Displaying publications 21 - 40 of 246 in total

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  1. Ge P, Li Q, Dong M, Niu Y, Han X, Xiong P, et al.
    Front Public Health, 2022;10:1074559.
    PMID: 36620260 DOI: 10.3389/fpubh.2022.1074559
    OBJECTIVE: To investigate the status of Chinese residents' self-medication behavior and the important factors to consider when purchasing OTC drugs, and to explore the related factors of the possibility that Chinese residents take medical staff's suggestions as important factors to consider when purchasing OTC drugs.

    STUDY DESIGN: A cross-sectional survey.

    METHODS: A questionnaire was developed for exploring the sociodemographic characteristics of the respondents, their self-medication status, and important considerations. The questionnaire includes several scales including Health Literacy Scale-Short Form (HLS-SF), EQ-5D Visual Analog Scale (EQ-5D-VAS), Big Five Inventary-10 Items (BFI-10), and New General Self Efficacy Scale (NGSES). After carrying out a multi-stage sampling method, the questionnaire was conducted nationwide from July 10 to September 15, 2021. Next, descriptive statistics were conducted to analyze the general features. Logistic regression was then used to analyze the related factors of the possibility that the respondents took the suggestions of medical staff as an important consideration when purchasing OTC drugs.

    RESULTS: Nine thousand two hundred fifty-six qualified questionnaires were received. 99.06% of Chinese adults had self-medication behaviors. The types of OTC drugs purchased most by the respondents were NSAIDs (5,421/9,256 people, 58.57%) and vitamins/minerals (4,851/9,256 people, 52.41%). 86.2% of the respondents took the suggestions of medical staff as an important consideration when purchasing OTC drugs. The results of multi-factor logistic regression showed that women, those living in the central and western regions of China, those suffering from chronic diseases, those with high agreeableness, high conscientiousness, high neuroticism and openness, high health literacy, high EQ-5D-VAS, and those with high self-efficacy are more likely to take medical staff's suggestions as important factors to consider.

    CONCLUSION: The vast majority of Chinese adults have self-medication behavior. Important considerations when purchasing OTC drugs include medical staff's suggestions, drug safety and drug efficacy. Whether residents take the suggestions of medical staff as an important consideration is related to their sociological characteristics, agreeableness, conscientiousness, neuroticism, openness, health literacy, self-assessment health status, and self-efficacy. When purchasing and using OTC drugs, residents should carefully listen to the suggestions from medical staff. They should also carefully consider their own conditions before buying OTC drugs.

  2. da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, et al.
    Gigascience, 2020 Jan 01;9(1).
    PMID: 31942620 DOI: 10.1093/gigascience/giz152
    BACKGROUND: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.

    FINDINGS: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

    CONCLUSIONS: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

  3. Luo H, Li Q, Pramanik J, Luo J, Guo Z
    Histol Histopathol, 2014 Oct;29(10):1287-93.
    PMID: 24515304
    Nanog is a potential stem cell marker and is considered a regeneration factor during tissue repair. In the present study, we investigated expression patterns of nanog in the rat heart after acute myocardial infarction by semi-quantitative RT-PCR, immunohistochemistry and Western blot analyses. Our results show that nanog at both mRNA and protein levels is positively expressed in myocardial cells, fibroblasts and small round cells in different myocardial zones at different stages after myocardial infarction, showing a spatio-temporal and dynamic change. After myocardial infarction, the nanog expression in fibroblasts and small round cells in the infarcted zone (IZ) is much stronger than that in the margin zone (MZ) and remote infarcted zone (RIZ). From day 7 after myocardial infarction, the fibroblasts and small cells strongly expressed nanog protein in the IZ, and a few myocardial cells in the MZ and the RIZ and the numbers of nanog-positive fibroblasts and small cells reached the highest peak at 21 days after myocardial infarction, but in this period the number of nanog-positive myocardial cells decreased gradually. At 28 days after myocardial infarction, the numbers of all nanog-positive cells decreased into a low level. Therefore, our data suggest that all myocardial cells, fibroblasts and small round cells are involved in myocardial reconstruction after cardiac infarction. The nanog-positive myocardial cells may respond to early myocardial repair, and the nanog-positive fibroblasts and small round cells are the main source for myocardial reconstruction after cardiac infarction.
  4. Tan T, Li Z, Liu H, Zanjani FG, Ouyang Q, Tang Y, et al.
    PMID: 30324036 DOI: 10.1109/JTEHM.2018.2865787
    Bronchoscopy inspection, as a follow-up procedure next to the radiological imaging, plays a key role in the diagnosis and treatment design for lung disease patients. When performing bronchoscopy, doctors have to make a decision immediately whether to perform a biopsy. Because biopsies may cause uncontrollable and life-threatening bleeding of the lung tissue, thus doctors need to be selective with biopsies. In this paper, to help doctors to be more selective on biopsies and provide a second opinion on diagnosis, we propose a computer-aided diagnosis (CAD) system for lung diseases, including cancers and tuberculosis (TB). Based on transfer learning (TL), we propose a novel TL method on the top of DenseNet: sequential fine-tuning (SFT). Compared with traditional fine-tuning (FT) methods, our method achieves the best performance. In a data set of recruited 81 normal cases, 76 TB cases and 277 lung cancer cases, SFT provided an overall accuracy of 82% while other traditional TL methods achieved an accuracy from 70% to 74%. The detection accuracy of SFT for cancers, TB, and normal cases are 87%, 54%, and 91%, respectively. This indicates that the CAD system has the potential to improve lung disease diagnosis accuracy in bronchoscopy and it may be used to be more selective with biopsies.
  5. Chen LC, Huang WC, Peng KY, Chen YY, Li SC, Syed Mohammed Nazri SK, et al.
    JACC Asia, 2023 Aug;3(4):664-675.
    PMID: 37614534 DOI: 10.1016/j.jacasi.2023.03.010
    BACKGROUND: Primary aldosteronism is characterized by inappropriate aldosterone production, and unilateral aldosterone-producing adenoma (uPA) is a common type of PA. KCNJ5 mutation is a protective factor in uPA; however, there is no preoperative approach to detect KCNJ5 mutation in patients with uPA.

    OBJECTIVES: This study aimed to provide a personalized surgical recommendation that enables more confidence in advising patients to pursue surgical treatment.

    METHODS: We enrolled 328 patients with uPA harboring KCNJ5 mutations (n = 158) or not (n = 170) who had undergone adrenalectomy. Eighty-seven features were collected, including demographics, various blood and urine test results, and clinical comorbidities. We designed 2 versions of the prediction model: one for institutes with complete blood tests (full version), and the other for institutes that may not be equipped with comprehensive testing facilities (condensed version).

    RESULTS: The results show that in the full version, the Light Gradient Boosting Machine outperformed other classifiers, achieving area under the curve and accuracy values of 0.905 and 0.864, respectively. The Light Gradient Boosting Machine also showed excellent performance in the condensed version, achieving area under the curve and accuracy values of 0.867 and 0.803, respectively.

    CONCLUSIONS: We simplified the preoperative diagnosis of KCNJ5 mutations successfully using machine learning. The proposed lightweight tool that requires only baseline characteristics and blood/urine test results can be widely applied and can aid personalized prediction during preoperative counseling for patients with uPA.

  6. Li P, Lei Y, Li Q, Lakshmipriya T, Gopinath SCB, Gong X
    J Anal Methods Chem, 2019;2019:6097375.
    PMID: 31534814 DOI: 10.1155/2019/6097375
    Every year, over 200 million adults are undergoing noncardiac surgery. These noncardiac surgery patients may face the risk of cardiac mortality and morbidity during the perioperative and recovery periods. Around ten million patients who underwent noncardiac surgery experience cardiac complications within the first 30 days of the postoperative period; the complications are myocardial infarction, cardiac death, and cardiac arrest. This cardiovascular risk is mostly faced by the patients having cerebrovascular or cardiac disease and the patients with the age greater than 50 years. Monitoring and treating cardiac diseases with a suitable biomarker during the perioperative period is necessary for the early recovery of noncardiac surgery patients. This review discussed the risk factors and the key guidelines to avoid the cardiovascular risks during the perioperative period of noncardiac surgery patients. In addition, the biomarkers and identification strategies for cardiac diseases are discussed.
  7. Chen J, Ahmad R, Suenaga H, Li W, Swain M, Li Q
    J Biomech, 2015 Feb 5;48(3):512-9.
    PMID: 25560272 DOI: 10.1016/j.jbiomech.2014.11.043
    Although implant-retained overdenture allows edentulous patients to take higher occlusal forces than the conventional complete dentures, the biomechanical influences have not been explored yet. Clinically, there is limited knowledge and means for predicting localized bone remodelling after denture treatment with and without implant support. By using finite element (FE) analysis, this article provides an in-silico approach to exploring the treatment effects on the oral mucosa and potential resorption of residual ridge under three different denture configurations in a patient-specific manner. Based on cone beam computerized tomography (CBCT) scans, a 3D heterogeneous FE model was created; and the supportive tissue, mucosa, was characterized as a hyperelastic material. A measured occlusal load (63N) was applied onto three virtual models, namely complete denture, two and four implant-retained overdentures. Clinically, the bone resorption was measured after one year in the two implant-retained overdenture treatment. Despite the improved stability and enhanced masticatory function, the implant-retained overdentures demonstrated higher hydrostatic stress in mucosa (43.6kPa and 39.9kPa for two and four implants) at the posterior ends of the mandible due to the cantilever effect, than the complete denture (33.4kPa). Hydrostatic pressure in the mucosa signifies a critical indicator and can be correlated with clinically measured bone resorption, pointing to severer mandibular ridge resorption posteriorly with implant-retained overdentures. This study provides a biomechanical basis for denture treatment planning to improve long-term outcomes with minimal residual ridge resorption.
  8. Zhu P, Li J, Wen X, Huang Y, Yang H, Wang S, et al.
    J Environ Manage, 2022 Feb 07;308:114682.
    PMID: 35144065 DOI: 10.1016/j.jenvman.2022.114682
    This study investigated the effects of biochar-based solid acids (SAs) on carbon conversion, alpha diversity and bacterial community succession during cow manure composting with the goal of providing a new strategy for rapid carbon conversion during composting. The addition of SA prolonged the thermophilic phase and accelerated the degradation of lignocellulose; in particular, the degradation time of cellulose was shortened by 50% and the humus content was increased by 22.56% compared with the control group (CK). In addition, high-throughput sequencing results showed that SA improved the alpha diversity and the relative abundance of thermophilic bacteria, mainly Actinobacteria, increased by 12.955% compared with CK. A redundancy analysis (RDA) showed that Actinobacteria was positively correlated with the transformation of carbon.
  9. Waqas MY, Lisi H, Yang P, Ullah S, Zhang L, Zhang Q, et al.
    J Exp Zool A Ecol Genet Physiol, 2015 Nov;323(9):655-65.
    PMID: 26350585 DOI: 10.1002/jez.1957
    The oviduct is the location of fertilization and sperm storage. We examined the ultrastructure of the oviduct epithelium and its glandular secretions in the isthmus, uterus and vagina of Chinese soft-shelled turtle Pelodiscus sinensis using light and transmission electron microscopy. The epithelium in these segments is lined with ciliated, secretory and other cells; the first two cell types span the entire epithelium, with secretory cells being predominant. The ciliated cells are characterized by the presence of a secretory vacuole that releases apocrine secretions into the lumen, whereas the secretory cells contain typical biphasic granules with both dark and light aspects. The third type of cells observed have wider proximal portion, abundant mitochondria, vacuoles, and narrow nuclei. The storage of spermatozoa is restricted to the isthmus, uterus, and vagina. In addition, the gland cells show prominent features, including the presence of granules of different shapes, sizes, and electron densities. The synthesis of these granules is described for the first time in this study. Mitochondria appear to play an important role in the formation of dense granules, the rough endoplasmic reticulum and microfilaments may also play a role in the maturation of these dense granules. After completing the maturation process, these granules are released into the lumen of the gland cells.
  10. Liu L, Sim SF, Lin S, Wan J, Zhang W, Li Q, et al.
    J Hazard Mater, 2021 Sep 05;417:126009.
    PMID: 34229376 DOI: 10.1016/j.jhazmat.2021.126009
    In this study, various HCl-supported hydrochar made from root powder of long-root Eichhornia crassipes were applied to adsorb aqueous sulfachloropyridazine (SCP). Adsorption capacity (qe μg g-1) was positively correlated with combined severity-CS. With CS increasing, carbonization degree, hydrophobicity, porosity and isoelectric point of hydrochar increased, but content of polar functional groups decreased. Hydrophobic interaction was important for SCP adsorption. A 24 × 36 peak area table was generated from 24 FT-IR absorbance spectra computed by peak detection algorithm. Afterwards, correlation analysis between qe μg g-1 and FT-IR peak area were conducted, indicating that wavenumbers at 555.4, 1227.47, 1374.51, 1604.5, 2901.4/2919.2 and 3514.63 cm-1 were helpful for SCP adsorption. Further, multivariate linear regression analyses showed that aromatic skeleton and phenolic hydroxyl were the two biggest contributors. Electrostatic attraction did not exist during the SCP adsorption process. Under strong acid condition, protonated amino groups in cationic SCP acting as a hydrogen donator interacted with electron-rich functional groups onto hydrochar by Hydrogen interaction. Under weak acid condition, neutral SCP served as an π electron donor to bond with hydrochar by π-π electron donator-acceptor interaction. This work could guide the functional groups modification strategy of hydrochar to make better use of it in water purification field.
  11. Yang C, Li X, Li Q, Li H, Qiao L, Guo Z, et al.
    J Mol Neurosci, 2018 Feb;64(2):287-299.
    PMID: 29285739 DOI: 10.1007/s12031-017-1019-5
    During nervous system development, neurons project axons over long distances to reach the appropriate targets for correct neural circuit formation. Sonic hedgehog (Shh) is a secreted protein and plays a key role in regulating vertebrate embryogenesis, especially in central nervous system (CNS) patterning, including neuronal migration and axonal projection in the brain and spinal cord. In the developing ventral midbrain, Shh is sufficient to specify a striped pattern of cell fates. Little is known about the molecular mechanisms underlying the Shh regulation of the neural precursor cell fate during the optic tectum development. Here, we aimed at studying how Shh might regulate chicken optic tectum patterning. In the present study, in ovo electroporation methods were employed to achieve the overexpression of Shh in the optic tectum during chicken embryo development. Besides, the study combined in ovo electroporation and neuron isolation culturing to study the function of Shh in vivo and in vitro. The fluorescent immunohistochemistry methods were used to check the related indicators. The results showed that Shh overexpression caused 87.8% of cells to be distributed to the stratum griseum central (SGC) layer, while only 39.3% of the GFP-transfected cells resided in the SGC layer in the control group. Shh overexpression also reduced the axon length in vivo and in vitro. In conclusion, we provide evidence that Shh regulates the neural precursor cell fate during chicken optic tectum development. Shh overexpression impairs neuronal migration and may affect the fate determination of transfected neurons.
  12. Chen J, Ahmad R, Li W, Swain M, Li Q
    J R Soc Interface, 2015 Aug 06;12(109):20150325.
    PMID: 26224566 DOI: 10.1098/rsif.2015.0325
    The prevalence of prosthodontic treatment has been well recognized, and the need is continuously increasing with the ageing population. While the oral mucosa plays a critical role in the treatment outcome, the associated biomechanics is not yet fully understood. Using the literature available, this paper provides a critical review on four aspects of mucosal biomechanics, including static, dynamic, volumetric and interactive responses, which are interpreted by its elasticity, viscosity/permeability, apparent Poisson's ratio and friction coefficient, respectively. Both empirical studies and numerical models are analysed and compared to gain anatomical and physiological insights. Furthermore, the clinical applications of such biomechanical knowledge on the mucosa are explored to address some critical concerns, including stimuli for tissue remodelling (interstitial hydrostatic pressure), pressure-pain thresholds, tissue displaceability and residual bone resorption. Through this review, the state of the art in mucosal biomechanics and their clinical implications are discussed for future research interests, including clinical applications, computational modelling, design optimization and prosthetic fabrication.
  13. Zhong J, Guazzato M, Chen J, Zhang Z, Sun G, Huo X, et al.
    J Mech Behav Biomed Mater, 2020 02;102:103490.
    PMID: 31877512 DOI: 10.1016/j.jmbbm.2019.103490
    Mechanical failure of zirconia-based full-arch implant-supported fixed dental prostheses (FAFDPs) remains a critical issue in prosthetic dentistry. The option of full-arch implant treatment and the biomechanical behaviour within a sophisticated screw-retained prosthetic structure have stimulated considerable interest in fundamental and clinical research. This study aimed to analyse the biomechanical responses of zirconia-based FAFDPs with different implant configurations (numbers and distributions), thereby predicting the possible failure sites and the optimum configuration from biomechanical aspect by using finite element method (FEM). Five 3D finite element (FE) models were constructed with patient-specific heterogeneous material properties of mandibular bone. The results were reported using volume-averaged von-Mises stresses (σVMVA) to eliminate numerical singularities. It was found that wider placement of multi-unit copings was preferred as it reduces the cantilever effect on denture. Within the limited areas of implant insertion, the adoption of angled multi-unit abutments allowed the insertion of oblique implants in the bone and wider distribution of the multi-unit copings in the prosthesis, leading to lower stress concentration on both mandibular bone and prosthetic components. Increasing the number of supporting implants in a FAFDPs reduced loading on each implant, although it may not necessarily reduce the stress concentration in the most posterior locations significantly. Overall, the 6-implant configuration was a preferable configuration as it provided the most balanced mechanical performance in this patient-specific case.
  14. Law JKC, Ng WM, Chong WH, Li Q, Zhang L, Khoerunnisa F, et al.
    Langmuir, 2023 Apr 11;39(14):4904-4916.
    PMID: 36992604 DOI: 10.1021/acs.langmuir.2c03164
    The possible magnetophoretic migration of iron oxide nanoparticles through the cellulosic matrix within a single layer of paper is challenging with its underlying mechanism remained unclear. Even with the recent advancements of theoretical understanding on magnetophoresis, mainly driven by cooperative and hydrodynamics phenomena, the contributions of these two mechanisms on possible penetration of magnetic nanoparticles through cellulosic matrix of paper have yet been proven. Here, by using iron oxide nanoparticles (IONPs), both nanospheres and nanorods, we have investigated the migration kinetics of these nanoparticles through grade 4 Whatman filter paper with a particle retention of 20-25 μm. By performing droplet tracking experiments, the real-time stained area growth of the particle droplet on the filter paper, under the influences of a grade N40 NdFeB magnet, were recorded. Our results show that the spatial and temporal expansion of the IONP stain is biased toward the magnet and such an effect is dependent on (i) particle concentration and (ii) particle shape. The kinetics data were first analyzed by treating it as a radial wicking fluid, and later the IONP distribution within the cellulosic matrix was investigated by optical microscopy. The macroscopic flow front velocities of the stained area ranged from 259 μm/s to 16 040 μm/s. Moreover, the microscopic magnetophoretic velocity of nanorod cluster was also successfully measured as ∼214 μm/s. Findings in this work have indirectly revealed the strong influence of cooperative magnetophoresis and the engineering feasibility of paper-based magnetophoretic technology by taking advantage of magnetoshape anisotropy effect of the particles.
  15. Yan G, Li Q, Hong X, Gopinath SCB, Anbu P, Li C, et al.
    Mikrochim Acta, 2021 05 11;188(6):185.
    PMID: 33977395 DOI: 10.1007/s00604-021-04836-8
    An abdominal aortic aneurysm (AAA) is abnormal swelling in the abdominal aorta and a prevalent life-threatening disease. This research introduces a new interdigitated microelectrode (IDME)-sensing surface modified by iron oxide nanoworms (IONWs) for detecting the AAA biomarker insulin-like growth factor-1 (IGF1). A sandwich pattern was formulated with the IGF1 aptamer and IGFBP1 (IGF binding protein-1) on the IONW-constructed IDME hybrid to identify IGF1. The surface morphology of the IONWs revealed a uniform distribution of worm-like structures (80-100 nm) as confirmed by FESEM and FETEM analyses. Further, the presence of the major elements, Fe and O, was confirmed by EDX and XPS studies. The crystal planes that appeared in the IONW reflect cubic magnetite. IONW-modified IDME attained a limit of detection for IGF1 of 1 fM (3σ) with an aptamer-IGF1-IGFBP1 sandwich. This sandwich with IGFBP1 enhanced the current level at all concentrations of IGF1 and displayed linearity in the range 1 fM to 100 pM with a determination coefficient of R2 = 0.9373 [y = 3.38221x - 4.79]. Control experiments with complementary aptamer sequences, IGF2 and IGFBP3 did not show notable signal changes, indicating the specific detection of IGF1. This IONW constructed electrode helps to achieve the detection of low amounts of IGF1 and diagnose AAA at the stage prior to rupture.
  16. Al-Hada NM, Md Kasmani R, Kasim H, Al-Ghaili AM, Saleh MA, Banoqitah EM, et al.
    Nanomaterials (Basel), 2021 Aug 22;11(8).
    PMID: 34443973 DOI: 10.3390/nano11082143
    In the present work, a thermal treatment technique is applied for the synthesis of CexSn1-xO2 nanoparticles. Using this method has developed understanding of how lower and higher precursor values affect the morphology, structure, and optical properties of CexSn1-xO2 nanoparticles. CexSn1-xO2 nanoparticle synthesis involves a reaction between cerium and tin sources, namely, cerium nitrate hexahydrate and tin (II) chloride dihydrate, respectively, and the capping agent, polyvinylpyrrolidone (PVP). The findings indicate that lower x values yield smaller particle size with a higher energy band gap, while higher x values yield a larger particle size with a smaller energy band gap. Thus, products with lower x values may be suitable for antibacterial activity applications as smaller particles can diffuse through the cell wall faster, while products with higher x values may be suitable for solar cell energy applications as more electrons can be generated at larger particle sizes. The synthesized samples were profiled via a number of methods, such as scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FT-IR). As revealed by the XRD pattern analysis, the CexSn1-xO2 nanoparticles formed after calcination reflect the cubic fluorite structure and cassiterite-type tetragonal structure of CexSn1-xO2 nanoparticles. Meanwhile, using FT-IR analysis, Ce-O and Sn-O were confirmed as the primary bonds of ready CexSn1-xO2 nanoparticle samples, whilst TEM analysis highlighted that the average particle size was in the range 6-21 nm as the precursor concentration (Ce(NO3)3·6H2O) increased from 0.00 to 1.00. Moreover, the diffuse UV-visible reflectance spectra used to determine the optical band gap based on the Kubelka-Munk equation showed that an increase in x value has caused a decrease in the energy band gap and vice versa.
  17. Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, et al.
    Nature, 2021 Apr;592(7856):E24.
    PMID: 33833441 DOI: 10.1038/s41586-021-03473-8
  18. Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, et al.
    Nature, 2020 11;587(7833):252-257.
    PMID: 33177665 DOI: 10.1038/s41586-020-2873-9
    Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
  19. Lawrenson K, Li Q, Kar S, Seo JH, Tyrer J, Spindler TJ, et al.
    Nat Commun, 2015 Sep 22;6:8234.
    PMID: 26391404 DOI: 10.1038/ncomms9234
    Genome-wide association studies have reported 11 regions conferring risk of high-grade serous epithelial ovarian cancer (HGSOC). Expression quantitative trait locus (eQTL) analyses can identify candidate susceptibility genes at risk loci. Here we evaluate cis-eQTL associations at 47 regions associated with HGSOC risk (P≤10(-5)). For three cis-eQTL associations (P<1.4 × 10(-3), FDR<0.05) at 1p36 (CDC42), 1p34 (CDCA8) and 2q31 (HOXD9), we evaluate the functional role of each candidate by perturbing expression of each gene in HGSOC precursor cells. Overexpression of HOXD9 increases anchorage-independent growth, shortens population-doubling time and reduces contact inhibition. Chromosome conformation capture identifies an interaction between rs2857532 and the HOXD9 promoter, suggesting this SNP is a leading causal variant. Transcriptomic profiling after HOXD9 overexpression reveals enrichment of HGSOC risk variants within HOXD9 target genes (P=6 × 10(-10) for risk variants (P<10(-4)) within 10 kb of a HOXD9 target gene in ovarian cells), suggesting a broader role for this network in genetic susceptibility to HGSOC.
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