department of Pharmacology, College of Pharmacy, Dali University, Dali, China.

1. Breviscapine was an active ingredient of flavonoid glycosides. Our present study was conducted to evaluate the impact of breviscapine on the pharmacokinetics of losartan and its active metabolite E-3174, and that relationship with the gene polymorphism of CYP2C9 in healthy Chinese volunteers, to provide a basis for clinical rational drug use. 2. The genotypes of 217 healthy Chinese subjects were determined using PCR-RFLP. Twelve healthy subjects were selected and were known CYP2C9 genotypes (six CYP2C9*1/*3 and six CYP2C9*1/*1) in a two-phase randomised crossover design study. These subjects were given daily doses of 120 mg (40 mg, three times a day) of breviscapine or a placebo for 14 days, followed by 50 mg losartan on day 15. 3. Compared with individuals carrying the CYP2C9*1/*1 genotype, the CYP2C9*1/*3 genotype showed an increase in the AUC (833.6 ± 379.8 ng h ml vs. 526.1 ± 140.1 ng h ml,  < 0.05) and a decrease in the MR (the metabolic ratio of losartan, AUC/AUC) (2.67 ± 1.40 vs. 4.56 ± 0.83,  < 0.05) of losartan during the placebo treatment phase. Individuals with genotype CYP2C9*1/*3 showed a significant increase in AUC (2335 ± 851.8 ng h ml vs. 1927 ± 949.5 ng h ml,  < 0.05) and AUC (2363 ± 875.6 ng h ml vs. 1966 ± 966.1 ng h ml,  < 0.05) of E-3174 after breviscapine treatment compared to the placebo group. 4. In healthy subjects, breviscapine had no significant effect on the pharmacokinetics of losartan. The activity of CYP2C9 enzyme to losartan metabolism was more significant in subjects with CYP2C9*1/*3 than those with CYP2C9*1/*1 genotype.
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http://dx.doi.org/10.1080/00498254.2021.1880670DOI Listing
February 2021

Study of rapid reorganization of visual neurofunctions with the resting-state functional MRI in pituitary adenoma patients with vision improvement after transsphenoidal surgery.

Brain Behav 2021 Jan 27:e01917. Epub 2021 Jan 27.

Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China.

Introduction: To investigate changes of vision-related resting-state activity in pituitary adenoma (PA) patients with visual improvement after transsphenoidal surgery.

Methods: 14 PA patients with visual improvement after surgery were enrolled. The resting-state functional MRI and neuro-ophthalmologic evaluation were performed before and after the operation. The functional connectivity (FC) of 8 seeds (the primary visual cortex (V1), the secondary visual cortex (V2), the middle temporal visual cortex (MT+), and fusiform gyrus(FG)) was evaluated. A paired t test was conducted to identify the differences between the two groups.

Results: Compared with the preoperation counterparts, the PA patients with improved vision exhibited decreased FC with the V1, V2, MT+, FG in the left paracentral lobule, bilateral lingual gyrus, precentral gyrus(BA 4), right superior temporal gyrus(BA 22), left fusiform gyrus, bilateral middle occipital gyrus (BA 19), left cuneus, right inferior occipital gyrus, left superior frontal gyrus, right cuneus, left superior parietal lobule(BA 7),the medulla, right postcentral gyrus, and increased FC in the right middle frontal gyrus, left inferior parietal lobule (BA 40), left declive, right lentiform nucleus, inferior frontal gyrus, right superior frontal gyrus(BA 11), cingulate gyrus(BA 32), right putamen, right thalamus, left medial frontal gyrus, left claustrum, left superior frontal Medial, right rectal gyrus(BA 25) and right parahippocampal gyrus.

Conclusions: The results show most subareas within the visual cortex exhibit decreased functional connectivity. The functional changes in subareas within default mode network (DMN), action observation network (AON) and the multisensory system in PAs propose that vision improvement may lead to function remodeling in higher-order cortex.
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http://dx.doi.org/10.1002/brb3.1917DOI Listing
January 2021

NSCR-Based DenseNet for Lung Tumor Recognition Using Chest CT Image.

Biomed Res Int 2020 16;2020:6636321. Epub 2020 Dec 16.

Urinary Surgery, General Hospital of Ningxia Medical University, Yinchuan 750004, China.

Nonnegative sparse representation has become a popular methodology in medical analysis and diagnosis in recent years. In order to resolve network degradation, higher dimensionality in feature extraction, data redundancy, and other issues faced when medical images parameters are trained using convolutional neural networks. Lung tumors in chest CT image based on nonnegative, sparse, and collaborative representation classification of DenseNet (DenseNet-NSCR) are proposed by this paper: firstly, initialization parameters of pretrained DenseNet model using transfer learning; secondly, training DenseNet using CT images to extract feature vectors for the full connectivity layer; thirdly, a nonnegative, sparse, and collaborative representation (NSCR) is used to represent the feature vector and solve the coding coefficient matrix; fourthly, the residual similarity is used for classification. The experimental results show that the DenseNet-NSCR classification is better than the other models, and the various evaluation indexes such as specificity and sensitivity are also high, and the method has better robustness and generalization ability through comparison experiment using AlexNet, GoogleNet, and DenseNet-201 models.
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http://dx.doi.org/10.1155/2020/6636321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787714PMC
December 2020

Tumor-tagging by oncolytic viruses: A novel strategy for CAR-T therapy against solid tumors.

Cancer Lett 2021 Jan 19;503:69-74. Epub 2021 Jan 19.

State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China. Electronic address:

Chimeric antigen receptor (CAR) T cell therapy is one of the most promising immunotherapies in the past decade. It brings hope for cure to patients with previously refractory hematological malignancies. However, when translating this strategy into non-hematologic malignancies, the antitumor activity from multiple clinical studies seemed to be subtle or transient. The less satisfying efficacy in solid tumors might at least due to antigen heterogeneity, suboptimal CAR-T cell trafficking and tumor immunosuppressive environment. Here, we will review the updating strategies to challenge the therapeutic impediments of CAR-T therapy in non-hematologic malignancies. We mainly focus on the combination with oncolytic viruses (OV), the born allies for CAR-T cells. In addition to previously reported OVs-arming strategy, we discuss recently proposed tumor-tagging concept by OVs as CAR-T targets, as well as the possible improvements. Overall, tumor-tagging strategy by OVs combination with CAR-T would be a novel and promising solution for the heterogeneity and immunosuppressive microenvironment of solid tumors.
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http://dx.doi.org/10.1016/j.canlet.2021.01.014DOI Listing
January 2021

CEP55 promotes cilia disassembly through stabilizing Aurora A kinase.

J Cell Biol 2021 Feb;220(2)

State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.

Primary cilia protrude from the cell surface and have diverse roles during development and disease, which depends on the precise timing and control of cilia assembly and disassembly. Inactivation of assembly often causes cilia defects and underlies ciliopathy, while diseases caused by dysfunction in disassembly remain largely unknown. Here, we demonstrate that CEP55 functions as a cilia disassembly regulator to participate in ciliopathy. Cep55-/- mice display clinical manifestations of Meckel-Gruber syndrome, including perinatal death, polycystic kidneys, and abnormalities in the CNS. Interestingly, Cep55-/- mice exhibit an abnormal elongation of cilia on these tissues. Mechanistically, CEP55 promotes cilia disassembly by interacting with and stabilizing Aurora A kinase, which is achieved through facilitating the chaperonin CCT complex to Aurora A. In addition, CEP55 mutation in Meckel-Gruber syndrome causes the failure of cilia disassembly. Thus, our study establishes a cilia disassembly role for CEP55 in vivo, coupling defects in cilia disassembly to ciliopathy and further suggesting that proper cilia dynamics are critical for mammalian development.
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http://dx.doi.org/10.1083/jcb.202003149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7829976PMC
February 2021

Purification and Biological Activities of Enzymatically Degraded Sargassum fusiforme Polysaccharides.

Chem Biodivers 2021 Jan 20. Epub 2021 Jan 20.

School of Food Science and Biotechnology, Zhejiang Gongshang University, Xiasha, Hangzhou, 310018, P. R. China.

Enzymatic hydrolysate of the crude polysaccharide (SFP) extracted from Sargassum fusiforme was purified by column DEAE-52 and Sephadex G-100 to yield four components, namely, ESFP1, ESFP2, ESFP3 and ESFP4. These components were characterized by chemical composition assay, GC/MS, HPGPC, UV and FT-IR techniques. The in vitro antioxidant activities of the four purified fractions were investigated by measuring their radical scavenging activity and reducing power. The results suggested that all the four components possess good antioxidant activities. Among them, ESFP1 was found to possess the strongest 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical and hydroxyl radical-scavenging activity, and the greatest ferric reducing power. The immunomodulatory effect of these four polysaccharides was demonstrated by their ability to promote proliferation, and to enhance both phagocytic activity and NO release in a macrophage RAW264.7 model. The results revealed that the bioactivities of the polysaccharides are related to their molecular weight, and the uronic acid and sulfate contents.
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http://dx.doi.org/10.1002/cbdv.202000930DOI Listing
January 2021

Incomplete multi-modal representation learning for Alzheimer's disease diagnosis.

Med Image Anal 2021 Jan 1;69:101953. Epub 2021 Jan 1.

School of Biomedical Engineering, Shanghai Tech University, Shanghai, China; Shanghai United Imaging Intelligence Co., Ltd., Shanghai, China; Department of Artificial Intelligence, Korea University, Seoul 02841, Republic of Korea. Electronic address:

Alzheimers disease (AD) is a complex neurodegenerative disease. Its early diagnosis and treatment have been a major concern of researchers. Currently, the multi-modality data representation learning of this disease is gradually becoming an emerging research field, attracting widespread attention. However, in practice, data from multiple modalities are only partially available, and most of the existing multi-modal learning algorithms can not deal with the incomplete multi-modality data. In this paper, we propose an Auto-Encoder based Multi-View missing data Completion framework (AEMVC) to learn common representations for AD diagnosis. Specifically, we firstly map the original complete view to a latent space using an auto-encoder network framework. Then, the latent representations measuring statistical dependence learned from the complete view are used to complement the kernel matrix of the incomplete view in the kernel space. Meanwhile, the structural information of original data and the inherent association between views are maintained by graph regularization and Hilbert-Schmidt Independence Criterion (HSIC) constraints. Finally, a kernel based multi-view method is applied to the learned kernel matrix for the acquisition of common representations. Experimental results achieved on Alzheimers Disease Neuroimaging Initiative (ADNI) datasets validate the effectiveness of the proposed method.
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http://dx.doi.org/10.1016/j.media.2020.101953DOI Listing
January 2021

A novel pathogenicity determinant hijacks maize catalase 1 to enhance viral multiplication and infection.

New Phytol 2021 Jan 18. Epub 2021 Jan 18.

State Kay Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China.

Pathogens have evolved various strategies to overcome host immunity for successful infection. Maize chlorotic mottle virus (MCMV) can cause lethal necrosis in maize (Zea mays) when it coinfects with a virus in the Potyviridae family. However, the MCMV pathogenicity determinant remains largely unknown. Here we show that the P31 protein of MCMV is important for viral accumulation and essential for symptom development. Ectopic expression of P31 using foxtail mosaic virus or potato virus X induced necrosis in systemically infected maize or Nicotiana benthamiana leaves. Maize catalases (CATs) were shown to interact with P31 in yeast and in planta. P31 accumulation was elevated through its interaction with ZmCAT1. P31 attenuated the expression of salicylic acid (SA)-responsive pathogenesis-related (PR) genes by inhibiting catalase activity during MCMV infection. In addition, silencing of ZmCATs using a brome mosaic virus-based gene silencing vector facilitated MCMV RNA and coat protein accumulation. This study reveals an important role for MCMV P31 in counteracting host defence and inducing systemic chlorosis and necrosis. Our results have implications for understanding the mechanisms in defence and counter-defence during infection of plants by various pathogens.
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http://dx.doi.org/10.1111/nph.17206DOI Listing
January 2021

Deep learning-based automatic delineation of the hippocampus by MRI: geometric and dosimetric evaluation.

Radiat Oncol 2021 Jan 14;16(1):12. Epub 2021 Jan 14.

Department of Radiation Oncology, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, China.

Background: Whole brain radiotherapy (WBRT) can impair patients' cognitive function. Hippocampal avoidance during WBRT can potentially prevent this side effect. However, manually delineating the target area is time-consuming and difficult. Here, we proposed a credible approach of automatic hippocampal delineation based on convolutional neural networks.

Methods: Referring to the hippocampus contouring atlas proposed by RTOG 0933, we manually delineated (MD) the hippocampus on the MRI data sets (3-dimensional T1-weighted with slice thickness of 1 mm, n = 175), which were used to construct a three-dimensional convolutional neural network aiming for the hippocampus automatic delineation (AD). The performance of this AD tool was tested on three cohorts: (a) 3D T1 MRI with 1-mm slice thickness (n = 30); (b) non-3D T1-weighted MRI with 3-mm slice thickness (n = 19); (c) non-3D T1-weighted MRI with 1-mm slice thickness (n = 11). All MRIs confirmed with normal hippocampus has not been violated by any disease. Virtual radiation plans were created for AD and MD hippocampi in cohort c to evaluate the clinical feasibility of the artificial intelligence approach. Statistical analyses were performed using SPSS version 23. P < 0.05 was considered significant.

Results: The Dice similarity coefficient (DSC) and Average Hausdorff Distance (AVD) between the AD and MD hippocampi are 0.86 ± 0.028 and 0.18 ± 0.050 cm in cohort a, 0.76 ± 0.035 and 0.31 ± 0.064 cm in cohort b, 0.80 ± 0.015 and 0.24 ± 0.021 cm in cohort c, respectively. The DSC and AVD in cohort a were better than those in cohorts b and c (P < 0.01). There is no significant difference between the radiotherapy plans generated using the AD and MD hippocampi.

Conclusion: The AD of the hippocampus based on a deep learning algorithm showed satisfying results, which could have a positive impact on improving delineation accuracy and reducing work load.
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http://dx.doi.org/10.1186/s13014-020-01724-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807715PMC
January 2021

Preliminary clinical experience applying donor-derived cell-free DNA to discern rejection in pediatric liver transplant recipients.

Sci Rep 2021 Jan 13;11(1):1138. Epub 2021 Jan 13.

Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, No. 1630 Dongfang Road, Shanghai, 200127, People's Republic of China.

Donor-derived cell-free DNA (dd-cfDNA) has been of major interest recently as a non-invasive marker of graft injury, but has not yet been extensively tested in children. From May to September in 2019, a total of 76 pediatric patients receiving a liver graft were enrolled and there were 27 patients excluded. Ultimately plasma samples and matched liver specimens from 49 patients were successfully collected whenever rejection was suspected clinically. Dd-cfDNA were analyzed and then compared to biopsy. Of these, 11 (22.4%) patients were found to have rejection by biopsy. Dd-cfDNA levels were higher among patients with rejection compared to those with no rejection. In subgroup analysis, dd-cfDNA% among patients with rejection differed from those with EBV/CMV infection and DILI patients. Similarly, observations were available concerning dd-cfDNA (cp/mL). The AUC for dd-cfDNA% and dd-cfDNA (cp/mL) were 0.878, 0.841, respectively, both of which were higher than conventional LFTs. For rejection, dd-cfDNA% ≥ 28.7% yielded a sensitivity of 72.7%, specificity 94.7% and dd-cfDNA (cp/mL) ≥ 2076 cp/mL, yielded a sensitivity of 81.8%, specificity 81.9%. Of note, the dd-cfDNA distribution was significantly different between whole liver and LLS transplantation. In the setting of pediatric LTx, dd-cfDNA appears to be a sensitive biomarker indicating the presence of rejection.International Clinical Trails Registry Platform: ChiCTR1900022406.
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http://dx.doi.org/10.1038/s41598-020-80845-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807012PMC
January 2021

Cyclopeptides from the Mushroom Pathogen Fungus .

J Nat Prod 2021 Feb 13;84(2):327-338. Epub 2021 Jan 13.

Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.

Three new cyclopeptides with serial Phe residues were identified with the aid of HPLC-DAD analysis, from the culture broth of , a fungal pathogen causing mushroom cobweb disease. Cladoamides A () and B () have two consecutive -methylphenylalanine units in the destruxin class cyclic depsipentapeptide framework, while cladoamide C () has a three consecutive Phe motif in a cyclopentapeptide structure. Of these three cyclopeptides, showed potent autophagy-inducing activity at 10 μg/mL, comparable to a positive control, rapamycin. For the determination of the absolute configurations of the Ile residues in and , new conditions for separating Ile and -Ile, using a pentafluorophenyl-bonded solid phase and methanolic solvent, were established within the analytical scheme of the advanced Marfey's method, thus offering a convenient alternative to the C Marfey's method, which requires elution with a three-solvent mixture. The sequence of two d-Phe and one l-Phe in was determined through NMR chemical shift prediction by DFT-based calculations and chemical synthesis, which demonstrated the significance of noncovalent interactions in the accurate calculation of stable conformers for peptides with multiple aromatic rings.
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http://dx.doi.org/10.1021/acs.jnatprod.0c00980DOI Listing
February 2021

RGB-D salient object detection: A survey.

Comput Vis Media (Beijing) 2021 Jan 7:1-33. Epub 2021 Jan 7.

Inception Institute of Artificial Intelligence (IIAI), Abu Dhabi, United Arab Emirates.

Salient object detection, which simulates human visual perception in locating the most significant object(s) in a scene, has been widely applied to various computer vision tasks. Now, the advent of depth sensors means that depth maps can easily be captured; this additional spatial information can boost the performance of salient object detection. Although various RGB-D based salient object detection models with promising performance have been proposed over the past several years, an in-depth understanding of these models and the challenges in this field remains lacking. In this paper, we provide a comprehensive survey of RGB-D based salient object detection models from various perspectives, and review related benchmark datasets in detail. Further, as light fields can also provide depth maps, we review salient object detection models and popular benchmark datasets from this domain too. Moreover, to investigate the ability of existing models to detect salient objects, we have carried out a comprehensive attribute-based evaluation of several representative RGB-D based salient object detection models. Finally, we discuss several challenges and open directions of RGB-D based salient object detection for future research. All collected models, benchmark datasets, datasets constructed for attribute-based evaluation, and related code are publicly available at https://github.com/taozh2017/RGBD-SODsurvey.
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http://dx.doi.org/10.1007/s41095-020-0199-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7788385PMC
January 2021

Full genome sequence of a new three-segment gammapartitivirus from the phytopathogenic fungus Alternaria tenuissima on cotton in China.

Arch Virol 2021 Mar 11;166(3):973-976. Epub 2021 Jan 11.

College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.

In this study, a new double-stranded RNA (dsRNA) virus, Alternaria tenuissima partitivirus 1 (AttPV1), was isolated from Alternaria tenuissima strain XJ-BZ-2-6, a phytopathogenic fungus infecting cotton in China. The genome of AttPV1 comprised three dsRNAs of 1,785 nt (dsRNA1), 1,545 nt (dsRNA2), and 1,537 nt (dsRNA3) in length, the nucleotide sequence of which was determined using reverse transcription polymerase chain reaction, random-primed clones, and RNA-ligase-mediated rapid amplification of cDNA ends. dsRNA1 had a single open reading frame encoding a putative 61.54-kDa RNA-dependent RNA polymerase (RdRp). dsRNA2 and dsRNA3 were predicted to encode putative coat proteins (CPs) of 47.90 kDa and 46.25 kDa, respectively. The RdRp domain shared 63.54-73.17% amino acid sequence identity with members of the genus Gammapartitivirus. Phylogenetic trees based on RdRp or CP sequences showed that AttPV1 clustered with members of the genus Gammapartitivirus. Hence, these results indicate that AttPV1 is a new gammapartitivirus from A. tenuissima.
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http://dx.doi.org/10.1007/s00705-020-04937-4DOI Listing
March 2021