Displaying publications 1 - 20 of 26 in total

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  1. iSegMSI: An Interactive Strategy to Improve Spatial Segmentation of Mass Spectrometry Imaging Data
    Guo L, Liu X, Zhao C, Hu Z, Xu X, Cheng KK, et al.
    Anal Chem, 2022 Oct 25;94(42):14522-14529.
    PMID: 36223650 DOI: 10.1021/acs.analchem.2c01456
    Spatial segmentation is a critical procedure in mass spectrometry imaging (MSI)-based biochemical analysis. However, the commonly used unsupervised MSI segmentation methods may lead to inappropriate segmentation results as the MSI data is characterized by high dimensionality and low signal-to-noise ratio. This process can be improved by the incorporation of precise prior knowledge, which is hard to obtain in most cases. In this study, we show that the incorporation of partial or coarse prior knowledge from different sources such as reference images or biological knowledge may also help to improve MSI segmentation results. Here, we propose a novel interactive segmentation strategy for MSI data called iSegMSI, which incorporates prior information in the form of scribble-regularization of the unsupervised model to fine-tune the segmentation results. By using two typical MSI data sets (including a whole-body mouse fetus and human thyroid cancer), the present results demonstrate the effectiveness of the iSegMSI strategy in improving the MSI segmentations. Specifically, the method can be used to subdivide a region into several subregions specified by the user-defined scribbles or to merge several subregions into a single region. Additionally, these fine-tuned results are highly tolerant to the imprecision of the scribbles. Our results suggest that the proposed iSegMSI method may be an effective preprocessing strategy to facilitate the analysis of MSI data.
  2. Validation of the Chinese version of the Rosenberg Self-Esteem Scale: evidence from a three-wave longitudinal study
    Jiang C, Zhu Y, Luo Y, Tan CS, Mastrotheodoros S, Costa P, et al.
    BMC Psychol, 2023 Oct 18;11(1):345.
    PMID: 37853499 DOI: 10.1186/s40359-023-01293-1
    BACKGROUND: The 10-item Rosenberg Self-Esteem Scale (RSES) is a widely used tool for individuals to self-report their self-esteem; however, the factorial structures of translated versions of the RSES vary across different languages. This study aimed to validate the Chinese version of the RSES in the Chinese mainland using a longitudinal design.

    METHODS: A group of healthcare university students completed the RSES across three waves: baseline, 1-week follow-up, and 15-week follow-up. A total of 481 valid responses were collected through the three-wave data collection process. Exploratory factor analysis (EFA) was performed on the baseline data to explore the potential factorial structure, while confirmatory factor analysis (CFA) was performed on the follow-up data to determine the best-fit model. Additionally, the cross-sectional and longitudinal measurement invariances were tested to assess the measurement properties of the RSES for different groups, such as gender and age, as well as across different time points. Convergent validity was assessed against the Self-Rated Health Questionnaire (SRHQ) using Spearman's correlation. Internal consistency was examined using Cronbach's alpha and McDonald's omega coefficients, while test-retest reliability was assessed using intraclass correlation coefficient.

    RESULTS: The results of EFA revealed that Items 5, 8, and 9 had inadequate or cross-factor loadings, leading to their removal from further analysis. Analysis of the remaining seven items using EFA suggested a two-factor solution. A comparison of several potential models for the 10-item and 7-item RSES using CFA showed a preference for the 7-item form (RSES-7) with two factors. Furthermore, the RSES-7 exhibited strict invariance across different groups and time points, indicating its stability and consistency. The RSES-7 also demonstrated adequate convergent validity, internal consistency, and test-retest reliability, which further supported its robustness as a measure of self-esteem.

    CONCLUSIONS: The findings suggest that the RSES-7 is a psychometrically sound and brief self-report scale for measuring self-esteem in the Chinese context. More studies are warranted to further verify its usability.

  3. Fulltext Turnovers of Sex-Determining Mutation in the Golden Pompano and Related Species Provide Insights into Microevolution of Undifferentiated Sex Chromosome
    Guo L, Malara D, Battaglia P, Waiho K, Davis DA, Deng Y, et al.
    Genome Biol Evol, 2024 Mar 02;16(3).
    PMID: 38408866 DOI: 10.1093/gbe/evae037
    The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within the same gene Hsd17b1. We propose an evolutionary model elucidating the turnover of sex-determining mutations by highlighting the contrasting dynamics between purifying selection, responsible for maintaining W-linked Hsd17b1, and neutral evolution, which drives Z-linked Hsd17b1. Additionally, sporadic loss-of-function mutations in W-linked Hsd17b1 contribute to the conversion of W chromosomes into Z chromosomes. This model was directly supported by simulations, closely related species, and indirectly by zebrafish mutants. These findings shed new light on the early stages of sex chromosome evolution.
  4. The incompatibility between industrial restructuring and low-carbon economy: a comprehensive analysis
    Zhang X, Zhu H, Sang B, Guo L
    Environ Sci Pollut Res Int, 2023 Aug;30(36):85611-85625.
    PMID: 37389755 DOI: 10.1007/s11356-023-28316-z
    Numerous studies have demonstrated that the development of low-carbon economy and industrial restructuring cannot occur in a coordinated manner. However, academic literature does not provide further explanations for this phenomenon. In this paper, we introduce a novel decomposition method to reassess the relationship between industrial restructuring and low-carbon economy, which yields similar findings. Next, we construct a straightforward theoretical model to investigate two fundamental reasons that interrelate with this issue: excessively high proportion of secondary sector and excessive carbon intensity of tertiary sector. Finally, we implement a rigorous causal identification using three-dimensional panel data at the provincial, industrial, and yearly levels by undergoing multiple robustness tests and mitigating endogeneity issues. Our heterogeneity tests suggest that the impact of industrial restructuring is greater in high-polluting industries, the Eastern region, and non-digital pilot regions. Overall, our theoretical and empirical analysis serves as a vital reference for other developing and developed countries to attain harmonious development between low-carbon economy and industrial restructuring.
  5. Fulltext The impact of digital healthcare systems on pain and body function in patients with knee joint pain: a systematic review and meta-analysis
    Guo L, Li S, Xie S, Bian L, Shaharudin S
    Sci Rep, 2024 Feb 09;14(1):3310.
    PMID: 38331984 DOI: 10.1038/s41598-024-53853-z
    The digital healthcare (DH) system has recently emerged as an advanced rehabilitation approach that promotes rehabilitation training based on virtual reality (VR) and augmented reality (AR). The purpose of this meta-analysis study is to review and assess the impact of DH systems on pain and physical function among patients diagnosed with knee joint pain. Between January 2003 and September 2023, studies that met the listed inclusion criteria were gathered from Scopus, PubMed, Web of Science, and EBSCO databases. The analysis of standardized mean difference (SMD) was carried out with 95% confidence interval (95% CI) (PROSPERO registration number: CRD42023462538). Eight research papers were selected, which collectively involved 194 males and 279 females. The meta-analysis outcomes revealed that DH intervention significantly improved balance (SMD, 0.41 [0.12, 0.69], p 
  6. Fulltext SLC25A13 gene analysis in citrin deficiency: sixteen novel mutations in East Asian patients, and the mutation distribution in a large pediatric cohort in China
    Song YZ, Zhang ZH, Lin WX, Zhao XJ, Deng M, Ma YL, et al.
    PLoS One, 2013;8(9):e74544.
    PMID: 24069319 DOI: 10.1371/journal.pone.0074544
    The human SLC25A13 gene encodes citrin, the liver-type mitochondrial aspartate/glutamate carrier isoform 2 (AGC2), and SLC25A13 mutations cause citrin deficiency (CD), a disease entity that encompasses different age-dependant clinical phenotypes such as Adult-onset Citrullinemia Type II (CTLN2) and Neonatal Intrahepatic Cholestasis caused by Citrin Deficiency (NICCD). The analyses of SLC25A13 gene and its protein/mRNA products remain reliable tools for the definitive diagnoses of CD patients, and so far, the SLC25A13 mutation spectrum in Chinese CD patients has not been well-characterized yet.
  7. Robotic Mounted Rail Arm System for implementing effective workplace safety for migrant workers
    Wei H, Rahman MA, Hu X, Zhang L, Guo L, Tao H, et al.
    Work, 2021;68(3):845-852.
    PMID: 33612527 DOI: 10.3233/WOR-203418
    BACKGROUND: The selection of orders is the method of gathering the parts needed to assemble the final products from storage sites. Kitting is the name of a ready-to-use package or a parts kit, flexible robotic systems will significantly help the industry to improve the performance of this activity. In reality, despite some other limitations on the complexity of components and component characteristics, the technological advances in recent years in robotics and artificial intelligence allows the treatment of a wide range of items.

    OBJECTIVE: In this article, we study the robotic kitting system with a Robotic Mounted Rail Arm System (RMRAS), which travels narrowly to choose the elements.

    RESULTS: The objective is to evaluate the efficiency of a robotic kitting system in cycle times through modeling of the elementary kitting operations that the robot performs (pick and room, move, change tools, etc.). The experimental results show that the proposed method enhances the performance and efficiency ratio when compared to other existing methods.

    CONCLUSION: This study with the manufacturer can help him assess the robotic area performance in a given design (layout and picking a policy, etc.) as part of an ongoing project on automation of kitting operations.

  8. Nanomedicines guided nanoimaging probes and nanotherapeutics for early detection of lung cancer and abolishing pulmonary metastasis: Critical appraisal of newer developments and challenges to clinical transition
    Gao X, Guo L, Li J, Thu HE, Hussain Z
    J Control Release, 2018 12 28;292:29-57.
    PMID: 30359665 DOI: 10.1016/j.jconrel.2018.10.024
    Lung cancer (LC) is the second most prevalent type of cancer and primary cause of mortality among both men and women, worldwide. The most commonly employed diagnostic modalities for LC include chest X-ray (CXR), magnetic-resonance-imaging (MRI), computed tomography (CT-scan), and fused-positron-emitting-tomography-CT (PET-CT). Owing to several limitations associated with the use of conventional diagnostic tools such as radiation burden to the patient, misleading diagnosis ("missed lung cancer"), false staging and low sensitivity and resolution, contemporary diagnostic regimen needed to be employed for screening of LC. In recent decades, nanotechnology-guided interventions have been transpired as emerging nanoimaging probes for detection of LC at advanced stages, while producing signal amplification, better resolution for surface and deep tissue imaging, and enhanced translocation and biodistribution of imaging probes within the cancerous tissues. Besides enormous potential of nanoimaging probes, nanotechnology-based advancements have also been evidenced for superior efficacy for treatment of LC and abolishing pulmonary metastasis (PM). The success of nanotherapeutics is due to their ability to maximise translocation and biodistribution of anti-neoplastic agents into the tumor tissues, improve pharmacokinetic profiles of anti-metastatic agents, optimise target-specific drug delivery, and control release kinetics of encapsulated moieties in target tissues. This review aims to overview and critically discuss the superiority of nanoimaging probes and nanotherapeutics over conventional regimen for early detection of LC and abolishing PM. Current challenges to clinical transition of nanoimaging probes and therapeutic viability of nanotherapeutics for treatment for LC and PM have also been pondered.
  9. Multimodal Image Fusion Offers Better Spatial Resolution for Mass Spectrometry Imaging
    Guo L, Zhu J, Wang K, Cheng KK, Xu J, Dong L, et al.
    Anal Chem, 2023 Jun 27;95(25):9714-9721.
    PMID: 37296503 DOI: 10.1021/acs.analchem.3c02002
    High-resolution reconstruction has attracted increasing research interest in mass spectrometry imaging (MSI), but it remains a challenging ill-posed problem. In the present study, we proposed a deep learning model to fuse multimodal images to enhance the spatial resolution of MSI data, namely, DeepFERE. Hematoxylin and eosin (H&E) stain microscopy imaging was used to pose constraints in the process of high-resolution reconstruction to alleviate the ill-posedness. A novel model architecture was designed to achieve multi-task optimization by incorporating multi-modal image registration and fusion in a mutually reinforced framework. Experimental results demonstrated that the proposed DeepFERE model is able to produce high-resolution reconstruction images with rich chemical information and a detailed structure on both visual inspection and quantitative evaluation. In addition, our method was found to be able to improve the delimitation of the boundary between cancerous and para-cancerous regions in the MSI image. Furthermore, the reconstruction of low-resolution spatial transcriptomics data demonstrated that the developed DeepFERE model may find wider applications in biomedical fields.
  10. Fulltext Multi-platform discovery of haplotype-resolved structural variation in human genomes
    Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, et al.
    Nat Commun, 2019 04 16;10(1):1784.
    PMID: 30992455 DOI: 10.1038/s41467-018-08148-z
    The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies.
  11. Fulltext Mesenchymal stem cell-derived extracellular vesicles for immunomodulation and regeneration: a next generation therapeutic tool?
    Kou M, Huang L, Yang J, Chiang Z, Chen S, Liu J, et al.
    Cell Death Dis, 2022 Jul 04;13(7):580.
    PMID: 35787632 DOI: 10.1038/s41419-022-05034-x
    Mesenchymal stem cells (MSCs) can be widely isolated from various tissues including bone marrow, umbilical cord, and adipose tissue, with the potential for self-renewal and multipotent differentiation. There is compelling evidence that the therapeutic effect of MSCs mainly depends on their paracrine action. Extracellular vesicles (EVs) are fundamental paracrine effectors of MSCs and play a crucial role in intercellular communication, existing in various body fluids and cell supernatants. Since MSC-derived EVs retain the function of protocells and have lower immunogenicity, they have a wide range of prospective therapeutic applications with advantages over cell therapy. We describe some characteristics of MSC-EVs, and discuss their role in immune regulation and regeneration, with emphasis on the molecular mechanism and application of MSC-EVs in the treatment of fibrosis and support tissue repair. We also highlight current challenges in the clinical application of MSC-EVs and potential ways to overcome the problem of quality heterogeneity.
  12. Fulltext Irigenin treatment alleviates doxorubicin (DOX)-induced cardiotoxicity by suppressing apoptosis, inflammation and oxidative stress via the increase of miR-425
    Guo L, Zheng X, Wang E, Jia X, Wang G, Wen J
    Biomed Pharmacother, 2020 May;125:109784.
    PMID: 32092815 DOI: 10.1016/j.biopha.2019.109784
    Doxorubicin (DOX) is an eff ;ective chemotherapeutic drug to suppress the progression of various types of tumors. However, its clinical application has been largely limited due to its potential cardiotoxicity. MicroRNAs (miRNAs) are emerged as critical regulators of cardiac injury. This study was aimed to explore the effects of irigenin (IR), as an isoflavonoid isolated from the rhizome of Belamcanda chinensis, on DOX-induced cardiotoxicity using the in vivo and in vitrostudies. The results indicated that DOX-induced fibrosis, cardiac dysfunction and injury were markedly attenuated by IR through reducing apoptosis, oxidative stress and inflammation in heart tissue samples. Importantly, DOX resulted in a remarkable decrease of miR-425 in heart tissues and cells, which was significantly rescued by IR. Receptor-interacting protein kinase 1 (RIPK1) was discovered to be a direct target of miR-425. DOX induced over-expression of RIPK1 both in vivo and in vitro, which were greatly decreased by IR. Transfection with miR-425 mimic could inhibit RIPK1 expression, whereas reducing miR-425 increased RIPK1 expression levels. In parallel to miR-425 over-expression, RIPK1 knockdown could attenuate apoptosis, reactive oxygen species (ROS) production and inflammation in HL-1 cells. However, over-expression of RIPK1 markedly abolished miR-425 mimic-induced apoptosis, ROS accumulation and inflammatory response in DOX-exposed cells. Herein, miR-425 could ameliorate cardiomyocyte injury through directly targeting RIPK1. Furthermore, activation of miR-425 by IR markedly improved DOX-induced cardiotoxicity, and therefore IR could be considered as a promising therapeutic agent for the treatment of cardiac injury.
  13. Fulltext Immunity and clinical efficacy of an inactivated enterovirus 71 vaccine in healthy Chinese children: a report of further observations
    Liu L, Mo Z, Liang Z, Zhang Y, Li R, Ong KC, et al.
    BMC Med, 2015;13:226.
    PMID: 26381232 DOI: 10.1186/s12916-015-0448-7
    To investigate the long-term effects on immunity of an inactivated enterovirus 71 (EV71) vaccine and its protective efficacy.
  14. Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)
    Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.
    Autophagy, 2016;12(1):1-222.
    PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
  15. Fulltext Genomic insights into the evolution of Echinochloa species as weed and orphan crop
    Wu D, Shen E, Jiang B, Feng Y, Tang W, Lao S, et al.
    Nat Commun, 2022 02 03;13(1):689.
    PMID: 35115514 DOI: 10.1038/s41467-022-28359-9
    As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.
  16. Fulltext Genetic structure of Phytophthora infestans populations in China indicates multiple migration events
    Guo L, Zhu XQ, Hu CH, Ristaino JB
    Phytopathology, 2010 Oct;100(10):997-1006.
    PMID: 20839935 DOI: 10.1094/PHYTO-05-09-0126
    One hundred isolates of Phytophthora infestans collected from 10 provinces in China between 1998 and 2004 were analyzed for mating type, metalaxyl resistance, mitochondrial DNA (mtDNA) haplotype, allozyme genotype, and restriction fragment length polymorphism (RFLP) with the RG-57 probe. In addition, herbarium samples collected in China, Russia, Australia, and other Asian countries were also typed for mtDNA haplotype. The Ia haplotype was found during the first outbreaks of the disease in China (1938 and 1940), Japan (1901, 1930, and 1931), India (1913), Peninsular Malaysia (1950), Nepal (1954), The Philippines (1910), Australia (1917), Russia (1917), and Latvia (1935). In contrast, the Ib haplotype was found after 1950 in China on both potato and tomato (1952, 1954, 1956, and 1982) and in India (1968 and 1974). Another migration of a genotype found in Siberia called SIB-1 (Glucose-6-phosphate isomerase [Gpi] 100/100, Peptidase [Pep] 100/100, IIa mtDNA haplotype) was identified using RFLP fingerprints among 72% of the isolates and was widely distributed in the north and south of China and has also been reported in Japan. A new genotype named CN-11 (Gpi 100/111, Pep 100/100, IIb mtDNA haplotype), found only in the south of China, and two additional genotypes (Gpi 100/100, Pep 100/100, Ia mtDNA haplotype) named CN-9 and CN-10 were identified. There were more diverse genotypes among isolates from Yunnan province than elsewhere. The SIB-1 (IIa) genotype is identical to those from Siberia, suggesting later migration of this genotype from either Russia or Japan into China. The widespread predominance of SIB-1 suggests that this genotype has enhanced fitness compared with other genotypes found. Movement of the pathogen into China via infected seed from several sources most likely accounts for the distribution of pathogen genotypes observed. MtDNA haplotype evidence and RFLP data suggest multiple migrations of the pathogen into China after the initial introduction of the Ia haplotype in the 1930s.
  17. Flotation separation of poly (ethylene terephthalate and vinyl chloride) mixtures based on clean corona modification: Optimization using response surface methodology
    Zhao Y, Han F, Guo L, Zhang J, Zhang H, Abdelaziz IIM, et al.
    Waste Manag, 2021 Dec;136:184-194.
    PMID: 34689097 DOI: 10.1016/j.wasman.2021.10.018
    Postconsumer polyethylene terephthalate (PET) has potential applications in many areas of manufacturing, but contamination by hazardous polyvinyl chloride (PVC) in common waste streams can reduce its recyclable value. Separating collected PET-PVC mixtures before recycling remains very challenging because of the similar physicochemical properties of PET and PVC. Herein, we describe a novel flotation process with corona modification pretreatment to facilitate the separation of PET-PVC mixtures. Through water contact angle, surface free energy, X-ray photoelectron and FT-IR characterization, we found that polar hydroxyl groups can be more easily introduced on the PVC surface than on the PET surface induced by corona modification. This selective wetting can suppress the floatability of PVC, leading to the separation of PET as floating product. A reliable mechanism including two different hydrogen-abstraction pathways was established. Response surface methodology consisting of Plackett-Burman and Box-Behnken designs was adopted for optimization of the combined process, and control parameters were solved based on high-quality prediction models, with fitting from significant variables and interactions. For physical or chemical circulation strategies with PET purity prioritization, the validated purity of the product reached 96.05% at a 626 W corona power, 5.42 m/min passing speed, 24.78 mg/L frother concentration and 286 L/h air flow rate. For the energy recuperation strategy with PET recovery prioritization, the factual recovery reached 98.08% under a 601 W corona power, 6.04 m/min passing speed, 27.55 mg/L frother concentration and 184 L/h air flow rate. The current work provides technological insights into the cleaner disposal of waste plastics.
  18. Evidence for the Higgs Boson Decay to a Z Boson and a Photon at the LHC
    Aad G, Abbott B, Abeling K, Abicht NJ, Abidi SH, Aboulhorma A, et al.
    Phys Rev Lett, 2024 Jan 12;132(2):021803.
    PMID: 38277607 DOI: 10.1103/PhysRevLett.132.021803
    The first evidence for the Higgs boson decay to a Z boson and a photon is presented, with a statistical significance of 3.4 standard deviations. The result is derived from a combined analysis of the searches performed by the ATLAS and CMS Collaborations with proton-proton collision datasets collected at the CERN Large Hadron Collider (LHC) from 2015 to 2018. These correspond to integrated luminosities of around 140  fb^{-1} for each experiment, at a center-of-mass energy of 13 TeV. The measured signal yield is 2.2±0.7 times the standard model prediction, and agrees with the theoretical expectation within 1.9 standard deviations.
  19. Efficient detection of copy-number variations using exome data: Batch- and sex-based analyses
    Uchiyama Y, Yamaguchi D, Iwama K, Miyatake S, Hamanaka K, Tsuchida N, et al.
    Hum Mutat, 2021 01;42(1):50-65.
    PMID: 33131168 DOI: 10.1002/humu.24129
    Many algorithms to detect copy number variations (CNVs) using exome sequencing (ES) data have been reported and evaluated on their sensitivity and specificity, reproducibility, and precision. However, operational optimization of such algorithms for a better performance has not been fully addressed. ES of 1199 samples including 763 patients with different disease profiles was performed. ES data were analyzed to detect CNVs by both the eXome Hidden Markov Model (XHMM) and modified Nord's method. To efficiently detect rare CNVs, we aimed to decrease sequencing biases by analyzing, at the same time, the data of all unrelated samples sequenced in the same flow cell as a batch, and to eliminate sex effects of X-linked CNVs by analyzing female and male sequences separately. We also applied several filtering steps for more efficient CNV selection. The average number of CNVs detected in one sample was <5. This optimization together with targeted CNV analysis by Nord's method identified pathogenic/likely pathogenic CNVs in 34 patients (4.5%, 34/763). In particular, among 142 patients with epilepsy, the current protocol detected clinically relevant CNVs in 19 (13.4%) patients, whereas the previous protocol identified them in only 14 (9.9%) patients. Thus, this batch-based XHMM analysis efficiently selected rare pathogenic CNVs in genetic diseases.
  20. Fulltext Diverse genetic mechanisms underlie worldwide convergent rice feralization
    Qiu J, Jia L, Wu D, Weng X, Chen L, Sun J, et al.
    Genome Biol, 2020 03 26;21(1):70.
    PMID: 32213201 DOI: 10.1186/s13059-020-01980-x
    BACKGROUND: Worldwide feralization of crop species into agricultural weeds threatens global food security. Weedy rice is a feral form of rice that infests paddies worldwide and aggressively outcompetes cultivated varieties. Despite increasing attention in recent years, a comprehensive understanding of the origins of weedy crop relatives and how a universal feralization process acts at the genomic and molecular level to allow the rapid adaptation to weediness are still yet to be explored.

    RESULTS: We use whole-genome sequencing to examine the origin and adaptation of 524 global weedy rice samples representing all major regions of rice cultivation. Weed populations have evolved multiple times from cultivated rice, and a strikingly high proportion of contemporary Asian weed strains can be traced to a few Green Revolution cultivars that were widely grown in the late twentieth century. Latin American weedy rice stands out in having originated through extensive hybridization. Selection scans indicate that most genomic regions underlying weedy adaptations do not overlap with domestication targets of selection, suggesting that feralization occurs largely through changes at loci unrelated to domestication.

    CONCLUSIONS: This is the first investigation to provide detailed genomic characterizations of weedy rice on a global scale, and the results reveal diverse genetic mechanisms underlying worldwide convergent rice feralization.

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