Publications by authors named "An Zhang"

88 Publications

Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam).

BMC Genomics 2021 Apr 13;22(1):262. Epub 2021 Apr 13.

Jiangsu Xuzhou Sweetpotato Research Center/Sweetpotato Research Institute, China Agricultural Academy of Sciences, Xuzhou, 221131, China.

Background: Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato.

Results: The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages.

Conclusions: Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato.
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http://dx.doi.org/10.1186/s12864-021-07544-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042981PMC
April 2021

Cytokine-induced killer cells/dendritic cells and cytokine-induced killer cells immunotherapy for the treatment of esophageal cancer: A meta-analysis.

Medicine (Baltimore) 2021 Apr;100(13):e24519

Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education)/ Department of Pathology, the First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang.

Objectives: This meta-analysis was designed to systematically evaluate whether autologous cytokine-induced killer cells (CIK) or dendritic cells and cytokine-induced killer cells (DC-CIK) immunotherapy combined with chemotherapy can improve the therapeutic effect and safety of chemotherapy in esophageal cancer (EC).

Materials And Methods: Randomized controlled trials (RCTs) were electronically searched databases including CNKI, WanFang, WeiPu, CBMDisc, PubMed, Web of Science, EMbase, the Cochrane Library, and Clinical Trials. The databases were searched for articles published until June 2019. Two researchers independently screened the literature, extracted data, and evaluated the quality of the included literature. Meta-analysis was performed using RevMan5.3.

Results: Seventeen studies (1416 participants) were included. The differences between CIK/DC-CIK combination chemotherapy and chemotherapy alone were significant. The results displayed that the number of CD3+, CD4+, CD4+/CD8+, and NK cells was significantly increased after 1 to 2 weeks of treatment with CIK/DC-CIK cells in the treatment group (all P < .05). In addition, the results shown that 1-year overall survival was significantly prolonged (P < .0001) and quality of life was improved (P = .001) in EC chemotherapy combined with immunotherapy groups compared with conventional treatment. Furthermore, cytokine expression levels of interleukin 2 (IL-2), tumor necrosis factor α (TNF-α), and interleukin 12 (IL-12) were significantly increased (P = .0003) as well as the levels of immunoglobulins were elevated (P < .00001). Serum levels of tumor marker molecules, carcinoembryonic antigen (CEA), carbohydrate antigen (CA)-199, and CA-125 were lower in treatment groups than that of control groups (P < .00001). No fatal adverse reactions were noted (P = .04).

Conclusions: It is safe and effective for patients to use chemotherapy combined with CIK/DC-CIK immunotherapy. Immunotherapy can simultaneously improve the antitumor immune response. Specifically, DC-CIK cells can increase T lymphocyte subsets, CIK cells, NK cells, and immunoglobulins in peripheral blood to enhance antitumor immunity. Therefore, combination therapy enhances the immune function and improves the therapeutic efficacy of patients with EC.
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http://dx.doi.org/10.1097/MD.0000000000024519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8021386PMC
April 2021

Factoring distinct materials and nitrogen-related microbes into assessments of nitrogen pollution risks during composting.

Bioresour Technol 2021 Jun 26;329:124896. Epub 2021 Feb 26.

Heilongjiang Province Environmental Science Research Institute, Harbin 150056, China.

The aim of this study was to evaluate nitrogen pollution risks from distinct materials composting with the discrepancy of component, including chicken manure, municipal solid and straw waste (CM, MSW, SW). Results showed total nitrogen maximum mean concentrations were observed in CM (39.57 g/kg). Pollution risks in CM were continuous, while MSW and SW mainly concentrated during heating phases. Microbial analysis confirmed that pollution risks from ammonification and nitrification were more prevalent in CM. The risks of pollution caused by nitrate reduction accompanied NO were the most serious in MSW. The multifunctional nitrogen-related microbes Pseudomonas and Bacillus were affected by microenvironments and contributed to different pollution risks. Furthermore, PICRUSt analysis identified the "inferred" key genes (pmoC-amoC, nrfH, nifD etc.) related to nitrogen pollution risks. This study evaluated nitrogen pollution risks and proposed the future directions, providing theoretical basis and feasible optimization measures for the mitigation of nitrogen pollution during composting.
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http://dx.doi.org/10.1016/j.biortech.2021.124896DOI Listing
June 2021

Early Improvement of Acute Respiratory Distress Syndrome in Patients With COVID-19 in the Intensive Care Unit: Retrospective Analysis.

JMIR Public Health Surveill 2021 03 9;7(3):e24843. Epub 2021 Mar 9.

Department of Intensive Care Unit, Chongqing Sixth People's Hospital, Chongqing, China.

Background: Since the start of the COVID-19 pandemic, there have been over 2 million deaths globally. Acute respiratory distress syndrome (ARDS) may be the main cause of death.

Objective: This study aimed to describe the clinical features, outcomes, and ARDS characteristics of patients with COVID-19 admitted to the intensive care unit (ICU) in Chongqing, China.

Methods: The epidemiology of COVID-19 from January 21, 2020, to March 15, 2020, in Chongqing, China, was analyzed retrospectively, and 75 ICU patients from two hospitals were included in this study. On day 1, 56 patients with ARDS were selected for subgroup analysis, and a modified Poisson regression was performed to identify predictors for the early improvement of ARDS (eiARDS).

Results: Chongqing reported a 5.3% case fatality rate for the 75 ICU patients. The median age of these patients was 57 (IQR 25-75) years, and no bias was present in the sex ratio. A total of 93% (n=70) of patients developed ARDS during ICU stay, and more than half had moderate ARDS. However, most patients (n=41, 55%) underwent high-flow nasal cannula oxygen therapy, but not mechanical ventilation. Nearly one-third of patients with ARDS improved (arterial blood oxygen partial pressure/oxygen concentration >300 mm Hg) in 1 week, which was defined as eiARDS. Patients with eiARDS had a higher survival rate and a shorter length of ICU stay than those without eiARDS. Age (<55 years) was the only variable independently associated with eiARDS, with a risk ratio of 2.67 (95% CI 1.17-6.08).

Conclusions: A new subphenotype of ARDS-eiARDS-in patients with COVID-19 was identified. As clinical outcomes differ, the stratified management of patients based on eiARDS or age is highly recommended.
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http://dx.doi.org/10.2196/24843DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7945975PMC
March 2021

Spatial-Temporal Distribution Variation of Ground-Level Ozone in China's Pearl River Delta Metropolitan Region.

Int J Environ Res Public Health 2021 01 20;18(3). Epub 2021 Jan 20.

State Key Laboratory of Resources and Environmental Information System, Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.

Long-term exposure to ozone pollution will cause severe threats to residents' physical and mental health. Ground-level ozone is the most severe air pollutant in China's Pearl River Delta Metropolitan Region (PRD). It is of great significance to accurately reveal the spatial-temporal distribution characteristics of ozone pollution exposure patterns. We used the daily maximum 8-h ozone concentration data from PRD's 55 air quality monitoring stations in 2015 as input data. We used six models of STK and ordinary kriging (OK) for the simulation of ozone concentration. Then we chose a better ozone pollution prediction model to reveal the ozone exposure characteristics of the PRD in 2015. The results show that the Bilonick model (BM) model had the highest simulation precision for ozone in the six models for spatial-temporal kriging (STK) interpolation, and the STK model's simulation prediction results are significantly better than the OK model. The annual average ozone concentrations in the PRD during 2015 showed a high spatial variation in the north and east and low in the south and west. Ozone concentrations were relatively high in summer and autumn and low in winter and spring. The center of gravity of ozone concentrations tended to migrate to the north and west before moving to the south and then finally migrating to the east. The ozone's spatial autocorrelation was significant and showed a significant positive correlation, mainly showing high-high clustering and low-low clustering. The type of clustering undergoes temporal migration and conversion over the four seasons, with spatial autocorrelation during winter the most significant.
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http://dx.doi.org/10.3390/ijerph18030872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7908513PMC
January 2021

Increases in the seaward river flux of nutrients driven by human migration and land-use changes in the tide-influenced delta.

Sci Total Environ 2021 Mar 14;761:144501. Epub 2020 Dec 14.

Key Laboratory of Marine Chemistry Theory and Technology, Ocean University of China, 238 Songling Road, Qingdao 266100, China.

Most large megacities are located on areas adjacent to tide-influenced deltas. However, contribution of megacities to seaward nutrient fluxes in tide-influenced deltas are poorly quantified in regional and global levels. We analyzed nutrient concentrations and water current data for a large and tide-influenced delta, the Changjiang (Yangtze River) since 1980. Concentrations, species ratios and fluxes of nutrients in tide-influenced delta has been found to differ dramatically from those at upstream. Over the period 2004 to 2015, the seaward nutrient fluxes of dissolved inorganic nitrogen and dissolved silica increased by 5%-10%, but dissolved inorganic phosphorus increased by 15%-20%, in the tide-influenced delta of the Changjiang. Consequently, the DIP/DIN decreases by 11% and DIP/DSi increases by 14% at the river mouth relative to those farther upstream the tidal limit. The legacy and/or recycled contribution accounts for 10%-30% of this increased nutrient flux, hence additional sources are predominantly those involving anthropogenic land-use changes. These findings have implications not only for the Changjiang but also for other riverine systems with respect to management strategy. Nutrient dynamics in tide-influenced deltas near urban areas should receive increased research and policy attention. By not considering nutrient sources in tide-influenced deltas, knowledge of the seaward fluxes and species ratios of nutrients from land sources is incomplete and can be biased, to the point that assessments of their impacts on adjacent marine environments may be inaccurate and mitigation policies therefore ineffective.
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http://dx.doi.org/10.1016/j.scitotenv.2020.144501DOI Listing
March 2021

Tumor-associated macrophage polarization promotes the progression of esophageal carcinoma.

Aging (Albany NY) 2020 12 15;13(2):2049-2072. Epub 2020 Dec 15.

Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang 832000, China.

The immune response facilitated by tumor-associated macrophages is a vital determinant of tumor progression. We identified differentially expressed genes between various macrophage phenotypes in the Gene Expression Omnibus, and used Kaplan-Meier Plotter to determine which of them altered the prognosis of esophageal carcinoma patients. Fibrinogen-like protein 2 (), an immunosuppressive factor in the tumor microenvironment of various cancers, was upregulated in M2 macrophages, and higher expression was associated with poorer survival in esophageal carcinoma patients. Using the TIMER database, we found that expression correlated positively with the levels of immune markers of infiltrating B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils and dendritic cells in esophageal carcinoma samples. Correlation analyses in cBioPortal revealed that the mRNA levels of correlated strongly with those of interleukin 10, matrix metalloproteinase 9, C-C motif chemokine ligand 5, T-cell immunoglobulin mucin 3, interleukin 13, vascular cell adhesion molecule 1, macrophage colony-stimulating factor and fibroblast growth factor 7 in esophageal carcinoma tissues. The same cytokines were upregulated when esophageal squamous cell carcinoma cells were co-cultured with M2-like tumor-associated macrophages. Thus, by secreting FGL2, M2-like tumor-associated macrophages may create an immunosuppressive tumor microenvironment that induces the occurrence and progression of esophageal carcinoma.
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http://dx.doi.org/10.18632/aging.202201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7880404PMC
December 2020

Distribution and prognostic impact of M1 macrophage on esophageal squamous cell carcinoma.

Carcinogenesis 2020 Dec 3. Epub 2020 Dec 3.

Department of Pathology and Key Laboratory of Xinjiang Endemic and Ethnic Diseases (Ministry of Education) / Department of Pathology, the First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, China.

Macrophages are a double-edged sword with potential cancer-promoting and anti-cancer effects. Controversy remains regarding the effect of macrophages, especially M1 macrophages, on tumor promotion and suppression. We aimed to investigate the role of M1 macrophages in the occurrence and progression of esophageal squamous cell carcinoma (ESCC). Analyzing the data in Gene Expression Omnibus (GEO) database by The CIBERSORT algorithm found that M1 macrophages were one of the important components of many immune cells in ESCCs, and the increased in their number was obviously negatively correlated with tumor T staging. This result was verified by our experimental data: the density of CD68/HLA-DR double-stained M1 macrophages in ESCC tumor nest and tumor stroma were significantly higher than that in cancer-adjacent normal (CAN) tissues. The density of M1 macrophages in ESCC tumor nest was negatively correlated with the patient's lymph node metastasis and clinical stage (P < 0.05), and the negative tendency was more obvious for M1 macrophages in ESCC tumor stroma (P < 0.001). Exposure to M1 macrophage CM inhibited ESCC cell migration and invasion ability significantly (P < 0.05). Moreover, the increased M1 macrophage density in ESCC tumor stroma correlated positively with good prognosis of ESCC. M1 macrophages were involved in inhibiting ESCC cell migration and invasion, which could serve as a good prognostic factor in patients with ESCC.
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http://dx.doi.org/10.1093/carcin/bgaa128DOI Listing
December 2020

The COVID-19 Infodemic: Infodemiology Study Analyzing Stigmatizing Search Terms.

J Med Internet Res 2020 11 16;22(11):e22639. Epub 2020 Nov 16.

State Key Laboratory of Resources and Environmental Information System, Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.

Background: In the context of the COVID-19 infodemic, the global profusion of monikers and hashtags for COVID-19 have found their way into daily communication and contributed to a backlash against China and the Chinese people.

Objective: This study examines public engagement in crisis communication about COVID-19 during the early epidemic stage and the practical strategy of social mobilization to mitigate the infodemic.

Methods: We retrieved the unbiased values of the top-ranked search phrases between December 30, 2019, and July 15, 2020, which normalized the anonymized, categorized, and aggregated samples from Google Search data. This study illustrates the most-searched terms, including the official COVID-19 terms, the stigmatized terms, and other controls, to measure the collective behavioral propensities to stigmatized terms and to explore the global reaction to the COVID-19 epidemic in the real world. We calculated the ratio of the cumulative number of COVID-19 cases to the regional population as the cumulative rate (R) of a specific country or territory and calculated the Gini coefficient (G) to measure the collective heterogeneity of crowd behavior.

Results: People around the world are using stigmatizing terms on Google Search, and these terms were used earlier than the official names. Many stigmatized monikers against China (eg, "Wuhan pneumonia," G=0.73; "Wuhan coronavirus," G=0.60; "China pneumonia," G=0.59; "China coronavirus," G=0.52; "Chinese coronavirus," G=0.50) had high collective heterogeneity of crowd behavior between December 30, 2019, and July 15, 2020, while the official terms "COVID-19" (G=0.44) and "SARS-CoV-2" (G=0.42) have not become de facto standard usages. Moreover, the pattern of high consistent usage was observed in 13 territories with low cumulative rates (R) between January 16 and July 15, 2020, out of 58 countries and territories that have reported confirmed cases of COVID-19. In the scientific literature, multifarious naming practices may have provoked unintended negative impacts by stigmatizing Chinese people. The World Health Organization; the United Nations Educational, Scientific and Cultural Organization; and the media initiated campaigns for fighting back against the COVID-19 infodemic with the same mission but in diverse voices.

Conclusions: Infodemiological analysis can articulate the collective propensities to stigmatized monikers across search behaviors, which may reflect the collective sentiment of backlash against China and Chinese people in the real world. The full-fledged official terms are expected to fight back against the resilience of negative perceptual bias amid the COVID-19 epidemic. Such official naming efforts against the infodemic should be met with a fair share of identification in scientific conventions and sociocultural paradigms. As an integral component of preparedness, appropriate nomenclatures should be duly assigned to the newly identified coronavirus, and social mobilization in a uniform voice is a priority for combating the next infodemic.
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http://dx.doi.org/10.2196/22639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7674145PMC
November 2020

Inflammatory cytokines, T lymphocyte subsets, and ritonavir involved in liver injury of COVID-19 patients.

Signal Transduct Target Ther 2020 10 31;5(1):255. Epub 2020 Oct 31.

Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 400010, Chongqing, China.

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http://dx.doi.org/10.1038/s41392-020-00363-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7599975PMC
October 2020

Surface Reconstruction of InN Nanosheets for Efficient CO Electroreduction into Formate.

Nano Lett 2020 Nov 15;20(11):8229-8235. Epub 2020 Oct 15.

Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.

Probing and understanding the intrinsic active sites of electrocatalysts is crucial to unravel the underlying mechanism of CO electroreduction and provide a prospective for the rational design of high-performance electrocatalysts. However, their structure-activity relationships are not straightforward because electrocatalysts might reconstruct under realistic working conditions. Herein, we employ measurements to unveil the intrinsic origin of the InN nanosheets which served as an efficient electrocatalyst for CO reduction with a high faradaic efficiency of 95% for carbonaceous product. During the CO electroreduction, InN nanosheets reconstructed to form the In-rich surface. Density functional theory calculations revealed that the reconstruction of InN led to the redistribution of surface charge that significantly promoted the adsorption of HCOO* intermediates and thus benefited the formation of formate toward CO electroreduction. This work establishes a fundamental understanding on the mechanism associated with self-reconstruction of heterogeneous catalysts toward CO electroreduction.
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http://dx.doi.org/10.1021/acs.nanolett.0c03345DOI Listing
November 2020

[Impact of the Timing of Traditional Chinese Medicine Therapy on the Therapeutic Effect and Prognosis of Severe Coronavirus Disease 2019].

Zhongguo Yi Xue Ke Xue Yuan Xue Bao 2020 Aug;42(4):521-530

Department of Critical Care Medicine,the Second Affiliated Hospital of Chongqing Medical University,Chongqing 400010,China.

To explore the optimal therapy time for the treatment of severe coronavirus disease 2019(COVID-19)by traditional Chinese medicine(TCM)and its influence on the therapeutic effect and prognosis. The clinical data,laboratory findings,and outcomes of 64 patients with severe COVID-19 treated with TCM and western medicine in Chongqing from January 20,2020, to March 11,2020 were retrospectively analyzed.Patients were divided into early intervention group[TCM was initiated within 3 days (including day 3) after the first diagnosis of severe type/critical type COVID-19]and late intervention group[TCM was initiated after 7 days (including day 7) after the first diagnosis of severe type /critical type COVID-19].The changes in clinical parameters during the course of disease were compared between the two groups. On day 14,the oxygenation index was 292.5(252.0,351.0)mmHg in the early intervention group,which was significantly higher than that in the late intervention group [246.0(170.0,292.5)mmHg](=0.005).The length of hospital stay [(18.56±1.11)d (24.87±1.64)d,=0.001],duration of ICU stay [(14.12±0.91)d (20.00±1.53)d,=0.000] and time to negativity [(16.77±1.04)d (22.48±1.66)d,=0.001] in the early intervention group were significantly shorter than those in the late intervention group.The intubation rate(7.3%)in the early intervention group was significantly lower than that in the late intervention group(30.4%)(=0.028). Early TCM therapy within three days after a diagnosis of severe COVID-19 can shorten the length of hospital stay,duration of ICU stay,and time to negativity and decrease intubation rate.
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http://dx.doi.org/10.3881/j.issn.1000-503X.12915DOI Listing
August 2020

Assessment of the role of afucosylated glycoforms on the antibody-dependent phagocytosis activity of an antibody to Aβ aggregates.

MAbs 2020 Jan-Dec;12(1):1803645

Pharmaceutical Operations and Technology, Biogen , Cambridge, MA, USA.

The terminal sugars of Fc glycans can influence the Fc-dependent biological activities of monoclonal antibody therapeutics. Afucosylated N-glycans have been shown to significantly alter binding to FcγRIIIa and affect antibody-dependent cell-mediated cytotoxicity (ADCC). Therefore, in order to maintain and ensure safety and efficacy for antibodies whose predominant mechanism of action (MOA) is ADCC, afucosylation is routinely monitored and controlled within appropriate limits. However, it is unclear how the composition and levels of afucosylated N-glycans can modulate the biological activities for a recombinant antibody whose target is not a cell surface receptor, as is the case with ADCC. The impact of different types and varying levels of enriched afucosylated N-glycan species on the bioactivities is assessed for an antibody whose target is aggregated amyloid beta (Aβ). While either the presence of complex biantennary or high mannose afucosylated glycoforms significantly increased FcγRIIIa binding activity compared to fucosylated glycoforms, they did not similarly increase aggregated Aβ uptake activity mediated by different effector cells. These experiments suggest that afucosylated N-glycans are not critical for the phagocytic activity of a recombinant antibody whose target is aggregated Aβ and uses Fc effector function as part of its MOA.
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http://dx.doi.org/10.1080/19420862.2020.1803645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7531570PMC
August 2020

Trifunctional metasurface based on spoof surface plasmon polaritons.

Opt Express 2020 Jul;28(14):21260-21267

In this paper, we propose the design of a metasurface that can achieve three functions in different frequency bands. The proposed metasurface is composed of two kinds of unit cells which are designed on the basis of the spatial k-dispersion engineering of spoof surface plasmon polaritons (SSPPs). By arranging these two kinds of unit cells in the chessboard configuration, the three functions of transmission, anomalous refraction and absorption can be integrated into one metasurface. High transmission and strong absorption can be achieved in 2.0-9.0 GHz and 12.6-20.0 GHz, respectively. Meanwhile, anomalous refraction can be achieved in 10-11.7 GHz due to forward scattering cancellation of two unit cells. To verify the design, a prototype was fabricated and measured. The measured results are consistent with the simulation ones. The metasurface can integrate multiple functions into one aperture and therefore has potential application values in multifunctional microwave devices such as shared-aperture antennas, etc.
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http://dx.doi.org/10.1364/OE.395123DOI Listing
July 2020

Risk factors in patients with COVID-19 developing severe liver injury during hospitalisation.

Gut 2021 03 22;70(3):628-629. Epub 2020 Jun 22.

Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China

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http://dx.doi.org/10.1136/gutjnl-2020-321913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873415PMC
March 2021

Online searching platform for the antibiotic resistome in bacterial tree of life and global habitats.

FEMS Microbiol Ecol 2020 07;96(7)

Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China.

Metagenomic analysis reveals that antibiotic-resistance genes (ARGs) are widely distributed in both human-associated and non-human-associated habitats. However, it is difficult to equally compare ARGs between samples without a standard method. Here, we constructed a comprehensive profile of the distribution of potential ARGs in bacterial tree of life and global habitats by investigating ARGs in 55 000 bacterial genomes, 16 000 bacterial plasmid sequences, 3000 bacterial integron sequences and 850 metagenomes using a standard pipeline. We found that >80% of all known ARGs are not carried by any plasmid or integron sequences. Among potential mobile ARGs, tetracycline and beta-lactam resistance genes (such as tetA, tetM and class A beta-lactamase gene) distribute in multiple pathogens across bacterial phyla, indicating their clinical relevance and importance. We showed that class 1 integrases (intI1) display a poor linear relationship with total ARGs in both non-human-associated and human-associated environments. Furthermore, both total ARGs and intI1 genes show little correlation with the degree of anthropogenicity. These observations highlight the need to differentiate ARGs of high clinical relevance. This profile is published on an online platform (ARGs-OSP, http://args-osp.herokuapp.com/) as a valuable resource for the most challenging topics in this field, i.e. the risk, evolution and emergence of ARGs.
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http://dx.doi.org/10.1093/femsec/fiaa107DOI Listing
July 2020

A retrospective study on the epidemiological characteristics and establishment of an early warning system of severe COVID-19 patients.

J Med Virol 2020 10 2;92(10):2173-2180. Epub 2020 Jun 2.

Department of Critical Care Medicine, Three Gorges Center Hospital of Chongqing University, Chongqing, China.

This paper estimates the magnitude of an informational friction limiting credit reallocation to firms during the 2007-2009 financial crisis. Because lenders rely on private information when deciding which relationship to end, borrowers looking for a new lender are adversely selected. I show how to identify private information separately from information common to all lenders but unobservable to the econometrician by using bank shocks within a discrete choice model of relationships. Quantitatively, these informational frictions seem too small to explain the credit crunch in the U.S. syndicated corporate loan market.
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http://dx.doi.org/10.1002/jmv.26022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272979PMC
October 2020

Early forecasting of the potential risk zones of COVID-19 in China's megacities.

Sci Total Environ 2020 Aug 26;729:138995. Epub 2020 Apr 26.

State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.

Recently, the coronavirus disease 2019 (COVID-19) has become a worldwide public health threat. Early and quick identification of the potential risk zones of COVID-19 infection is increasingly vital for the megacities implementing targeted infection prevention and control measures. In this study, the communities with confirmed cases during January 21-February 27 were collected and considered as the specific epidemic data for Beijing, Guangzhou, and Shenzhen. We evaluated the spatiotemporal variations of the epidemics before utilizing the ecological niche models (ENM) to assemble the epidemic data and nine socioeconomic variables for identifying the potential risk zones of this infection in these megacities. Three megacities were differentiated by the spatial patterns and quantities of infected communities, average cases per community, the percentages of imported cases, as well as the potential risks, although their COVID-19 infection situations have been preliminarily contained to date. With higher risks that were predominated by various influencing factors in each megacity, the potential risk zones coverd about 75% to 100% of currently infected communities. Our results demonstrate that the ENM method was capable of being employed as an early forecasting tool for identifying the potential COVID-19 infection risk zones on a fine scale. We suggest that local hygienic authorities should keep their eyes on the epidemic in each megacity for sufficiently implementing and adjusting their interventions in the zones with more residents or probably crowded places. This study would provide useful clues for relevant hygienic departments making quick responses to increasingly severe epidemics in similar megacities in the world.
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http://dx.doi.org/10.1016/j.scitotenv.2020.138995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252152PMC
August 2020

Materials and Microenvironments for Engineering the Intestinal Epithelium.

Ann Biomed Eng 2020 Jul 4;48(7):1916-1940. Epub 2020 Feb 4.

Department of Chemical Engineering, Northeastern University, Boston, MA, 02115, USA.

The barrier functions of the gastrointestinal tract rely in large part on a single layer of columnar intestinal epithelial cells. These epithelial cells are mediators of intestinal homeostasis, regulating and communicating biochemical signals between underlying stromal cells and luminal cues. The development of representative in vitro models to recapitulate the gastrointestinal epithelium is crucial to understanding cell-cell interactions during intestinal homeostasis and dysfunction. Ideally, models would contain microbiota/immune cells, polarized intestinal architecture, multilayered cellular complexity, extracellular matrix, biochemical cues, and mechanical deformation. This review focuses on historical and state of the art biomaterials and substrates used in the field to establish static and fluidic models of the intestinal epithelium. A discussion of conventional adenocarcinoma colon cancer cell lines, primary intestinal epithelial cells derived from organoids, and stromal support cells such as enteric neurons, myofibroblasts, and immune cells, as well as the importance of increasing cellular complexity and future outlook is included.
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http://dx.doi.org/10.1007/s10439-020-02470-8DOI Listing
July 2020

Bioinformatics-based screening of key genes for transformation of liver cirrhosis to hepatocellular carcinoma.

J Transl Med 2020 01 30;18(1):40. Epub 2020 Jan 30.

Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases (Ministry of Education), Shihezi University School of Medicine, Xinjiang, 832002, China.

Background: Hepatocellular carcinoma (HCC) is the most common type of liver tumour, and is closely related to liver cirrhosis. Previous studies have focussed on the pathogenesis of liver cirrhosis developing into HCC, but the molecular mechanism remains unclear. The aims of the present study were to identify key genes related to the transformation of cirrhosis into HCC, and explore the associated molecular mechanisms.

Methods: GSE89377, GSE17548, GSE63898 and GSE54236 mRNA microarray datasets from Gene Expression Omnibus (GEO) were analysed to obtain differentially expressed genes (DEGs) between HCC and liver cirrhosis tissues, and network analysis of protein-protein interactions (PPIs) was carried out. String and Cytoscape were used to analyse modules and identify hub genes, Kaplan-Meier Plotter and Oncomine databases were used to explore relationships between hub genes and disease occurrence, development and prognosis of HCC, and the molecular mechanism of the main hub gene was probed using Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis.

Results: In total, 58 DEGs were obtained, of which 12 and 46 were up- and down-regulated, respectively. Three hub genes (CDKN3, CYP2C9 and LCAT) were identified and associated prognostic information was obtained. CDKN3 may be correlated with the occurrence, invasion, and recurrence of HCC. Genes closely related to changes in the CDKN3 hub gene were screened, and Kyoto Encyclopedia of Genes and Genomes (KEGGs) pathway analysis identified numerous cell cycle-related genes.

Conclusion: CDKN3 may affect the transformation of liver cirrhosis into HCC, and represents a new candidate molecular marker of the occurrence and progression of HCC.
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http://dx.doi.org/10.1186/s12967-020-02229-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6993496PMC
January 2020

Enhanced Coherent Emission from Ionized Nitrogen Molecules by Femtosecond Laser Pulses.

J Phys Chem Lett 2019 Nov 15;10(21):6598-6603. Epub 2019 Oct 15.

State Key Laboratory for Mesoscopic Physics, School of Physics , Peking University , Beijing 100871 , China.

The forward emission spectra were experimentally measured for ionized nitrogen molecules by an 800 nm pump laser and a delayed seed laser. It was found that emission lines around both 428 and 391 nm are greatly enhanced upon use of a 391 or 428 nm seed laser. The emission lines around 391 and 428 nm can be assigned to the rotational transitions of N [BΣ(' = 0) → XΣ( = 0)] and N [BΣ(' = 0) → XΣ( = 1)], respectively. They originate from seed-induced superfluorescence and resonant stimulated Raman scattering. The genetic algorithm was utilized to simulate the experimental observations and determine the relative population of BΣ(' = 0), XΣ( = 1), and XΣ( = 0). The result verifies that vibrational population inversion is achieved between BΣ(' = 0) and XΣ( = 0) by the 800 nm pump laser. Our finding provides new insights into controlling the coherent emission of ionized nitrogen molecules, which has promising application in filamentation-based remote atmospheric sensing.
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http://dx.doi.org/10.1021/acs.jpclett.9b02581DOI Listing
November 2019

Three CNGC Family Members, CNGC5, CNGC6, and CNGC9, Are Required for Constitutive Growth of Root Hairs as Ca-Permeable Channels.

Plant Commun 2020 Jan 16;1(1):100001. Epub 2019 Sep 16.

National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.

The genetic identities of Ca channels in root hair (RH) tips essential for constitutive RH growth have remained elusive for decades. Here, we report the identification and characterization of three cyclic nucleotide-gated channel (CNGC) family members, CNGC5, CNGC6, and CNGC9, as Ca channels essential for constitutive RH growth in . We found that the triple mutant (designated ) showed significantly shorter and branching RH phenotypes as compared with the wild type. The defective RH growth phenotype of could be rescued by either the expression of , , or single gene or by the supply of high external Ca, but could not be rescued by external K supply. Cytosolic Ca imaging and patch-clamp data in HEK293T cells showed that these three CNGCs all function as Ca-permeable channels. Cytosolic Ca imaging in growing RHs further showed that the Ca gradients and their oscillation in RH tips were dramatically attenuated in compared with those in the wild type. Phenotypic analysis revealed that these three CNGCs are Ca channels essential for constitutive RH growth, with different roles in RHs from the conditional player CNGC14. Moreover, we found that these three CNGCs are involved in auxin signaling in RHs. Taken together, our study identified CNGC5, CNGC6, and CNGC9 as three key Ca channels essential for constitutive RH growth and auxin signaling in .

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http://dx.doi.org/10.1016/j.xplc.2019.100001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7748020PMC
January 2020

A cyclic nucleotide-gated channel mediates cytoplasmic calcium elevation and disease resistance in rice.

Cell Res 2019 Oct 23;29(10):820-831. Epub 2019 Aug 23.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

The transient elevation of cytoplasmic calcium is essential for pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI). However, the calcium channels responsible for this process have remained unknown. Here, we show that rice CDS1 (CELL DEATH and SUSCEPTIBLE to BLAST 1) encoding OsCNGC9, a cyclic nucleotide-gated channel protein, positively regulates the resistance to rice blast disease. We show that OsCNGC9 mediates PAMP-induced Ca influx and that this event is critical for PAMPs-triggered ROS burst and induction of PTI-related defense gene expression. We further show that a PTI-related receptor-like cytoplasmic kinase OsRLCK185 physically interacts with and phosphorylates OsCNGC9 to activate its channel activity. Our results suggest a signaling cascade linking pattern recognition to calcium channel activation, which is required for initiation of PTI and disease resistance in rice.
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http://dx.doi.org/10.1038/s41422-019-0219-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796908PMC
October 2019

Long non-coding RNA is associated with the progression and prognosis of advanced gastric cancer.

Aging (Albany NY) 2019 08 15;11(15):5829-5847. Epub 2019 Aug 15.

Second Clinical Medical College, Lanzhou University, Lanzhou 730030, Gansu, P.R. China.

Evidence indicates that aberrantly expressed long non-coding RNAs (lncRNAs) are involved in the development and progression of advanced gastric cancer (AGC). Using RNA sequencing data and clinical information obtained from The Cancer Gene Atlas, we combined differential lncRNA expression profiling and weighted gene co-expression network analysis to identify key lncRNAs associated with AGC progression and prognosis. Cancer susceptibility 19 () was the top hub lncRNA among the lncRNAs included in the gene module most significantly correlated with AGC's pathological variables. was upregulated in AGC clinical samples and was significantly associated with higher pathologic TNM stage, pathologic T stage, lymph node metastasis, and poor overall survival. Multivariable Cox analysis confirmed that overexpression is an independent prognostic factor for overall survival. Furthermore, quantitative real-time PCR assay confirmed that expression in four human gastric cancer cells (AGS, BGC-823, MGC-803, and HGC-27) was significantly upregulated compared with human normal gastric mucosal epithelial cell line (GES-1). Functionally, knockdown inhibited GC cell proliferation and migration in vitro. These findings suggest that may be a novel prognostic biomarker and a potential therapeutic target for AGC.
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http://dx.doi.org/10.18632/aging.102190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6710062PMC
August 2019

Harmonizing the Electronic Structures of the Adsorbate and Catalysts for Efficient CO Reduction.

Nano Lett 2019 Sep 16;19(9):6547-6553. Epub 2019 Aug 16.

Hefei National Laboratory for Physical Sciences at the Microscale, Key Laboratory of Strongly-Coupled Quantum Matter Physics of Chinese Academy of Sciences, National Synchrotron Radiation Laboratory, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , P.R. China.

In CO electroreduction, the critical bottleneck lies in the CO activation which requires high overpotentials. CO activation is related to both the electronic structures of catalysts and those of adsorbates, thus an ideal catalyst should match its electronic structures with those of the adsorbate. Here, we harmonized the electronic structures of the adsorbate and Mn-doped InS nanosheets for efficient CO reduction. The introduction of Mn dopants into InS nanosheets enhanced both the Faradaic efficiency (FE) for carbonaceous products and current density (). At -0.9 V vs RHE, Mn-doped InS nanosheets exhibited a remarkable FE of 92% for carbonaceous product at a high of 20.1 mA cm. Mechanistic studies revealed that Mn doping enabled the harmonic overlaps between the orbitals of O atoms and orbitals of Mn atoms near the conduction band edge of Mn-doped InS nanosheets during the activation of CO. Due to the unique electronic structures of the coadsorbed configurations, Mn-doped InS nanosheets exhibited an energy barrier for CO activation into HCOO* lower than that over pristine InS nanosheets.
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http://dx.doi.org/10.1021/acs.nanolett.9b02782DOI Listing
September 2019

Anti-quorum sensing activity of Forsythia suspense extract against Chromobacterium violaceum by targeting CviR receptor.

Int Microbiol 2020 May 24;23(2):215-224. Epub 2019 Jul 24.

Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.

The increasing incidence of antimicrobial-resistant bacterial pathogens has focused researchers on quorum sensing inhibition strategies instead of those conventional approaches to fight bacterial infections. Anti-quorum sensing (QS) activity of aqueous extract from Forsythia suspense (FSE) was assessed, and its potential QS inhibition mechanisms were also analyzed. The minimal inhibitory concentration (MIC) of FSE to Chromobacterium violaceum 12472 is 0.5 mg mL. Inhibition of QS-regulated violacein production and biofilm formation in C. violaceum 12472 by FSE occurred in a concentration-dependent manner at sub-MIC, with > 70.12 and > 85.31% inhibition at 0.25 mg mL, respectively. N-Acyl homoserine lactones (AHLs) extracted from cultures of C. violaceum 31532 grown in the presence of FSE could not change the violacein production in C. violaceum 026, which indicated that FSE did not inhibit AHL synthesis. We also found that FSE cannot degrade AHLs. Finally, in silico molecular docking was conducted. The computed binding energy data suggested that components of F. suspense have a tendency to inhibit CviR with varying binding affinities and the energy score of Pinoresinol (- 26.02 kcal/mol) is higher than that of C6-HSL (- 16.09 kcal mol). We concluded that FSE acts as an antagonist of bacterial quorum sensing by competing with AHL receptor binding site.
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http://dx.doi.org/10.1007/s10123-019-00091-3DOI Listing
May 2020

Subfemtosecond-resolved modulation of superfluorescence from ionized nitrogen molecules by 800-nm femtosecond laser pulses.

Opt Express 2019 May;27(10):14922-14930

Superfluorescence emission around 391 nm is generated when nitrogen molecules are irradiated by a strong 800-nm pump laser and a delayed seed laser. The emission corresponds to the transition between N2+(BΣu+,ν=0) and N2+(XΣg+,ν=0). When another weak 800-nm probe laser is injected and scanned after the pump laser, the superfluorescence intensity is observed to exhibit periodical modulation. The period is determined to be ~2.63 fs, corresponding to the transition frequency between N2+(AΠ,ν=2) and N2+(XΣg+,ν=0). Based on theoretical derivation, these observations can be attributed to the laser-induced population transfer and polarization variation between the relevant electronic states of ionized nitrogen molecules.
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http://dx.doi.org/10.1364/OE.27.014922DOI Listing
May 2019

Beyond dealloying: development of nanoporous gold via metal-induced crystallization and its electrochemical properties.

Nanotechnology 2019 Sep 31;30(37):375601. Epub 2019 May 31.

School of Materials Science and Engineering, Tianjin University, Tianjin, People's Republic of China.

Nanoporous metals (NPMs) possess a number of intriguing properties that result in NPMs being an important family of nanomaterials for many advanced applications. However, the methods of preparing NPMs are relatively complicated and have many limitations, which have hindered the commercial application of NPMs thus far. By introducing metal-induced crystallization, a solid-phase reaction method for preparing NPMs was developed in this study, which is highly efficient and environmentally friendly. The microstructure of the prepared nanoporous gold (NPG) was characterized on an atomic scale by scanning electron microscopy and high-resolution transmission electron microscopy. The results confirmed that the solid-phase reaction method is an effective alternative means of preparing highly pure NPG. The results of electrochemical tests demonstrated that thus-prepared NPG possesses higher electrocatalytic activity than other types of gold electrodes toward oxygen reduction in alkaline media. The combination of a simple preparation process and higher activity suggests that the developed method may promote the future use of NPG in new energy applications, such as fuel cells and metal-air batteries.
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http://dx.doi.org/10.1088/1361-6528/ab2616DOI Listing
September 2019

Coherent modulation of superradiance from nitrogen ions pumped with femtosecond pulses.

Opt Express 2019 Apr;27(9):12638-12646

Singly ionized nitrogen molecules in ambient air pumped by 800 nm femtosecond laser give rise to superradiant emission. Here, we study this superradiance by injecting a pair of resonant seeding pulses at different intensity ratios inside the nitrogen gas plasma. Strong modulation of the 391.4 nm superradiant emission with a period of 1.3 fs is observed when the delay between the two seeding pulses is finely tuned. The modulation contrast is increased and then decreased with the delay time when the second seed pulse is stronger than the first one, and the maximum modulation contrast occurs at longer delay time when the second seeding pulse is stronger. This reveals the increase of the macroscopic polarization with time after the seeding pulse. Moreover, these observations provide a new level of control on the "air lasing" based on nitrogen ions, which can find potential applications in optical remote sensing.
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http://dx.doi.org/10.1364/OE.27.012638DOI Listing
April 2019

Comparative karyotype analysis among six species of based on two newly identified repetitive sequences.

Genome 2019 Apr 20;62(4):243-252. Epub 2019 Feb 20.

a Institute of Integrative Plant Biology, School of Life Science, Jiangsu Normal University, Xuzhou, China.

Sweet potato is one of the most important crops worldwide; however, basic research in this crop is limited. In this study, we aimed to construct a detailed karyotype of six species of (hexaploid and five related species, namely, one tetraploid, and four diploids, , , , and × ) and understand the relationship among these species. Two satellite repeats (viz., and ) were identified from the diploid genome sequence using RepeatExplorer on Galaxy. Together with the ribosomal DNA (rDNA), although without distinguishable chromosomes, a detailed karyotype was constructed for the six species. Our results showed a similar karyotype between and × , indicating their close relationship. The signal distribution pattern of , 45S rDNA combination, detected only in , , and , implied their close relationships. The chromosomes carrying 5S rDNA could be conserved among the six species as they always carried the _2 signals, which generated a similar signal distribution pattern. The results enabled a detailed comparative cytogenetic analysis, providing valuable information to understand the relationship among these species and help assemble the genome sequence of the six species of .
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http://dx.doi.org/10.1139/gen-2018-0169DOI Listing
April 2019