Publications by authors named "Liqing Zhang"

158 Publications

Memorize, Associate and Match: Embedding Enhancement via Fine-Grained Alignment for Image-Text Retrieval.

IEEE Trans Image Process 2021 10;30:9193-9207. Epub 2021 Nov 10.

Image-text retrieval aims to capture the semantic correlation between images and texts. Existing image-text retrieval methods can be roughly categorized into embedding learning paradigm and pair-wise learning paradigm. The former paradigm fails to capture the fine-grained correspondence between images and texts. The latter paradigm achieves fine-grained alignment between regions and words, but the high cost of pair-wise computation leads to slow retrieval speed. In this paper, we propose a novel method named MEMBER by using Memory-based EMBedding Enhancement for image-text Retrieval (MEMBER), which introduces global memory banks to enable fine-grained alignment and fusion in embedding learning paradigm. Specifically, we enrich image (resp., text) features with relevant text (resp., image) features stored in the text (resp., image) memory bank. In this way, our model not only accomplishes mutual embedding enhancement across two modalities, but also maintains the retrieval efficiency. Extensive experiments demonstrate that our MEMBER remarkably outperforms state-of-the-art approaches on two large-scale benchmark datasets.
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http://dx.doi.org/10.1109/TIP.2021.3123553DOI Listing
November 2021

Depth Privileged Scene Recognition via Dual Attention Hallucination.

IEEE Trans Image Process 2021 10;30:9164-9178. Epub 2021 Nov 10.

RGB-D scene recognition has achieved promising performance because depth could provide complementary geometric information to RGB images. However, the inaccessibility of depth sensors severely limits RGB-D applications. In this paper, we focus on depth privileged setting, in which depth information is only available during training but not available during testing. Considering that the information obtained from RGB and depth images are complementary while attention is informative and transferable, our idea is using RGB input to hallucinate depth attention. We build our model upon modulated deformable convolutional layer and hallucinate dual attention: post-hoc importance weight and trainable spatial transformation. Specifically, we use modulation (resp., offset) learned from RGB to mimic Grad-CAM (resp., offset) learned from depth, to combine the strength of dual attention. We also design a weighted loss to avoid negative transfer according to the quality of depth attention. Extensive experiments on two benchmarks, i.e., SUN RGB-D and NYUDv2, demonstrate that our method outperforms the state-of-the-art methods for depth privileged scene recognition.
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http://dx.doi.org/10.1109/TIP.2021.3122955DOI Listing
November 2021

MetaMLP: A Fast Word Embedding Based Classifier to Profile Target Gene Databases in Metagenomic Samples.

J Comput Biol 2021 Nov 19;28(11):1063-1074. Epub 2021 Oct 19.

Department of Computer Science and Virginia Tech, Blacksburg, Virginia, USA.

The functional profile of metagenomic samples enables improved understanding of microbial populations in the environment. Such analysis consists of assigning short sequencing reads to a particular functional category. Normally, manually curated databases are used for functional assignment, and genes are arranged into different classes. Sequence alignment has been widely used to profile metagenomic samples against curated databases. However, this method is time consuming and requires high computational resources. While several alignment-free methods based on -mer composition have been developed in recent years, they still require large amounts of computer main memory. In this article, MetaMLP (Metagenomics Machine Learning Profiler), a machine learning method that represents sequences as numerical vectors (embeddings) and uses a simple one hidden layer neural network to profile functional categories, is developed. Unlike other methods, MetaMLP enables partial matching by using a reduced alphabet to build sequence embeddings from full and partial -mers. MetaMLP is able to identify a slightly larger number of reads compared with DIAMOND (one of the fastest sequence alignment methods), as well as to perform accurate predictions with 0.99 precision and 0.99 recall. MetaMLP can process 100M reads in ∼10 minutes on a laptop computer, which is 50 times faster than DIAMOND.
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http://dx.doi.org/10.1089/cmb.2021.0273DOI Listing
November 2021

Data Analytics for Environmental Science and Engineering Research.

Environ Sci Technol 2021 08 2;55(16):10895-10907. Epub 2021 Aug 2.

Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States.

The advent of new data acquisition and handling techniques has opened the door to alternative and more comprehensive approaches to environmental monitoring that will improve our capacity to understand and manage environmental systems. Researchers have recently begun using machine learning (ML) techniques to analyze complex environmental systems and their associated data. Herein, we provide an overview of data analytics frameworks suitable for various Environmental Science and Engineering (ESE) research applications. We present current applications of ML algorithms within the ESE domain using three representative case studies: (1) Metagenomic data analysis for characterizing and tracking antimicrobial resistance in the environment; (2) Nontarget analysis for environmental pollutant profiling; and (3) Detection of anomalies in continuous data generated by engineered water systems. We conclude by proposing a path to advance incorporation of data analytics approaches in ESE research and application.
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http://dx.doi.org/10.1021/acs.est.1c01026DOI Listing
August 2021

Speciation and environmental risk of heavy metals in biochars produced by pyrolysis of chicken manure and water-washed swine manure.

Sci Rep 2021 06 7;11(1):11994. Epub 2021 Jun 7.

College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan, 410128, People's Republic of China.

This study was conducted to investigate the speciation, bioavailability and environmental risk of heavy metals (HMs) in chicken manure (CM) and water-washed swine manure (WSM) and their biochars produced at different pyrolysis temperatures (200 to 800 °C). As the pyrolysis temperature increased, the remaining proportion, toxicity characteristic leaching procedure (TCLP), HCl and diethylenetriamine pentaacetic acid (DTPA) of HMs gradually declined. This result proved that the speciation of HMs in chicken manure biochars (CMB) and water-washed swine manure biochars (WSMB) was influenced by pyrolysis temperature. The proportions of stable fractions were enhanced with increased pyrolysis temperature and weakened the HM validity for vegetation at 800 °C. Finally, the results of the risk assessment showed that the environmental risk of HMs in CMB and WSMB decreased with increasing pyrolysis temperature. Therefore, pyrolysis at 800 °C can provide a practical approach to lessen the initial and underlying heavy metal toxicity of CMB and WSMB to the environment.
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http://dx.doi.org/10.1038/s41598-021-91440-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8185107PMC
June 2021

1,25-Dihydroxyvitamin D3 Supplementation during Pregnancy Is Associated with Allergic Rhinitis in the Offspring by Modulating Immunity.

J Immunol Res 2021 14;2021:6638119. Epub 2021 Apr 14.

Department of Otolaryngology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China.

Background: Maternal supplementation with 1,25-dihydroxyvitamin D3 (VD3) has immunologic effects on the developing fetus through multiple pathways. This study was aimed at investigating the effects of VD3 supplementation on immune dysregulation in the offspring during allergic rhinitis.

Methods: Different doses of VD3 as well as control were given to pregnant female mice. Ovalbumin (OVA) challenge and aluminum hydroxide gel in sterile saline were used to induce allergic rhinitis in offspring mice. Nasal lavage fluids (NLF) were collected, and eosinophils were counted in NLF 24 hours after the OVA challenge. Th1, Th2, Th17, and Treg subtype-relevant cytokines, including IFN-, IL-4, IL-10, IL-17, TGF-, and OVA-IgE levels from the blood and NLF of offspring mice, were detected by the enzyme-linked immunosorbent assay (ELISA) method. The Treg subtype was analyzed by flow cytometry. Treg cells were purified from offspring and were adoptively transferred to OVA-sensitized allogenic offspring mice. The outcomes were assessed in allogenic offspring.

Results: Our data showed that VD3 supplementation significantly decreased the number of eosinophils, basophils, and lymphocytes in the peripheral blood and NLF. The proportion of CD4CD25FoxP3Tregs had a positive correlation with VD3 in a dose-dependent manner. The levels of serum IgE, IL-4, and IL-17 were decreased while the expressions of IFN-, IL-10, and TGF- were significantly enhanced in VD3 supplementation groups. Adoptive transfer CD4CD25FoxP3Tregs of VD3 supplementation groups promoted Th1 and suppressed Th2 responses in the offspring during allergic rhinitis.

Conclusion: Our findings indicated that low dose VD3 supply in pregnant mice's diet suppressed Th2 and Th17 responses in allergic rhinitis by elevating the Th1 subtype and the proportion of CD4CD25FoxP3Tregs in offspring. It suggested that low dose VD3 supply may have the potential to act as a new therapeutic strategy for allergic rhinitis.
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http://dx.doi.org/10.1155/2021/6638119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8062205PMC
November 2021

HSP17.4 mediates salicylic acid and jasmonic acid pathways in the regulation of resistance to Colletotrichum gloeosporioides in strawberry.

Mol Plant Pathol 2021 07 5;22(7):817-828. Epub 2021 May 5.

Institute of Forestry and Pomology, Shanghai Academy of Agricultural Sciences, Shanghai, China.

In this study, we used virus-mediated gene silencing technology and found that the HSP17.4 gene-silenced cultivar Sweet Charlie plants were more susceptible to Colletotrichum gloeosporioides than the wild-type Sweet Charlie, and the level of infection was even higher than that of the susceptible cultivar Benihopp. The results of differential quantitative proteomics showed that after infection with the pathogen, the expression of the downstream response genes NPR1, TGA, and PR-1 of the salicylic acid (SA) signalling pathway was fully up-regulated in the wild-type Sweet Charlie, and the expression of the core transcription factor MYC2 of the jasmonic acid (JA) pathway was significantly down-regulated. The expression of the proteins encoded by these genes did not change significantly in the HSP17.4-silenced Sweet Charlie, indicating that the expression of HSP17.4 activated the up-regulation of downstream signals of SA and inhibited the JA signal pathway. The experiments that used SA, methyl jasmonate, and their inhibitors to treat plants provide additional evidence that the antagonism between SA and JA regulates the resistance of strawberry plants to C. gloeosporioides.
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http://dx.doi.org/10.1111/mpp.13065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8232031PMC
July 2021

The Prevalence of Post-Traumatic Stress Disorder in the General Population during the COVID-19 Pandemic: A Systematic Review and Single-Arm Meta-Analysis.

Psychiatry Investig 2021 May 30;18(5):426-433. Epub 2021 Apr 30.

Department of Psychiatry, The First Affiliated Hospital of Jinan University, Guangzhou, China.

Objective: To investigate the prevalence of post-traumatic stress disorder (PTSD) in the general population during the COVID-19 pandemic by a systematic review and single-arm meta-analysis.

Methods: CNKI, PubMed, EMBASE, and MEDLINE were searched to collect literature on the prevalence of PTSD in the general population during the epidemic. The retrieval time is from the database construction to 31/08/2020. Meta-analysis was performed on the included articles by using Review Manger 5.3 and Stata 16.0 software.

Results: The prevalence of PTSD in the general population during the COVID-19 pandemic was 15% (95% CI: 11-21%, p<0.001).

Conclusion: The COVID-19 pandemic brought certain mental pain to general population, leading to a rise in the incidence of PTSD in a short time.
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http://dx.doi.org/10.30773/pi.2020.0458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8169329PMC
May 2021

Bioinformatics analysis of a TF-miRNA-lncRNA regulatory network in major depressive disorder.

Psychiatry Res 2021 05 28;299:113842. Epub 2021 Feb 28.

School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou, China.

Major depressive disorder (MDD) is a highly prevalent disease and one of the main causes of disability worldwide. Although many studies have partially revealed the occurrence and development process of MDD, the pathogeny and molecular mechanisms are not fully understood. Weighted gene coexpression network analysis (WGCNA) was used to explore the co-expression modules and hub genes in MDD. A protein-protein interaction (PPI) network of the most significant module and a TF-miRNA-lncRNA regulatory network of MDD were constructed using bioinformatics analysis tools. A KEGG pathway and gene ontology (GO) functional enrichment analysis of the genes in the significant module was performed using DAVID. Five hub genes in the PPI network and 10 genes in the TF-miRNA-lncRNA regulatory network with high degree values were identified, which may provide new insights for the investigation of key pathways, diagnostic bio-markers, and therapeutic targets of MDD. This study brings a novel perspective and provides valuable information to explore the molecular mechanism of MDD.
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http://dx.doi.org/10.1016/j.psychres.2021.113842DOI Listing
May 2021

AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata.

BMC Bioinformatics 2021 Mar 10;22(1):117. Epub 2021 Mar 10.

Department of Computer Science, Virginia Polytechnic Institute and State University, 24061, Blacksburg, USA.

Background: Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance.

Results: Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis.

Conclusion: AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
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http://dx.doi.org/10.1186/s12859-021-04035-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7944603PMC
March 2021

Next generation sequencing approaches to evaluate water and wastewater quality.

Water Res 2021 Apr 4;194:116907. Epub 2021 Feb 4.

Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States. Electronic address:

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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http://dx.doi.org/10.1016/j.watres.2021.116907DOI Listing
April 2021

Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes.

Sci Rep 2021 02 12;11(1):3753. Epub 2021 Feb 12.

Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, VA, 24060, USA.

In the fight to limit the global spread of antibiotic resistance, the assembly of environmental metagenomes has the potential to provide rich contextual information (e.g., taxonomic hosts, carriage on mobile genetic elements) about antibiotic resistance genes (ARG) in the environment. However, computational challenges associated with assembly can impact the accuracy of downstream analyses. This work critically evaluates the impact of assembly leveraging short reads, nanopore MinION long-reads, and a combination of the two (hybrid) on ARG contextualization for ten environmental metagenomes using seven prominent assemblers (IDBA-UD, MEGAHIT, Canu, Flye, Opera-MS, metaSpades and HybridSpades). While short-read and hybrid assemblies produced similar patterns of ARG contextualization, raw or assembled long nanopore reads produced distinct patterns. Based on an in-silico spike-in experiment using real and simulated reads, we show that low to intermediate coverage species are more likely to be incorporated into chimeric contigs across all assemblers and sequencing technologies, while more abundant species produce assemblies with a greater frequency of inversions and insertion/deletions (indels). In sum, our analyses support hybrid assembly as a valuable technique for boosting the reliability and accuracy of assembly-based analyses of ARGs and neighboring genes at environmentally-relevant coverages, provided that sufficient short-read sequencing depth is achieved.
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http://dx.doi.org/10.1038/s41598-021-83081-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7881036PMC
February 2021

Enhancing cadmium extraction potential of Brassica napus: Effect of rhizosphere interactions.

J Environ Manage 2021 Apr 3;284:112056. Epub 2021 Feb 3.

College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan, 410128, PR China; Key Laboratory for Rural Ecosystem Health in the Dongting Lake Area of Hunan Province, Changsha, 410128, PR China. Electronic address:

Brassica napus L. (oilseed rape) was grown with daikon and white lupin in a polyvinyl chloride split pot experiment (with no barrier between the compartments or by a nylon mesh barrier (37 μm) to license partial root interaction, or a solid barrier to stop any root interactions) to examine the effect of rhizosphere interaction on the cadmium uptake. The results showed that shoot and root biomasses of oilseed rape were 40.66% and 26.94% less than that of the monocropped treatment (solid barrier) when intercropping with daikon under the rhizosphere complete interaction. However, the intermingling of roots between oilseed rape and white lupin notably enhanced the dry biomass of oilseed rape by 40.23% and decreased with the reduction of root contact. Oilseed rape intercropping with daikon enhanced the shoot Cd concentration of oilseed rape. The shoot Cd concentration (44.8 mg/kg) of oilseed rape when intercropped white lupin under complete rhizosphere interaction were greater than those of other treatments. Additionally, the intermingling of roots played a positive role in the content of citric and malic acids when intercropping with white lupin. In all systems, the BCF values of oilseed rape >5. Therefore, intercropping with white lupin may contribute to higher biomass and increased uptake Cd by oilseed rape. We can toward sustainable positive effects on phytoremediation that based on a better understanding of rhizosphere processes.
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http://dx.doi.org/10.1016/j.jenvman.2021.112056DOI Listing
April 2021

Person Re-Identification With Reinforced Attribute Attention Selection.

IEEE Trans Image Process 2021 25;30:603-616. Epub 2020 Nov 25.

Person re-identification (Re-ID) aims to match pedestrian images across various scenes in video surveillance. There are a few works using attribute information to boost Re-ID performance. Specifically, those methods leverage attribute information to boost Re-ID performance by introducing auxiliary tasks like verifying the image level attribute information of two pedestrian images or recognizing identity level attributes. Identity level attribute annotations cost less manpower and are well-fitted for person re-identification task compared with image-level attribute annotations. However, the identity attribute information may be very noisy due to incorrect attribute annotation or lack of discriminativeness to distinguish different persons, which is probably unhelpful for the Re-ID task. In this paper, we propose a novel Attribute Attentional Block (AAB), which can be integrated into any backbone network or framework. Our AAB adopts reinforcement learning to drop noisy attributes based on our designed reward and then utilizes aggregated attribute attention of the remaining attributes to facilitate the Re-ID task. Experimental results demonstrate that our proposed method achieves state-of-the-art results on three benchmark datasets.
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http://dx.doi.org/10.1109/TIP.2020.3036762DOI Listing
November 2020

Delinquent Events Prediction in Temporal Networked-Guarantee Loans.

IEEE Trans Neural Netw Learn Syst 2020 Oct 13;PP. Epub 2020 Oct 13.

Under debt obligation promises, small- and medium-sized enterprises (SMEs) can guarantee each other to enhance their financial security to get loans from commercial banks. When the economy rises, the banks may reduce the threshold to some extent, which may introduce default risk during the economy down period, especially when many SMEs bind together and form complex networks. The risk may diffuse across the guarantee network and may result in a financial crisis. Macroprudential oversight of the guarantee network to eliminate any potential systematics financial risk is the central task of the regulatory commission and the commercial banks. Based on our observation, the delinquent probability of an SME depends not only on self-financial status but also highly related to its temporal behaviors and structural position in networks. The classic approach for loan assessment criteria face challenges in extracting temporal and structural patterns from dynamic networks. To address these issues, we propose a temporal delinquent event prediction (TDEP) framework that preserves temporal network structures and credit behavior sequences in an end-to-end model. In particular, we first employ a graph attention layer to learn the representation of nodes in temporal guarantee networks. We then design a recursive and self-attention mechanism to integrate both credit behavior and network structure information. The learned attentional weights are leveraged to uncover high-risk guarantee patterns that effectively accelerate the risk assessment process. Afterward, we conduct extensive experiments in a real-world guaranteed-loan data set to evaluate its performance. The results show the effectiveness of our proposed approach compared with the state-of-the-art baselines. Finally, we integrate the proposed model in a real-world loan risk management system. We present the implementation details of each subcomponent of the system and report out the performance after online deployment.
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http://dx.doi.org/10.1109/TNNLS.2020.3027346DOI Listing
October 2020

Cadmium accumulation in oilseed rape is promoted by intercropping with faba bean and ryegrass.

Ecotoxicol Environ Saf 2020 Dec 21;205:111162. Epub 2020 Aug 21.

College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan, 410128, PR China; Key Laboratory for Rural Ecosystem Health in the Dongting Lake Area of Hunan Province, Changsha, 410128, PR China. Electronic address:

The mechanisms of intercropping increasing plant biomass, cadmium accumulation, and organic acids secreted in rhizosphere soil are still unclear. Oilseed rape and intercrops were grown in boxes separated either with no barrier between the compartments or by a nylon mesh barrier (37 μm) to license partial root interaction, or a solid barrier to stop any root interactions. Two intercropping systems (oilseed rape-faba bean and oilseed rape-ryegrass) were carried out in soil with Cd content of 5 mg/kg. The intermingling of roots between oilseed rape and faba bean enhanced the biomass of oilseed rape. However, the biomass was negatively affected implying the higher nutrient apportionment to the ryegrass than oilseed rape. Oilseed rape intercropping with both faba bean and ryegrass played a positive role in the shoot Cd concentration of oilseed rape. The intermingling of roots played a positive role in the citric and malic acids when intercropping with faba bean. A remarkable increase in water-soluble Cd and DTPA-Cd content was observed during oilseed rape-faba bean complete root interaction treatment, up to 175.00% and 46.65%, respectively, which compare with the monoculture treatment. In both systems, the translocation factor values were higher for oilseed rape (O-F system) than for the other test plants and were always >1. Thus the Cd removal potential of oilseed rape can be further improved in the future by optimizing agronomic practices and intercropping with faba bean.
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http://dx.doi.org/10.1016/j.ecoenv.2020.111162DOI Listing
December 2020

Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro.

PLoS One 2020 25;15(6):e0234046. Epub 2020 Jun 25.

United States Department of Agriculture, Dairy and Functional Foods Research Unit, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America.

The recent ban of the antimicrobial compound triclosan from use in consumer soaps followed research that showcased the risk it poses to the environment and to human health. Triclosan has been found in human plasma, urine and milk, demonstrating that it is present in human tissues. Previous work has also demonstrated that consumption of triclosan disrupts the gut microbial community of mice and zebrafish. Due to the widespread use of triclosan and ubiquity in the environment, it is imperative to understand the impact this chemical has on the human body and its symbiotic resident microbes. To that end, this study is the first to explore how triclosan impacts the human gut microbial community in vitro both during and after treatment. Through our in vitro system simulating three regions of the human gut; the ascending colon, transverse colon, and descending colon regions, we found that treatment with triclosan significantly impacted the community structure in terms of reduced population, diversity, and metabolite production, most notably in the ascending colon region. Given a 2 week recovery period, most of the population levels, community structure, and diversity levels were recovered for all colon regions. Our results demonstrate that the human gut microbial community diversity and population size is significantly impacted by triclosan at a high dose in vitro, and that the community is recoverable within this system.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234046PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7316517PMC
August 2020

The Anxiety Status of Chinese Medical Workers During the Epidemic of COVID-19: A Meta-Analysis.

Psychiatry Investig 2020 May 15;17(5):475-480. Epub 2020 May 15.

Department of Psychiatry, The First Affiliated Hospital of Jinan University, Guangzhou, China.

Objective: To analysis the anxiety status of Chinese medical workers during the epidemic of COVID-19 by meta-analysis method.

Methods: CNKI, VIP, WanFang Data, SinoMed, PubMed, Cochrane, EMBASE, MEDLINE, Scopus, Google Scholar and other databases were searched to collect literature on the anxiety status of Chinese medical workers during the epidemic of COVID-19. The retrieval time is from the database construction to 11/03/2020. Meta-analysis was performed on the included articles by using Stata 16.0 software.

Results: A total of 7 articles were included, with a total sample size of 7,741 people. Meta-analysis using the random effects model showed that the anxiety score of Chinese medical during the epidemic of COVID-19 was significantly higher than that of the national norm in each study, the difference was statistically significant [SMD (95% CI)=1.145 (0.705-1.584), p<0.001].

Conclusion: The anxiety level of Chinese medical workers has increased significantly during the epidemic of COVID-19.
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http://dx.doi.org/10.30773/pi.2020.0127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7265026PMC
May 2020

Characterization and Fungicide Sensitivity of Species Causing Strawberry Anthracnose in Eastern China.

Plant Dis 2020 Jul 13;104(7):1960-1968. Epub 2020 May 13.

Shanghai Key Laboratory of Protected Horticultural Technology, Forestry and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.

Strawberry anthracnose caused by spp. is one of the most serious diseases in the strawberry fields of China. In total, 196 isolates of were obtained from leaves, stolons, and crowns of strawberry plants with anthracnose symptoms in eastern China and were characterized based on morphology, internal transcribed spacer (ITS), and β- () gene sequences. All 196 isolates were identified as the species complex. In total, 62 strains were further identified at the species level by phylogenetic analyses of multilocus sequences of ITS, (), (), (), (), and . Three species from the species complex were identified: , . , and . . Isolates of . were tolerant to high temperatures, with a significantly larger colony diameter than the other two species when grown above 36°C. The inoculation of strawberry plants confirmed the pathogenicity of all three species. . isolates resulted in the highest disease severity. The in vitro sensitivities of . and . isolates to azoxystrobin and three demethylation-inhibitor (DMI) fungicides (difenoconazole, tebuconazole, and prochloraz) were determined. Both species were sensitive to DMI fungicides but not to azoxystrobin. . isolates were more sensitive to prochloraz, while isolates were more sensitive to difenoconazole and tebuconazole. The present study provides valuable information for the effective management of strawberry anthracnose.
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http://dx.doi.org/10.1094/PDIS-10-19-2241-REDOI Listing
July 2020

Identification of Potential Biomarkers for Thyroid Cancer Using Bioinformatics Strategy: A Study Based on GEO Datasets.

Biomed Res Int 2020 1;2020:9710421. Epub 2020 Apr 1.

Department of Otorhinolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu, China.

Background: The molecular mechanisms and genetic markers of thyroid cancer are unclear. In this study, we used bioinformatics to screen for key genes and pathways associated with thyroid cancer development and to reveal its potential molecular mechanisms.

Methods: The GSE3467, GSE3678, GSE33630, and GSE53157 expression profiles downloaded from the Gene Expression Omnibus database (GEO) contained a total of 164 tissue samples (64 normal thyroid tissue samples and 100 thyroid cancer samples). The four datasets were integrated and analyzed by the RobustRankAggreg (RRA) method to obtain differentially expressed genes (DEGs). Using these DEGs, we performed gene ontology (GO) functional annotation, pathway analysis, protein-protein interaction (PPI) analysis and survival analysis. Then, CMap was used to identify the candidate small molecules that might reverse thyroid cancer gene expression.

Results: By integrating the four datasets, 330 DEGs, including 154 upregulated and 176 downregulated genes, were identified. GO analysis showed that the upregulated genes were mainly involved in extracellular region, extracellular exosome, and heparin binding. The downregulated genes were mainly concentrated in thyroid hormone generation and proteinaceous extracellular matrix. Pathway analysis showed that the upregulated DEGs were mainly attached to ECM-receptor interaction, p53 signaling pathway, and TGF-beta signaling pathway. Downregulation of DEGs was mainly involved in tyrosine metabolism, mineral absorption, and thyroxine biosynthesis. Among the top 30 hub genes obtained in PPI network, the expression levels of FN1, NMU, CHRDL1, GNAI1, ITGA2, GNA14 and AVPR1A were associated with the prognosis of thyroid cancer. Finally, four small molecules that could reverse the gene expression induced by thyroid cancer, namely ikarugamycin, adrenosterone, hexamethonium bromide and clofazimine, were obtained in the CMap database.

Conclusion: The identification of the key genes and pathways enhances the understanding of the molecular mechanisms for thyroid cancer. In addition, these key genes may be potential therapeutic targets and biomarkers for the treatment of thyroid cancer.
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http://dx.doi.org/10.1155/2020/9710421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152968PMC
January 2021

DeepMicro: deep representation learning for disease prediction based on microbiome data.

Authors:
Min Oh Liqing Zhang

Sci Rep 2020 04 7;10(1):6026. Epub 2020 Apr 7.

Department of Computer Science, Virginia Tech, Blacksburg, VA, USA.

Human microbiota plays a key role in human health and growing evidence supports the potential use of microbiome as a predictor of various diseases. However, the high-dimensionality of microbiome data, often in the order of hundreds of thousands, yet low sample sizes, poses great challenge for machine learning-based prediction algorithms. This imbalance induces the data to be highly sparse, preventing from learning a better prediction model. Also, there has been little work on deep learning applications to microbiome data with a rigorous evaluation scheme. To address these challenges, we propose DeepMicro, a deep representation learning framework allowing for an effective representation of microbiome profiles. DeepMicro successfully transforms high-dimensional microbiome data into a robust low-dimensional representation using various autoencoders and applies machine learning classification algorithms on the learned representation. In disease prediction, DeepMicro outperforms the current best approaches based on the strain-level marker profile in five different datasets. In addition, by significantly reducing the dimensionality of the marker profile, DeepMicro accelerates the model training and hyperparameter optimization procedure with 8X-30X speedup over the basic approach. DeepMicro is freely available at https://github.com/minoh0201/DeepMicro.
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http://dx.doi.org/10.1038/s41598-020-63159-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7138789PMC
April 2020

Draft Genome Sequence of the Strawberry Anthracnose Pathogen .

Microbiol Resour Announc 2020 Mar 19;9(12). Epub 2020 Mar 19.

Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom.

is a causal agent of strawberry anthracnose and a major economic pathogen of horticultural and ornamental crops worldwide. Here, we present an annotated draft genome sequence for a isolate previously used for transcriptomic analysis. The assembly totals 58.0 Mb in 477 contigs with 18,143 predicted genes.
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http://dx.doi.org/10.1128/MRA.01598-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082466PMC
March 2020

A Pilot Study of Chicago Waterways as Reservoirs of Multidrug-Resistant (MDR-Ent) in a High-Risk Region for Community-Acquired MDR-Ent Infection in Children.

Antimicrob Agents Chemother 2020 03 24;64(4). Epub 2020 Mar 24.

Virginia Tech University, Blacksburg, Virginia, USA.

Community-acquired multidrug resistant (MDR-Ent) infections continue to increase in the United States. In prior studies, we identified neighboring regions in Chicago, Illinois, where children have 5 to 6 times greater odds of MDR-Ent infections. To prevent community spread of MDR-Ent, we need to identify the MDR-Ent reservoirs. A pilot study of 4 Chicago waterways for MDR-Ent and associated antibiotic resistance genes (ARGs) was conducted. Three waterways (A1 to A3) are labeled safe for "incidental contact recreation" (e.g., kayaking), and A4 is a nonrecreational waterway that carries nondisinfected water. Surface water samples were collected and processed for standard bacterial culture and shotgun metagenomic sequencing. Generally, A3 and A4 (neighboring waterways which are not hydraulically connected) were strikingly similar in bacterial taxa, ARG profiles, and abundances of corresponding clades and genera within the Additionally, total ARG abundances recovered from the full microbial community were strongly correlated between A3 and A4 ( = 0.97). numbers (per 100 ml water) were highest in A4 (783 most probable number [MPN]) and A3 (200 MPN) relative to A2 (84 MPN) and A1 (32 MPN). We found concerning ARGs in such as MCR-1 (colistin), Qnr and OqxA/B (quinolones), CTX-M, OXA and ACT/MIR (beta-lactams), and AAC (aminoglycosides). We found significant correlations in microbial community composition between nearby waterways that are not hydraulically connected, suggesting cross-seeding and the potential for mobility of ARGs. and ARG profiles support the hypothesized concerns that recreational waterways are a potential source of community-acquired MDR-Ent.
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http://dx.doi.org/10.1128/AAC.02310-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179304PMC
March 2020

Preoperative platelet-lymphocyte ratio predicts recurrence of laryngeal squamous cell carcinoma.

Future Oncol 2020 Feb 27;16(6):209-217. Epub 2020 Jan 27.

Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China.

To evaluate the impact of preoperative platelet-lymphocyte ratio (PLR), neutrophil-lymphocyte ratio (NLR), derived NLR (dNLR) and lymphocyte-monocyte ratio (LMR) on the prognosis of laryngeal squamous cell carcinoma. Overall survival and recurrence-free survival (RFS) were analyzed using Kaplan-Meier estimates. Multivariable Cox regression model was used to evaluate the independent prognostic significance of variables. High PLR (>103.96), NLR (>1.96) and dNLR (>1.70) predicted lower RFS according to Kaplan-Meier method. In COX regression model, patients with high PLR had poor RFS estimates compared with those with lower PLR (p < 0.001). Preoperative PLR was a more valuable prognostic factor than NLR, dNLR and LMR for the recurrence of laryngeal squamous cell carcinoma.
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http://dx.doi.org/10.2217/fon-2019-0527DOI Listing
February 2020

Correction to: Functional analysis of GhCHS, GhANR and GhLAR in colored fiber formation of Gossypium hirsutum L.

BMC Plant Biol 2020 01 19;20(1):28. Epub 2020 Jan 19.

Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China.

In the original publication of this article [1], the authors pointed out the Fig. 4b was same with Fig. 4c. The correct Fig. 4b should be below.
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http://dx.doi.org/10.1186/s12870-019-2211-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6969971PMC
January 2020

Skin transcriptome profiles associated with black- and white-coated regions in Boer and Macheng black crossbred goats.

Genomics 2020 03 31;112(2):1853-1860. Epub 2019 Oct 31.

Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China. Electronic address:

To increase the current understanding of the gene-expression profiles in different skin regions associated with different coat colors and identify key genes for the regulation of color patterns in goats, we used the Illumina RNA-Seq method to compare the skin transcriptomes of the black- and white-coated regions containing hair follicles from the Boer and Macheng Black crossbred goat, which has a black head and a white body. Six cDNA libraries derived from skin samples of the white-coated region (n = 3) and black-coated region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for skin samples from black- and white-coated regions, respectively, of which 75.39% and 76.05% were covered in the genome database. A total of 165 differentially expressed genes (DEGs) were detected between these two color regions, among which 110 were upregulated and 55 were downregulated in the skin samples of white- vs. black-coated regions. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of these DEGs may play an important role in controlling the pigmentation of skin or hair follicles. We identified three key DEGs, i.e., Agouti, DCT, and TYRP1, in the pathway related to melanogenesis in the different skin regions of the crossbred goat. DCT and TYRP1 were downregulated and Agouti was upregulated in the skin of the white-coated region, suggesting a lack of mature melanocytes in this region and that Agouti might play a key developmental role in color-pattern formation. All data sets (Gene Expression Omnibus) are available via public repositories. In addition, MC1R was genotyped in 200 crossbred goats with a black head and neck. Loss-of-function mutations in MC1R as well as homozygosity for the mutant alleles were widely found in this population. The MC1R gene did not seem to play a major role in determining the black head and neck in our crossbred goats. Our study provides insights into the transcriptional regulation of two distinct coat colors, which might serve as a key resource for understanding coat color pigmentation in goats. The region-specific expression of Agouti may be associated with the distribution of pigments across the body in Boer and Macheng Black crossbred goats.
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http://dx.doi.org/10.1016/j.ygeno.2019.10.019DOI Listing
March 2020

Functional analysis of GhCHS, GhANR and GhLAR in colored fiber formation of Gossypium hirsutum L.

BMC Plant Biol 2019 Oct 29;19(1):455. Epub 2019 Oct 29.

Plant Genomics & Molecular Improvement of Colored Fiber Lab, Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310016, Zhejiang, China.

Background: The formation of natural colored fibers mainly results from the accumulation of different anthocyanidins and their derivatives in the fibers of Gossypium hirsutum L. Chalcone synthase (CHS) is the first committed enzyme of flavonoid biosynthesis, and anthocyanidins are transported into fiber cells after biosynthesis mainly by Anthocyanidin reductase (ANR) and Leucoanthocyanidin reductase (LAR) to present diverse colors with distinct stability. The biochemical and molecular mechanism of pigment formation in natural colored cotton fiber is not clear.

Results: The three key genes of GhCHS, GhANR and GhLAR were predominantly expressed in the developing fibers of colored cotton. In the GhCHSi, GhANRi and GhLARi transgenic cottons, the expression levels of GhCHS, GhANR and GhLAR significantly decreased in the developing cotton fiber, negatively correlated with the content of anthocyanidins and the color depth of cotton fiber. In colored cotton Zongxu1 (ZX1) and the GhCHSi, GhANRi and GhLARi transgenic lines of ZX1, HZ and ZH, the anthocyanidin contents of the leaves, cotton kernels, the mixture of fiber and seedcoat were all changed and positively correlated with the fiber color.

Conclusion: The three genes of GhCHS, GhANR and GhLAR were predominantly expressed early in developing colored cotton fibers and identified to be a key genes of cotton fiber color formation. The expression levels of the three genes affected the anthocyanidin contents and fiber color depth. So the three genes played a crucial part in cotton fiber color formation and has important significant to improve natural colored cotton quality and create new colored cotton germplasm resources by genetic engineering.
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http://dx.doi.org/10.1186/s12870-019-2065-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6819470PMC
October 2019

Comparison of Whole-Genome Sequences of Legionella pneumophila in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016.

Emerg Infect Dis 2019 11;25(11):2013-2020

During the water crisis in Flint, Michigan, USA (2014-2015), 2 outbreaks of Legionnaires' disease occurred in Genesee County, Michigan. We compared whole-genome sequences of 10 clinical Legionella pneumophila isolates submitted to a laboratory in Genesee County during the second outbreak with 103 water isolates collected the following year. We documented a genetically diverse range of L. pneumophila strains across clinical and water isolates. Isolates belonging to 1 clade (3 clinical isolates, 3 water isolates from a Flint hospital, 1 water isolate from a Flint residence, and the reference Paris strain) had a high degree of similarity (2-1,062 single-nucleotide polymorphisms), all L. pneumophila sequence type 1, serogroup 1. Serogroup 6 isolates belonging to sequence type 2518 were widespread in Flint hospital water samples but bore no resemblance to available clinical isolates. L. pneumophila strains in Flint tap water after the outbreaks were diverse and similar to some disease-causing strains.
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http://dx.doi.org/10.3201/eid2511.181032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6810188PMC
November 2019

Orbital Rosai-Dorfman disease: a case report and literature review.

Authors:
Xin Su Liqing Zhang

J Int Med Res 2019 Nov 15;47(11):5891-5895. Epub 2019 Oct 15.

Department of Radiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.

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http://dx.doi.org/10.1177/0300060519878086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862901PMC
November 2019

Four targeted genes for predicting the prognosis of colorectal cancer: A bioinformatics analysis case.

Oncol Lett 2019 Nov 13;18(5):5043-5054. Epub 2019 Sep 13.

Department of Computer Science, Virginia Tech, Blacksburg, VA 24060, USA.

The molecular mechanisms underlying the development and progression of colorectal cancer (CRC) have not been clarified. The purpose of the present study was to identify key genes that may serve as novel therapeutic targets or prognostic predictors in patients with CRC using bioinformatics analysis. Four gene expression datasets were downloaded from the Gene Expression Omnibus database, which revealed 19 upregulated and 34 downregulated differentially expressed genes (DEGs). The downregulated DEGs were significantly enriched in eight pathways according to Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. A protein-protein interaction network was constructed with 52 DEGs and 458 edges. Ten key genes were identified according to the degree value, betweenness centrality and closeness centrality. Survival analysis revealed that low expression of four of the ten genes, carcinoembryonic antigen related cell adhesion molecule 7 (CEACAM7), solute carrier family 4 member 4 (SLC4A4), glucagon (GCG) and chloride channel accessory 1 (CLCA1) genes, were associated with unfavorable prognosis in CRC. Furthermore, gene set enrichment analysis revealed that two pathways were significantly enriched in the CEACAM7 low-expression group. Thus, CEACAM7, SLC4A4, GCG and CLCA1 may be prognostic markers or therapeutic targets of CRC. Low CEACAM7 expression may be associated with the activation of glycosaminoglycan biosynthesis-chondroitin sulfate and extracellular matrix receptor interaction pathways and may affect the prognosis of CRC.
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http://dx.doi.org/10.3892/ol.2019.10866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781647PMC
November 2019
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