TCOD: an integrated resource for tropical crops.

Tropical crops are vital for tropical agriculture, with resource scarcity, functional diversity and extensive market demand, providing considerable economic benefits for the world's tropical agriculture-producing countries. The rapid development of sequencing technology has promoted a milestone in tropical crop research, resulting in the generation of massive amount of data, which urgently needs an effective platform for data integration and sharing. However, the existing databases cannot fully satisfy researchers' requirements due to the relatively limited integration level and untimely update. Here, we present the Tropical Crop Omics Database (TCOD, https://ngdc.cncb.ac.cn/tcod), a comprehensive multi-omics data platform for tropical crops. TCOD integrates diverse omics data from 15 species, encompassing 34 chromosome-level de novo assemblies, 1 255 004 genes with functional annotations, 282 436 992 unique variants from 2048 WGS samples, 88 transcriptomic profiles from 1997 RNA-Seq samples and 13 381 germplasm items. Additionally, TCOD not only employs genes as a bridge to interconnect multi-omics data, enabling cross-species comparisons based on homology relationships, but also offers user-friendly online tools for efficient data mining and visualization. In short, TCOD integrates multi-species, multi-omics data and online tools, which will facilitate the research on genomic selective breeding and trait biology of tropical crops.

McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks.

Haplotype networks are graphs used to represent evolutionary relationships between a set of taxa and are characterized by intuitiveness in analyzing genealogical relationships of closely related genomes. We here propose a novel algorithm termed McAN that considers mutation spectrum history (mutations in ancestry haplotype should be contained in descendant haplotype), node size (corresponding to sample count for a given node) and sampling time when constructing haplotype network. We show that McAN is two orders of magnitude faster than state-of-the-art algorithms without losing accuracy, making it suitable for analysis of a large number of sequences. Based on our algorithm, we developed an online web server and offline tool for haplotype network construction, community lineage determination, and interactive network visualization. We demonstrate that McAN is highly suitable for analyzing and visualizing massive genomic data and is helpful to enhance the understanding of genome evolution. Availability: Source code is written in C/C++ and available at https://github.com/Theory-Lun/McAN and https://ngdc.cncb.ac.cn/biocode/tools/BT007301 under the MIT license. Web server is available at https://ngdc.cncb.ac.cn/bit/hapnet/. SARS-CoV-2 dataset are available at https://ngdc.cncb.ac.cn/ncov/. Contact: songshh@big.ac.cn (Song S), zhaowm@big.ac.cn (Zhao W), baoym@big.ac.cn (Bao Y), zhangzhang@big.ac.cn (Zhang Z), ybxue@big.ac.cn (Xue Y).

Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2.

Genomic epidemiology is important to study the COVID-19 pandemic, and more than two million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challenges. Here, we present the Coronavirus GenBrowser (CGB) based on a highly efficient analysis framework and a node-picking rendering strategy. In total, 1,002,739 high-quality genomic sequences with the transmission-related metadata were analyzed and visualized. The size of the core data file is only 12.20 MB, highly efficient for clean data sharing. Quick visualization modules and rich interactive operations are provided to explore the annotated SARS-CoV-2 evolutionary tree. CGB binary nomenclature is proposed to name each internal lineage. The pre-analyzed data can be filtered out according to the user-defined criteria to explore the transmission of SARS-CoV-2. Different evolutionary analyses can also be easily performed, such as the detection of accelerated evolution and ongoing positive selection. Moreover, the 75 genomic spots conserved in SARS-CoV-2 but non-conserved in other coronaviruses were identified, which may indicate the functional elements specifically important for SARS-CoV-2. The CGB was written in Java and JavaScript. It not only enables users who have no programming skills to analyze millions of genomic sequences, but also offers a panoramic vision of the transmission and evolution of SARS-CoV-2.

Correlation between triglyceride glucose index and collateral circulation formation in patients with chronic total occlusion of coronary arteries in different glucose metabolic states.

BACKGROUND: To investigate the correlation between triglyceride glucose index (TyG) and collateral circulation in patients with chronic total occlusion (CTO) of coronary arteries in different glucose metabolic states. METHODS: A total of 681 patients who underwent coronary angiography between January 2020 and December 2021 to determine the presence of CTO lesions in at least one major coronary artery were retrospectively included in this study. Patients were categorized into a group with poor collateral circulation formation (Rentrop grade 0-1, n = 205) and a group with good collateral circulation formation (Rentrop grade 2-3, n = 476) according to the Rentrop scale. They were also categorized according to their glucose metabolism status: normal glucose regulation (NGR) (n = 139), prediabetes mellitus (Pre-DM) (n = 218), and diabetes mellitus (DM) (n = 324). Correlation between TyG index and collateral circulation formation was analyzed by logistic regression analysis and receiver operating characteristic (ROC) curves. RESULTS: Among patients with CTO, TyG index was significantly higher in the group with poor collateral circulation formation than in the group with good collateral circulation formation. Logistic regression analysis showed that TyG index was an independent risk factor for poor collateral circulation formation (OR 5.104, 95% CI 3.323-7.839, P < 0.001). The accuracy of TyG index in predicting collateral circulation formation was evaluated by the ROC curve, which had an area under the curve of 0.779 (95% CI 0.738-0.820, P < 0.001). The restrictive cubic spline curves showed that the risk of poor collateral circulation formation in the Pre-DM and DM groups was initially flat and finally increased rapidly, except for the NGR group. TyG index was significantly associated with an increased risk of poor collateral circulation formation in the Pre-DM and DM groups. CONCLUSIONS: TyG index was significantly associated with the risk of poor collateral circulation formation in patients with CTO, especially those with Pre-DM and DM.

An Overview of Image Generation of Industrial Surface Defects.

Intelligent defect detection technology combined with deep learning has gained widespread attention in recent years. However, the small number, and diverse and random nature, of defects on industrial surfaces pose a significant challenge to deep learning-based methods. Generating defect images can effectively solve this problem. This paper investigates and summarises traditional defect generation and deep learning-based methods. It analyses the various advantages and disadvantages of these methods and establishes a benchmark through classical adversarial networks and diffusion models. The performance of these methods in generating defect images is analysed through various indices. This paper discusses the existing methods, highlights the shortcomings and challenges in the field of defect image generation, and proposes future research directions. Finally, the paper concludes with a summary.

RETRACTED: CGVD: a genomic variation database for Chinese populations.

Precision medicine calls upon deeper coverage of population-based sequencing and thorough gene-content and phenotype-based analysis, which lead to a population-associated genomic variation map or database. The Chinese Genomic Variation Database (CGVD; https://bigd.big.ac.cn/cgvd/) is such a database that has combined 48.30 million (M) SNVs and 5.77 M small indels, identified from 991 Chinese individuals of the Chinese Academy of Sciences Precision Medicine Initiative Project (CASPMI) and 301 Chinese individuals of the 1000 Genomes Project (1KGP). The CASPMI project includes whole-genome sequencing data (WGS, 25-30×) from ∼1000 healthy individuals of the CASPMI cohort. To facilitate the usage of such variations for pharmacogenomics studies, star-allele frequencies of the drug-related genes in the CASPMI and 1KGP populations are calculated and provided in CGVD. As one of the important database resources in BIG Data Center, CGVD will continue to collect more genomic variations and to curate structural and functional annotations to support population-based healthcare projects and studies in China and worldwide.

Alterations of the Gut Microbiome in Recurrent Malignant Gliomas Patients Received Bevacizumab and Temozolomide Combination Treatment and Temozolomide Monotherapy.

This case-control study explored compositions of gut microbiome in recurrent malignant gliomas patients who had received bevacizumab and Temozolomide combination treatment and Temozolomide monotherapy. We investigated gut microbiota communities in feces of 29 recurrent malignant gliomas patients received combination treatment with bevacizumab and Temozolomide (Group 1) and monotherapy with Temozolomide alone (Group 2). We took advantage of the high-throughput Illumina Miseq sequencing technology by targeting the third and fourth hypervariable (V3-V4) regions of the 16S ribosomal RNA (rRNA) gene. We found that the structures and richness of the fecal microbiota in Group 1 were different from Group 2 with LEfSe analysis. The fecal microbiota in both Group 1 and Group 2 were mainly composed by Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. However, Group 1 patients had higher relative abundance of Firmicutes, Bacteroidetes, Actinobacteria and lower relative abundance of Bacteroidetes and Cyanobacteria in their fecal microbiota than that in Group 2 patients. To evaluate bevacizumab involved post-treatment state of the fecal microbiota profile, we used random forest predictive model and ensembled decision trees with an AUC of 0.54. This study confirmed that the gut microbiota was different in recurrent malignant gliomas patients received the combination therapy of bevacizumab and Temozolomide compared with Temozolomide monotherapy. Our discover can help better understand the influence of bevacizumab related treatment on recurrent malignant gliomas patients. Therefore, this finding may also support the potentially therapeutic options for recurrent malignant gliomas patients such as fecal microbiota transplant. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-021-00962-2.

GSA-Human: Genome Sequence Archive for Human.

The Genome Sequence Archive for Human (GSA-Human) is a data repository specialized for human genetic related data derived from biomedical researches, and also supports the data collection and management of National Key Research and Development Projects. GSA-Human has a data security management strategy according to the national regulations of human genetic resources. It provides two different models of data access: Open-access and Controlled-access. Open-access data are universally and freely accessible for global researchers, while Controlled-access ensures that data are accessed only by authorized users with the permission of the Data Access Committee (DAC). Till July 2021, GSA-Human has housed more than 5.27 PB of data from 750 datasets.

Methods for Surveying Stable Fly Populations.

Stable flies are among the most important pests of livestock throughout much of the world. Their painful bites induce costly behavioral and physiological stress responses and reduce productivity. Stable flies are anthropogenic and their population dynamics vary depending on agricultural and animal husbandry practices. Standardized sampling methods are needed to better identify the factors controlling stable fly populations, test novel control technologies, and determine optimal management strategies. The current study reviewed methods used for a long-term study of stable fly population dynamics in the central Great Plains. An additional study compared the relative size of flies sampled from the general population with that of flies sampled emerging from substrates associated with livestock production. Flies developing in livestock associated substrates are significantly larger than those in the general population indicating that other types of developmental sites are contributing significant numbers of flies to the general population. Because efforts to identify those sites have yet to be successful, we speculate that they may be sites with low densities of developing stable flies, but covering large areas such as croplands and grasslands. The stable fly surveillance methods discussed can be used and further improved for monitoring stable fly populations for research and management programs.

Secure State Estimation for Motion Monitoring of Intelligent Connected Vehicle Systems.

This paper considers the state estimation problem of intelligent connected vehicle systems under the false data injection attack in wireless monitoring networks. We propose a new secure state estimation method to reconstruct the motion states of the connected vehicles equipped with cooperative adaptive cruise control (CACC) systems. First, the set of CACC models combined with Proportion-Differentiation (PD) controllers are used to represent the longitudinal dynamics of the intelligent connected vehicle systems. Then the notion of sparseness is employed to model the false data injection attack of the wireless networks of the monitoring platform. According to the corrupted data of the vehicles' states, the compressed sensing principle is used to describe the secure state estimation problem of the connected vehicles. Moreover, the L1 norm optimization problem is solved to reconstruct the motion states of the vehicles based on the orthogonaldecomposition. Finally, the simulation experiments verify that the proposed method can effectively reconstruct the motion states of vehicles for remote monitoring of the intelligent connected vehicle system.

The 2019 novel coronavirus resource.

An ongoing outbreak of a novel coronavirus infection in Wuhan, China since December 2019 has led to 31,516 infected persons and 638 deaths across 25 countries (till 16:00 on February 7, 2020). The virus causing this pneumonia was then named as the 2019 novel coronavirus (2019-nCoV) by the World Health Organization. To promote the data sharing and make all relevant information of 2019-nCoV publicly available, we construct the 2019 Novel Coronavirus Resource (2019nCoVR, https://bigd.big.ac.cn/ncov). 2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the Global Initiative on Sharing All Influenza Data, National Center for Biotechnology Information, China National GeneBank, National Microbiology Data Center and China National Center for Bioinformation (CNCB)/National Genomics Data Center (NGDC). It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains. Moreover, by linking seamlessly with related databases in CNCB/NGDC, 2019nCoVR offers virus data submission and sharing services for raw sequence reads and assembled sequences. In this report, we provide comprehensive descriptions on data deposition, management, release and utility in 2019nCoVR, laying important foundations in aid of studies on virus classification and origin, genome variation and evolution, fast detection, drug development and pneumonia precision prevention and therapy.

DoGSD: the dog and wolf genome SNP database.

The rapid advancement of next-generation sequencing technology has generated a deluge of genomic data from domesticated dogs and their wild ancestor, grey wolves, which have simultaneously broadened our understanding of domestication and diseases that are shared by humans and dogs. To address the scarcity of single nucleotide polymorphism (SNP) data provided by authorized databases and to make SNP data more easily/friendly usable and available, we propose DoGSD (http://dogsd.big.ac.cn), the first canidae-specific database which focuses on whole genome SNP data from domesticated dogs and grey wolves. The DoGSD is a web-based, open-access resource comprising ∼ 19 million high-quality whole-genome SNPs. In addition to the dbSNP data set (build 139), DoGSD incorporates a comprehensive collection of SNPs from two newly sequenced samples (1 wolf and 1 dog) and collected SNPs from three latest dog/wolf genetic studies (7 wolves and 68 dogs), which were taken together for analysis with the population genetic statistics, Fst. In addition, DoGSD integrates some closely related information including SNP annotation, summary lists of SNPs located in genes, synonymous and non-synonymous SNPs, sampling location and breed information. All these features make DoGSD a useful resource for in-depth analysis in dog-/wolf-related studies.

Pheromone-Based Pest Management in China: Past, Present, and Future Prospects.

Semiochemical-based pest management technology has been widely used to monitor and control insect pests in agricultural, forestry, and public health sectors in the western world. It became a popular tool in the early 1970s with tremendous efforts in developing environment-friendly control technologies for the integrated pest management. However, in China, similar research lagged 15 to 20 years and was not initiated until the late 1980s. In this review, we present the early history of pheromone research that has led to the current practical applications in China, particularly in the development of pheromone-based pest management products. We also provide information regarding the current status of pheromone-based product manufacturing, marketing, and regulatory issues related to local semiochemical industries, which may be useful to other international companies interested in pursuing business in China. In addition, we share some research topics that represent new directions of the present pheromone research to explore novel tools for advancing semiochemical-based pest management in China.

Semiochemicals and natural repellents in biting fly management.

Biting flies, including stable flies and horn flies, are considered important pests of livestock, companion animals, and humans by inflicting painful bites and interrupting normal animal behavior and human recreational/outdoor activities. It is estimated that they cause an annual loss of over 3 billion dollars in the US livestock industry. Both groups of pest flies further transmit various infectious diseases to animals and humans. The present review summarizes recent research advancements in stable and horn fly chemical and sensory ecology, especially in the discovery of novel attractants and repellents, as well as their controls for these blood-sucking flies and beyond.

Effect of Tooth Mobility on the Accuracy of Conventional Impressions: A Pilot Study.

PURPOSE: To study the influence of tooth mobility on the accuracy of conventional impressions. MATERIALS AND METHODS: In total, 10 patients with mobile anterior teeth and 10 healthy patients were treated with conventional impressions and intraoral digital impressions. The digital impression group was recorded as standard data, the mobile teeth group was recorded as the experimental group, and the healthy anterior teeth group was recorded as the control group. We imported digital impression and irreversible hydrocolloid impression files into Geomagic Wrap and marked reference points to execute N-point alignment, then we recorded the coordinates. Paired-samples t test was used to analyze whether the point coordinates of mobile teeth were statistically significant (a = .05). One-way ANOVA was used to analyze whether there was a relationship between coordinate differences and tooth mobility in the distal, coronal, and buccal directions (a = .05). RESULTS: In the buccal and coronal directions, the difference was statistically significant between the conventional and digital impression groups. In the buccal direction, the accuracy differences of I-degree and II-degree mobile teeth were 0.149 mm and 0.401 mm, respectively. In the coronal direction, the differences were 0.128 mm and 0.233 mm, respectively. Meanwhile, ANOVA analysis showed that there was a relationship between point coordinate difference and tooth mobility in the buccal and coronal directions. CONCLUSIONS: Conventional impressions can influence the accuracy of mobile tooth impressions. Therefore, digital impressions should be adopted for mobile teeth impressions.

Crop DNA extraction with lab-made magnetic nanoparticles.

Molecular breeding methods, such as marker-assisted selection and genomic selection, require high-throughput and cost-effective methods for isolating genomic DNA from plants, specifically from crop tissue or seed with high polysaccharides, lipids, and proteins. A quick and inexpensive high-throughput method for isolating genomic DNA from seed and leaf tissue from multiple crops was tested with a DNA isolation method that combines CTAB extraction buffer and lab-made SA-coated magnetic nanoparticles. This method is capable of isolating quality genomic DNA from leaf tissue and seeds in less than 2 hours with fewer steps than a standard CTAB extraction method. The yield of the genomic DNA was 582-729 ng per 5 leaf discs or 216-1869 ng per seed in soybean, 2.92-62.6 ng per 5 leaf discs or 78.9-219 ng per seed in wheat, and 30.9-35.4 ng per 5 leaf discs in maize. The isolated DNA was tested with multiple molecular breeding methods and was found to be of sufficient quality and quantity for PCR and targeted genotyping by sequencing methods such as molecular inversion probes (MIPs). The combination of SA-coated magnetic nanoparticles and CTAB extraction buffer is a fast, simple, and environmentally friendly, high-throughput method for both leaf tissues and seed(s) DNA preparation at low cost per sample. The DNA obtained from this method can be deployed in applied breeding programs for marker-assisted selection or genomic selection.

High-protein high-konjac glucomannan diets changed glucose and lipid metabolism by modulating colonic microflora and bile acid profiles in healthy mouse models.

High protein and fiber diets are becoming increasingly popular for weight loss; however, the benefits or risks of high protein and fiber diets with a normal calorie level for healthy individuals still need to be elucidated. In this study, we explored the role and mechanisms of long-term high protein and/or konjac glucomannan diets on the metabolic health of healthy mouse models. We found that high konjac glucomannan contents improved the glucose tolerance of mice and both high protein and high konjac glucomannan contents improved the serum lipid profile but increased the TNF-α levels. In the liver, high dietary protein contents reduced the expression of the FASN gene related to fatty acid synthesis. Interactions of dietary protein and fiber were shown in the signaling pathways related to lipid and glucose metabolism of the liver and the inflammatory status of the colon, wherein the high protein and high konjac glucomannan diet downregulated the expression of the SREBF1 and FXR genes in the liver and downregulated the expression of TNF-α genes in the colon compared to the high protein diet. High konjac glucomannan contents reduced the colonic secondary bile acid levels including DCA and LCA; this was largely associated with the changed microbiota profile and also contributed to improved lipid and glucose homeostasis. In conclusion, high protein diets improved lipid homeostasis and were not a risk to metabolic health, while high fiber diets improved glucose and lipid homeostasis by modulating colonic microbiota and bile acid profiles, and a high protein diet supplemented with konjac glucomannan might improve hepatic lipid homeostasis and colonic inflammation in healthy mouse models through long-term intervention.

Surveillance for adverse events following immunization with DTaP-containing combination vaccines in Linping, China, 2019-2022.

Background: The DTaP-Hib and DTaP-IPV/Hib combination vaccine can be used as a substitute for the diphtheria, tetanus, and acellular pertussis combined vaccine (DTaP). We aimed to evaluate the safety of multi-component vaccines containing DTaP by analyzing the reporting rates and characteristics of adverse events following immunization (AEFIs) in Linping District during the years 2019 to 2022. Methods: We obtained data of AEFI and vaccination from the National AEFI Surveillance System of China and Zhejiang Municipal Immunization Information Management System, respectively, during 2019-2022 for a descriptive, epidemiological analysis. Results: The total number of AEFI reported following vaccinations with DTaP-containing combination vaccines was 802 in Linping District from 2019 to 2022. The overall reporting rates of AEFIs following DTaP, DTaP-Hib, and DTaP-IPV/Hib vaccinations were 445.72 (537 cases), 536.29 (45 cases), and 306.13 (220 cases) per 100,000 doses in Linping District from 2019 to 2022, respectively. Only one case of a serious AEFI following DTaP vaccination, with a reporting rate of 0.83 per 100,000 doses. The composition ratio of vaccine product-related reactions for DTaP, DTaP-Hib, and DTaP-IPV/Hib were 99.81, 97.78, and 100.00%, respectively. The composition ratio of coincidental events for DTaP and DTaP-Hib were 0.19 and 2.22%, respectively. The reporting rates of total AEFIs for DTaP-IPV/Hib were lower than for DTaP. The reporting rate of local induration for DTaP-Hib was lower than for DTaP, and the reporting rates of local redness & swelling and local induration for DTaP-IPV/Hib were both lower than for DTaP. DTaP-IPV/Hib had a higher proportion of AEFIs in first quarter compared to DTaP. The reporting rate after the second dose of DTaP-Hib was higher than that of DTaP, and the reporting rates of AEFIs after the first dose and third dose of DTaP-IPV/Hib were lower than DTaP. Conclusion: The reported AEFIs to multi-component vaccines containing DTaP components during 2019-2022 in Linping District were mainly mild vaccine reactions. DTaP-containing combination vaccines demonstrated a good safety profile.

Zebrafish cobll1a regulates lipid homeostasis via the RA signaling pathway.

Background: The COBLL1 gene has been implicated in human central obesity, fasting insulin levels, type 2 diabetes, and blood lipid profiles. However, its molecular mechanisms remain largely unexplored. Methods: In this study, we established cobll1a mutant lines using the CRISPR/Cas9-mediated gene knockout technique. To further dissect the molecular underpinnings of cobll1a during early development, transcriptome sequencing and bioinformatics analysis was employed. Results: Our study showed that compared to the control, cobll1a -/- zebrafish embryos exhibited impaired development of digestive organs, including the liver, intestine, and pancreas, at 4 days post-fertilization (dpf). Transcriptome sequencing and bioinformatics analysis results showed that in cobll1a knockout group, the expression level of genes in the Retinoic Acid (RA) signaling pathway was affected, and the expression level of lipid metabolism-related genes (fasn, scd, elovl2, elovl6, dgat1a, srebf1 and srebf2) were significantly changed (p < 0.01), leading to increased lipid synthesis and decreased lipid catabolism. The expression level of apolipoprotein genes (apoa1a, apoa1b, apoa2, apoa4a, apoa4b, and apoea) genes were downregulated. Conclusion: Our study suggest that the loss of cobll1a resulted in disrupted RA metabolism, reduced lipoprotein expression, and abnormal lipid transport, therefore contributing to lipid accumulation and deleterious effects on early liver development.