Displaying publications 21 - 40 of 59 in total

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  1. Fulltext NMF-Based Approach for Missing Values Imputation of Mass Spectrometry Metabolomics Data
    Xu J, Wang Y, Xu X, Cheng KK, Raftery D, Dong J
    Molecules, 2021 Sep 24;26(19).
    PMID: 34641330 DOI: 10.3390/molecules26195787
    In mass spectrometry (MS)-based metabolomics, missing values (NAs) may be due to different causes, including sample heterogeneity, ion suppression, spectral overlap, inappropriate data processing, and instrumental errors. Although a number of methodologies have been applied to handle NAs, NA imputation remains a challenging problem. Here, we propose a non-negative matrix factorization (NMF)-based method for NA imputation in MS-based metabolomics data, which makes use of both global and local information of the data. The proposed method was compared with three commonly used methods: k-nearest neighbors (kNN), random forest (RF), and outlier-robust (ORI) missing values imputation. These methods were evaluated from the perspectives of accuracy of imputation, retrieval of data structures, and rank of imputation superiority. The experimental results showed that the NMF-based method is well-adapted to various cases of data missingness and the presence of outliers in MS-based metabolic profiles. It outperformed kNN and ORI and showed results comparable with the RF method. Furthermore, the NMF method is more robust and less susceptible to outliers as compared with the RF method. The proposed NMF-based scheme may serve as an alternative NA imputation method which may facilitate biological interpretations of metabolomics data.
  2. Fulltext Estimating nutrient uptake requirements for soybean using QUEFTS model in China
    Yang F, Xu X, Wang W, Ma J, Wei D, He P, et al.
    PLoS One, 2017;12(5):e0177509.
    PMID: 28498839 DOI: 10.1371/journal.pone.0177509
    Estimating balanced nutrient requirements for soybean (Glycine max [L.] Merr) in China is essential for identifying optimal fertilizer application regimes to increase soybean yield and nutrient use efficiency. We collected datasets from field experiments in major soybean planting regions of China between 2001 and 2015 to assess the relationship between soybean seed yield and nutrient uptake, and to estimate nitrogen (N), phosphorus (P), and potassium (K) requirements for a target yield of soybean using the quantitative evaluation of the fertility of tropical soils (QUEFTS) model. The QUEFTS model predicted a linear-parabolic-plateau curve for the balanced nutrient uptake with a target yield increased from 3.0 to 6.0 t ha-1 and the linear part was continuing until the yield reached about 60-70% of the potential yield. To produce 1000 kg seed of soybean in China, 55.4 kg N, 7.9 kg P, and 20.1 kg K (N:P:K = 7:1:2.5) were required in the above-ground parts, and the corresponding internal efficiencies (IE, kg seed yield per kg nutrient uptake) were 18.1, 126.6, and 49.8 kg seed per kg N, P, and K, respectively. The QUEFTS model also simulated that a balanced N, P, and K removal by seed which were 48.3, 5.9, and 12.2 kg per 1000 kg seed, respectively, accounting for 87.1%, 74.1%, and 60.8% of the total above-ground parts, respectively. These results were conducive to make fertilizer recommendations that improve the seed yield of soybean and avoid excessive or deficient nutrient supplies. Field validation indicated that the QUEFTS model could be used to estimate nutrient requirements which help develop fertilizer recommendations for soybean.
  3. Fulltext Multi-dimensional psychosocial factors influencing the willingness to receive a COVID-19 vaccine booster: A survey among the public in Mainland China
    Lin Y, Huang Z, Xu X, Du W, Alias H, Hu Z, et al.
    Hum Vaccin Immunother, 2022 Nov 30;18(6):2126667.
    PMID: 36165498 DOI: 10.1080/21645515.2022.2126667
    This study aimed to investigate multi-dimensional psychological and social factors that influence the willingness to receive a COVID-19 vaccine booster in China. A nationwide cross-sectional online survey was conducted between March and April 2022. A total of 6375 complete responses were received. The majority were of age 18 to 40 years old (80.0%) and college-educated (49.2%). In total, 79% responded extremely willing to receive a COVID-19 vaccine booster. By demographics, younger age, females, higher education, and participants with the lowest income reported higher willingness. Having a very good health status (odds ratio [OR] 3.56, 95% confidence interval [CI] 2.92-4.34) and a higher score of vaccine confidence (OR 3.50, 95% CI 2.98-4.11) were associated with an increased willingness to receive a booster shot. Experiencing no side effects with primary COVID-19 vaccination (OR 2.46, 95% CI 1.89-3.20) and higher perceived susceptibility of COVID-19 infection (OR 2.38, 95% CI 1.92-2.95) were also associated with an increased willingness to receive a booster shot. A variety of psychosocial factors, namely having no chronic diseases, lower perceived concern over the safety of a booster shot, higher perceived severity of COVID-19 infection, and a higher level of institutional trust, were also significantly associated with greater willingness to get a booster shot. In conclusion, the present study adds evidence to the significant role of psychosocial factors in predicting COVID-19 vaccine booster acceptance and provides insights to design interventions to increase booster uptake in certain targeted demographic groups.
  4. Differential Correlations Informed Metabolite Set Enrichment Analysis to Decipher Metabolic Heterogeneity of Disease
    Lin G, Dong L, Cheng KK, Xu X, Wang Y, Deng L, et al.
    Anal Chem, 2023 Aug 22;95(33):12505-12513.
    PMID: 37557184 DOI: 10.1021/acs.analchem.3c02246
    Metabolic pathways are regarded as functional and basic components of the biological system. In metabolomics, metabolite set enrichment analysis (MSEA) is often used to identify the altered metabolic pathways (metabolite sets) associated with phenotypes of interest (POI), e.g., disease. However, in most studies, MSEA suffers from the limitation of low metabolite coverage. Random walk (RW)-based algorithms can be used to propagate the perturbation of detected metabolites to the undetected metabolites through a metabolite network model prior to MSEA. Nevertheless, most of the existing RW-based algorithms run on a general metabolite network constructed based on public databases, such as KEGG, without taking into consideration the potential influence of POI on the metabolite network, which may reduce the phenotypic specificities of the MSEA results. To solve this problem, a novel pathway analysis strategy, namely, differential correlation-informed MSEA (dci-MSEA), is proposed in this paper. Statistically, differential correlations between metabolites are used to evaluate the influence of POI on the metabolite network, so that a phenotype-specific metabolite network is constructed for RW-based propagation. The experimental results show that dci-MSEA outperforms the conventional RW-based MSEA in identifying the altered metabolic pathways associated with colorectal cancer. In addition, by incorporating the individual-specific metabolite network, the dci-MSEA strategy is easily extended to disease heterogeneity analysis. Here, dci-MSEA was used to decipher the heterogeneity of colorectal cancer. The present results highlight the clustering of colorectal cancer samples with their cluster-specific selection of differential pathways and demonstrate the feasibility of dci-MSEA in heterogeneity analysis. Taken together, the proposed dci-MSEA may provide insights into disease mechanisms and determination of disease heterogeneity.
  5. Spinal Cord Injury: From MicroRNAs to Exosomal MicroRNAs
    Xu X, Liu R, Li Y, Zhang C, Guo C, Zhu J, et al.
    Mol Neurobiol, 2024 Jan 23.
    PMID: 38261255 DOI: 10.1007/s12035-024-03954-7
    Spinal cord injury (SCI) is an unfortunate experience that may generate extensive sensory and motor disabilities due to the destruction and passing of nerve cells. MicroRNAs are small RNA molecules that do not code for proteins but instead serve to regulate protein synthesis by targeting messenger RNA's expression. After SCI, secondary damage like apoptosis, oxidative stress, inflammation, and autophagy occurs, and differentially expressed microRNAs show a function in these procedures. Almost all animal and plant cells release exosomes, which are sophisticated formations of lipid membranes. These exosomes have the capacity to deliver significant materials, such as proteins, RNAs and lipids, to cells in need, regulating their functions and serving as a way of communication. This new method offers a fresh approach to treating spinal cord injury. Obviously, the exosome has the benefit of conveying the transported material across performing regulatory activities and the blood-brain barrier. Among the exosome cargoes, microRNAs, which modulate their mRNA targets, show considerable promise in the pathogenic diagnosis, process, and therapy of SCI. Herein, we describe the roles of microRNAs in SCI. Furthermore, we emphasize the importance of exosomal microRNAs in this disease.
  6. Genetic characteristics of human enterovirus 71 and coxsackievirus A16 circulating from 1999 to 2004 in Shenzhen, People's Republic of China
    Li L, He Y, Yang H, Zhu J, Xu X, Dong J, et al.
    J Clin Microbiol, 2005 Aug;43(8):3835-9.
    PMID: 16081920
    The genetic and phylogenetic characteristics of human enterovirus 71 (EV71) and coxsackievirus A16 (CA16) sampled from children with hand, foot, and mouth disease in Shenzhen, People's Republic of China, over a 6-year period (1999 to 2004) were examined with reverse transcription-PCR and DNA sequencing. Out of 147 stool specimens, 60 showed positive signals when screened with EV71- and CA16-specific primers. EV71 was identified in 19 specimens, and CA16 was identified in 41 specimens; coinfection by EV71 and CA16 was not observed. Phylogenetic analysis of all EV71 strains isolated from the mainland Chinese samples established C4 as the predominant genotype. Only one other known strain (3254-TAI-98; AF286531), isolated in Taiwan in 1998, was identified as belonging to genotype C4. Phylogenetic analysis of CA16 strains allowed us to identify three new genetic lineages (A, B, and C), with lineage C recently predominating in Asian countries, such as the People's Republic of China, Malaysia, and Japan. These new observations indicate that CA16 circulating in the People's Republic of China is genetically diverse, and additional surveillance is warranted.
  7. Fulltext Proteomic analysis of milk fat globule membrane proteins in mature human milk of women with and without gestational diabetes mellitus
    Yao D, Shen C, Yu J, Tang J, Zhang H, Xu X, et al.
    Food Chem, 2024 Jul 01;445:138691.
    PMID: 38354646 DOI: 10.1016/j.foodchem.2024.138691
    Milk fat globule membrane proteins (MFGMP) in human milks have positive effects on infant's health. As gestational diabetes mellitus (GDM) causes variations in MFGMP, it is essential to understand the effects of GDMon MFGMP. This study aims to investigate and compare the MFGMP (>3 months postpartum) of GDM and non-GDM (NGDM) women using four-dimensional-data-independent-acquisition proteomics technology. Principal component analysis shows significant differences in the MFGMP of GDM and NGDM women. A total of 4747 MFGMP were identified in maturehuman milk of GDM and NGDM women. Among these proteins, 174 differentially expressed proteins (DEPs) were identified in MFGM of GDM and NGDM women. Albumin (FC = 7.96) and transthyretin (FC = 2.57) which are related to insulin resistance and involved in thyroid hormone synthesis, are significantly up-regulated in MFGMP of GDM mothers indicating insulin resistance, imbalance of glucose homeostasis and poor glucose metabolism might persist in postpartum period.
  8. Approaches for controlling illicit tobacco trade--nine countries and the European Union
    Ross H, Husain MJ, Kostova D, Xu X, Edwards SM, Chaloupka FJ, et al.
    MMWR Morb Mortal Wkly Rep, 2015 May 29;64(20):547-50.
    PMID: 26020137
    An estimated 11.6% of the world cigarette market is illicit, representing more than 650 billion cigarettes a year and $40.5 billion in lost revenue. Illicit tobacco trade refers to any practice related to distributing, selling, or buying tobacco products that is prohibited by law, including tax evasion (sale of tobacco products without payment of applicable taxes), counterfeiting, disguising the origin of products, and smuggling. Illicit trade undermines tobacco prevention and control initiatives by increasing the accessibility and affordability of tobacco products, and reduces government tax revenue streams. The World Health Organization (WHO) Protocol to Eliminate Illicit Trade in Tobacco Products, signed by 54 countries, provides tools for addressing illicit trade through a package of regulatory and governing principles. As of May 2015, only eight countries had ratified or acceded to the illicit trade protocol, with an additional 32 needed for it to become international law (i.e., legally binding). Data from multiple international sources were analyzed to evaluate the 10 most commonly used approaches for addressing illicit trade and to summarize differences in implementation across select countries and the European Union (EU). Although the WHO illicit trade protocol defines shared global standards for addressing illicit trade, countries are guided by their own legal and enforcement frameworks, leading to a diversity of approaches employed across countries. Continued adoption of the methods outlined in the WHO illicit trade protocol might improve the global capacity to reduce illicit trade in tobacco products.
  9. Patient- and caregiver-related factors affecting family caregiver burden of urologic cancer patients
    Wong LP, Xu X, Alias H, Ting CY, Tan HM, Lin Y
    Urol Oncol, 2024 Apr 25.
    PMID: 38670816 DOI: 10.1016/j.urolonc.2024.04.004
    OBJECTIVE: This study aimed to investigate the level of family caregivers' (FC) burden and the extent to which patient- and caregiver-related factors influence the caregiving burden among FCs of urologic cancer (UC) patients.

    METHOD: A cross-sectional survey was conducted on caregivers of UC patients who sought cancer care. The modified caregiver strain index (MCSI) was used to assess FC burden.

    RESULTS: Just over half (54.3%) of FCs had moderate/high MCSI scores (score 9-26). By demographics, FCs who were unemployed (OR = 5.55, 95%CI 1.50-20.60) and perceived their current health condition as moderate/poor (OR = 6.05, 95%CI 1.95-18.78) reported higher odds of increased FC burden. Patient performance status played a pivotal role in exacerbating FC burden, whereby the odds of higher FC burden was 13 times higher in caregivers of UC patients having an Eastern Cooperative Oncology Group (ECOG) performance rating score of 3-4 (OR = 13.06, 95%CI 1.44-111.26) than those with a score of 0. Perceived lower levels of confidence in care provision were significantly associated with a higher level of strain (OR = 6.76, 985%CI 1.02-44.90).

    CONCLUSION: Care recipient performance status was a strong patient-related factor associated with higher FC burden regardless of duration of caregiving and other caregiver-related factors after adjusting for caregiver demographics.

  10. Effect of freeze-thaw cycles pretreatment on the vacuum freeze-drying process and physicochemical properties of the dried garlic slices
    Feng Y, Ping Tan C, Zhou C, Yagoub AEA, Xu B, Sun Y, et al.
    Food Chem, 2020 Sep 15;324:126883.
    PMID: 32344350 DOI: 10.1016/j.foodchem.2020.126883
    Freeze-thaw cycles (FTC) pretreatment was employed before the vacuum freeze-drying of garlic slices, aimed at improving the drying process and the quality of the end product. Cell viability, water status, internal structure, flavor, chemical composition and thermogravimetric of garlic samples were evaluated. The results indicated that FTC pretreatment reduced the drying time (22.22%-33.33%) and the energy consumption (14.25%-15.50%), owing to the water loss, the increase in free water, and the formation of porous structures. The FTC pretreatment improved thermal stability, flavor and chemical composition content of dried products. The antioxidant activity of polysaccharides extracted from FTC pretreated dried products was higher than that of the unpretreated dried product due to the reduction in polysaccharide molecular weight. This research could pave a route for future production of dried garlic slices having good quality by using the FTC pretreatment, with lower energy consumption and shorter drying time.
  11. Parasitological and molecular detection of human fascioliasis in a young man from Guizhou, China
    Chen MX, Zhang RL, Xu XN, Yu Q, Huang DN, Liu W, et al.
    Trop Biomed, 2020 Mar 01;37(1):50-57.
    PMID: 33612717
    A 24-year-old man born in Guizhou province was diagnosed with obstructive jaundice and bile duct stones in 2013. Four living trematodes were found during laparotomy and cholecystectomy. Based on the morphology and molecular genetics analysis of internal transcribed spacer and pcox1 genes of the flatworm specimens, the trematodes from the patient were confirmed to be Fasciola hepatica. This report provided the clinical and molecular diagnosis information on human fascioliasis, which is an emerging sanitary problem still ignored in China. Human fascioliasis constantly occurs due to climatic changes and frequency of human travel. Therefore, it deserves more attention from physicians working in both developing and developed countries.
  12. Intercontinental circulation of human influenza A(H1N2) reassortant viruses during the 2001-2002 influenza season
    Xu X, Smith CB, Mungall BA, Lindstrom SE, Hall HE, Subbarao K, et al.
    J Infect Dis, 2002 Nov 15;186(10):1490-3.
    PMID: 12404167
    Reassortant influenza A viruses bearing the H1 subtype of hemagglutinin (HA) and the N2 subtype of neuraminidase (NA) were isolated from humans in the United States, Canada, Singapore, Malaysia, India, Oman, Egypt, and several countries in Europe during the 2001-2002 influenza season. The HAs of these H1N2 viruses were similar to that of the A/New Caledonia/20/99(H1N1) vaccine strain both antigenically and genetically, and the NAs were antigenically and genetically related to those of recent human H3N2 reference strains, such as A/Moscow/10/99(H3N2). All 6 internal genes of the H1N2 reassortants examined originated from an H3N2 virus. This article documents the first widespread circulation of H1N2 reassortants on 4 continents. The current influenza vaccine is expected to provide good protection against H1N2 viruses, because it contains the A/New Caledonia/20/99(H1N1) and A/Moscow/10/99(H3N2)-like viruses, which have H1 and N2 antigens that are similar to those of recent H1N2 viruses.
  13. 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.
  14. Co-encapsulation of curcumin and quercetin with zein/HP-β-CD conjugates to enhance environmental resistance and antioxidant activity
    Qiu C, Zhang Z, Li X, Sang S, McClements DJ, Chen L, et al.
    NPJ Sci Food, 2023 Jun 14;7(1):29.
    PMID: 37316567 DOI: 10.1038/s41538-023-00186-2
    In this study, composite nanoparticles consisting of zein and hydroxypropyl beta-cyclodextrin were prepared using a combined antisolvent co-precipitation/electrostatic interaction method. The effects of calcium ion concentration on the stability of the composite nanoparticles containing both curcumin and quercetin were investigated. Moreover, the stability and bioactivity of the quercetin and curcumin were characterized before and after encapsulation. Fluorescence spectroscopy, Fourier Transform infrared spectroscopy, and X-ray diffraction analyses indicated that electrostatic interactions, hydrogen bonding, and hydrophobic interactions were the main driving forces for the formation of the composite nanoparticles. The addition of calcium ions promoted crosslinking of the proteins and affected the stability of the protein-cyclodextrin composite particles through electrostatic screening and binding effects. The addition of calcium ions to the composite particles improved the encapsulation efficiency, antioxidant activity, and stability of the curcumin and quercetin. However, there was an optimum calcium ion concentration (2.0 mM) that provided the best encapsulation and protective effects on the nutraceuticals. The calcium crosslinked composite particles were shown to maintain good stability under different pH and simulated gastrointestinal digestion conditions. These results suggest that zein-cyclodextrin composite nanoparticles may be useful plant-based colloidal delivery systems for hydrophobic bio-active agents.
  15. A novel porous lignocellulosic standing hierarchical hydroxyapatite for enhanced aqueous copper(II) removal
    Liang Y, Jin X, Xu X, Wu Y, Ghfar AA, Lam SS, et al.
    Sci Total Environ, 2024 Feb 20;912:168873.
    PMID: 38016558 DOI: 10.1016/j.scitotenv.2023.168873
    Potentially toxic metal-polluted water resources are a heavily discussed topic the pollution by potentially toxic metals can cause significant health risks. Nanomaterials are actively developed towards providing high specific surface area and creating active adsorption sites for the treatment and remediation of these polluted waters. In an effort to tackle the limitations of conventional type adsorbents, nano-hydroxyapatite (HAp) was developed in this study by in situ generation onto wood powder, resulting in the formation of uniform hybrid powder (HAp@wood composite) structure consisting of HAp nanoparticles that showed the removal efficiency up to 80 % after 10 min; the maximum adsorption capacity for Cu(II) ions (98.95 mg/g-HAp) was higher compared to agglomerated nano-HAp (72.85 mg/g-HAp). The adsorption capacity of Cu(II) remained stable (89.85-107.66 mg/g-HAp) during the four adsorption-desorption cycles in multi-component system, thereby demonstrating high selectivity for Cu(II). This approach of using nanoparticle is relatively simple yet effective in improving the adsorption of potentially toxic metals and the developed approach can be used to develop advanced nanocomposites in commercial wastewater treatment.
  16. A wAlbB Wolbachia Transinfection Displays Stable Phenotypic Effects across Divergent Aedes aegypti Mosquito Backgrounds
    Ross PA, Gu X, Robinson KL, Yang Q, Cottingham E, Zhang Y, et al.
    Appl Environ Microbiol, 2021 09 28;87(20):e0126421.
    PMID: 34379518 DOI: 10.1128/AEM.01264-21
    Aedes mosquitoes harboring intracellular Wolbachia bacteria are being released in arbovirus and mosquito control programs. With releases taking place around the world, understanding the contribution of host variation to Wolbachia phenotype is crucial. We generated a Wolbachia transinfection (wAlbBQ) in Aedes aegypti and performed backcrossing to introduce the infection into Australian or Malaysian nuclear backgrounds. Whole Wolbachia genome sequencing shows that the wAlbBQ transinfection is nearly identical to the reference wAlbB genome, suggesting few changes since the infection was first introduced to A. aegypti over 15 years ago. However, these sequences were distinct from other available wAlbB genome sequences, highlighting the potential diversity of wAlbB in natural Aedes albopictus populations. Phenotypic comparisons demonstrate the effects of wAlbB infection on egg hatching and nuclear background on fecundity and body size but no interactions between wAlbB infection and nuclear background for any trait. The wAlbB infection was stable at high temperatures and showed perfect maternal transmission and cytoplasmic incompatibility regardless of the host background. Our results demonstrate the stability of wAlbB across host backgrounds and point to its long-term effectiveness for controlling arbovirus transmission and mosquito populations. IMPORTANCE Wolbachia bacteria are being used to control the transmission of dengue virus and other arboviruses by mosquitoes. For Wolbachia release programs to be effective globally, Wolbachia infections must be stable across mosquito populations from different locations. In this study, we transferred Wolbachia (strain wAlbB) to Aedes aegypti mosquitoes with an Australian genotype and introduced the infection to Malaysian mosquitoes through backcrossing. We found that the phenotypic effects of Wolbachia are stable across both mosquito backgrounds. We sequenced the genome of wAlbB and found very few genetic changes despite spending over 15 years in a novel mosquito host. Our results suggest that the effects of Wolbachia infections are likely to remain stable across time and host genotype.
  17. Fulltext Extant primitively segmented spiders have recently diversified from an ancient lineage
    Xu X, Liu F, Cheng RC, Chen J, Xu X, Zhang Z, et al.
    Proc Biol Sci, 2015 Jun 07;282(1808):20142486.
    PMID: 25948684 DOI: 10.1098/rspb.2014.2486
    Living fossils are lineages that have retained plesiomorphic traits through long time periods. It is expected that such lineages have both originated and diversified long ago. Such expectations have recently been challenged in some textbook examples of living fossils, notably in extant cycads and coelacanths. Using a phylogenetic approach, we tested the patterns of the origin and diversification of liphistiid spiders, a clade of spiders considered to be living fossils due to their retention of arachnid plesiomorphies and their exclusive grouping in Mesothelae, an ancient clade sister to all modern spiders. Facilitated by original sampling throughout their Asian range, we here provide the phylogenetic framework necessary for reconstructing liphistiid biogeographic history. All phylogenetic analyses support the monophyly of Liphistiidae and of eight genera. As the fossil evidence supports a Carboniferous Euramerican origin of Mesothelae, our dating analyses postulate a long eastward over-land dispersal towards the Asian origin of Liphistiidae during the Palaeogene (39-58 Ma). Contrary to expectations, diversification within extant liphistiid genera is relatively recent, in the Neogene and Late Palaeogene (4-24 Ma). While no over-water dispersal events are needed to explain their evolutionary history, the history of liphistiid spiders has the potential to play prominently in vicariant biogeographic studies.
  18. Fulltext Genomic evidence for the Chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats
    Yu H, Xing YT, Meng H, He B, Li WJ, Qi XZ, et al.
    Sci Adv, 2021 Jun;7(26).
    PMID: 34162544 DOI: 10.1126/sciadv.abg0221
    The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat (Felis silvestris) subspecies and whether it has contributed to cat (F. s. catus) domestication in East Asia. Here, we sampled F. silvestris lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes, and multilocus regions from 270 modern or museum specimens. Genome-wide analyses classified the Chinese mountain cat as a wildcat conspecific F. s. bieti, which was not involved in cat domestication of China, thus supporting a single domestication origin arising from the African wildcat (F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat (F. s. ornata) to F. s. bieti, and contemporary gene flow between F. s. bieti and sympatric domestic cats that are likely recent Plateau arrivals, raises the prospect of disrupted wildcat genetic integrity, an issue with profound conservation implications.
  19. Educational environments in Asian medical schools: A cross-national comparison between Malaysia, Singapore, and China
    Arokiamary B, Russell V, Lim HA, Koay JM, Xia J, Zhao XH, et al.
    Asia Pac Psychiatry, 2021 Jun;13(2):e12454.
    PMID: 33646626 DOI: 10.1111/appy.12454
    INTRODUCTION: Perceptions of the educational environment (EE) represent an important source of information on medical students' learning experience. Understanding and addressing these perceptions can help inform initiatives designed to improve the learning experience and educational outcomes, while comparison of student perceptions across medical schools can provide an added perspective. The aim of the study was to compare the EEs of three Asian medical schools: Royal College of Surgeons in Ireland and University College Dublin Malaysia Campus, Yong Loo Lin School of Medicine, Singapore and Xiangya School of Medicine, China.

    METHODS: Medical students in the clinical years (N = 1063) participated in a cross-sectional study using the Dundee Ready Educational Environment Measure (DREEM). Data were analyzed using SPSS version 22.

    RESULTS: There were significant differences between the three medical schools in the total DREEM scores (F [2, 1059] = 38.29, p 

  20. Phylogenomic Analysis of Ultraconserved Elements Resolves the Evolutionary and Biogeographic History of Segmented Trapdoor Spiders
    Xu X, Su YC, Ho SYW, Kuntner M, Ono H, Liu F, et al.
    Syst Biol, 2021 Oct 13;70(6):1110-1122.
    PMID: 33367903 DOI: 10.1093/sysbio/syaa098
    The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show that the crown group of Liphistiidae appeared in the mid-Cretaceous at 102 Ma (95% credibility interval 92-113 Ma), but it was not until the Neogene that much of the diversification within the family occurred in mainland Southeast and East Asia. This diversification was coincident with tectonic events such as the extension of the East Asian continental margin, as well as geological upheavals in Indochina induced by the collision between India and Asia. Our study highlights the important role of major tectonic events in shaping the evolutionary history, present-day diversity, and geographical distribution of mesothele and liphistiid spiders. [biogeography; concatenation; Liphistiidae; molecular dating; summary coalescent; UCEs.].
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