Displaying publications 1 - 20 of 246 in total

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  1. Fulltext A Deep Neural Network for Simultaneous Estimation of b Jet Energy and Resolution
    Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Bergauer T, Dragicevic M, et al.
    Comput Softw Big Sci, 2020;4(1):10.
    PMID: 33196702 DOI: 10.1007/s41781-020-00041-z
    We describe a method to obtain point and dispersion estimates for the energies of jets arising from b quarks produced in proton-proton collisions at an energy of s = 13 TeV at the CERN LHC. The algorithm is trained on a large sample of simulated b jets and validated on data recorded by the CMS detector in 2017 corresponding to an integrated luminosity of 41 fb - 1 . A multivariate regression algorithm based on a deep feed-forward neural network employs jet composition and shape information, and the properties of reconstructed secondary vertices associated with the jet. The results of the algorithm are used to improve the sensitivity of analyses that make use of b jets in the final state, such as the observation of Higgs boson decay to b b ¯ .
  2. A comparative study on complete and implant retained denture treatments: a biomechanics perspective
    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.
  3. Fulltext A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea
    Xu X, Shen Y, Zhang Y, Li Q, Wang W, Chen L, et al.
    Front Plant Sci, 2022;13:1075353.
    PMID: 36684775 DOI: 10.3389/fpls.2022.1075353
    In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
  4. A deep convolutional neural network for the automatic segmentation of glioblastoma brain tumor: Joint spatial pyramid module and attention mechanism network
    Liu H, Huang J, Li Q, Guan X, Tseng M
    Artif Intell Med, 2024 Feb;148:102776.
    PMID: 38325925 DOI: 10.1016/j.artmed.2024.102776
    This study proposes a deep convolutional neural network for the automatic segmentation of glioblastoma brain tumors, aiming sat replacing the manual segmentation method that is both time-consuming and labor-intensive. There are many challenges for automatic segmentation to finely segment sub-regions from multi-sequence magnetic resonance images because of the complexity and variability of glioblastomas, such as the loss of boundary information, misclassified regions, and subregion size. To overcome these challenges, this study introduces a spatial pyramid module and attention mechanism to the automatic segmentation algorithm, which focuses on multi-scale spatial details and context information. The proposed method has been tested in the public benchmarks BraTS 2018, BraTS 2019, BraTS 2020 and BraTS 2021 datasets. The Dice score on the enhanced tumor, whole tumor, and tumor core were respectively 79.90 %, 89.63 %, and 85.89 % on the BraTS 2018 dataset, respectively 77.14 %, 89.58 %, and 83.33 % on the BraTS 2019 dataset, and respectively 77.80 %, 90.04 %, and 83.18 % on the BraTS 2020 dataset, and respectively 83.48 %, 90.70 %, and 88.94 % on the BraTS 2021 dataset offering performance on par with that of state-of-the-art methods with only 1.90 M parameters. In addition, our approach significantly reduced the requirements for experimental equipment, and the average time taken to segment one case was only 1.48 s; these two benefits rendered the proposed network intensely competitive for clinical practice.
  5. Fulltext A draft genome sequence of the elusive giant squid, Architeuthis dux
    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.

  6. Fulltext A multi-dimensional search for new heavy resonances decaying to boosted W W , W Z , or Z Z boson pairs in the dijet final state at 13  Te
    Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Bergauer T, Brandstetter J, et al.
    Eur Phys J C Part Fields, 2020;80(3):237.
    PMID: 32215380 DOI: 10.1140/epjc/s10052-020-7773-5
    A search in an all-jet final state for new massive resonances decaying to W W , W Z , or Z Z boson pairs using a novel analysis method is presented. The analysis is performed on data corresponding to an integrated luminosity of 77.3 fb - 1 recorded with the CMS experiment at the LHC at a centre-of-mass energy of 13  Te . The search is focussed on potential narrow-width resonances with masses above 1.2  Te , where the decay products of each W or Z boson are expected to be collimated into a single, large-radius jet. The signal is extracted using a three-dimensional maximum likelihood fit of the two jet masses and the dijet invariant mass, yielding an improvement in sensitivity of up to 30% relative to previous search methods. No excess is observed above the estimated standard model background. In a heavy vector triplet model, spin-1 Z ' and W ' resonances with masses below 3.5 and 3.8   Te , respectively, are excluded at 95% confidence level. In a bulk graviton model, upper limits on cross sections are set between 27 and 0.2 fb for resonance masses between 1.2 and 5.2   Te , respectively. The limits presented in this paper are the best to date in the dijet final state.
  7. A search for decays of the Higgs boson to invisible particles in events with a top-antitop quark pair or a vector boson in proton-proton collisions at s=13TeV
    Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, Damanakis K, et al.
    Eur Phys J C Part Fields, 2023;83(10):933.
    PMID: 37855556 DOI: 10.1140/epjc/s10052-023-11952-7
    A search for decays to invisible particles of Higgs bosons produced in association with a top-antitop quark pair or a vector boson, which both decay to a fully hadronic final state, has been performed using proton-proton collision data collected at s=13TeV by the CMS experiment at the LHC, corresponding to an integrated luminosity of 138fb-1. The 95% confidence level upper limit set on the branching fraction of the 125GeV Higgs boson to invisible particles, B(H→inv), is 0.54 (0.39 expected), assuming standard model production cross sections. The results of this analysis are combined with previous B(H→inv) searches carried out at s=7, 8, and 13TeV in complementary production modes. The combined upper limit at 95% confidence level on B(H→inv) is 0.15 (0.08 expected).
  8. Fulltext A search for new phenomena in pp collisions at [Formula: see text] in final states with missing transverse momentum and at least one jet using the [Formula: see text] variable
    Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2017;77(5):294.
    PMID: 28579921 DOI: 10.1140/epjc/s10052-017-4787-8
    A search for new phenomena is performed in final states containing one or more jets and an imbalance in transverse momentum in pp collisions at a centre-of-mass energy of 13[Formula: see text]. The analysed data sample, recorded with the CMS detector at the CERN LHC, corresponds to an integrated luminosity of 2.3[Formula: see text]. Several kinematic variables are employed to suppress the dominant background, multijet production, as well as to discriminate between other standard model and new physics processes. The search provides sensitivity to a broad range of new-physics models that yield a stable weakly interacting massive particle. The number of observed candidate events is found to agree with the expected contributions from standard model processes, and the result is interpreted in the mass parameter space of fourteen simplified supersymmetric models that assume the pair production of gluinos or squarks and a range of decay modes. For models that assume gluino pair production, masses up to 1575 and 975[Formula: see text] are excluded for gluinos and neutralinos, respectively. For models involving the pair production of top squarks and compressed mass spectra, top squark masses up to 400[Formula: see text] are excluded.
  9. Fulltext Air quality changes during the COVID-19 lockdown over the Yangtze River Delta Region: An insight into the impact of human activity pattern changes on air pollution variation
    Li L, Li Q, Huang L, Wang Q, Zhu A, Xu J, et al.
    Sci Total Environ, 2020 Aug 25;732:139282.
    PMID: 32413621 DOI: 10.1016/j.scitotenv.2020.139282
    The outbreak of COVID-19 has spreaded rapidly across the world. To control the rapid dispersion of the virus, China has imposed national lockdown policies to practise social distancing. This has led to reduced human activities and hence primary air pollutant emissions, which caused improvement of air quality as a side-product. To investigate the air quality changes during the COVID-19 lockdown over the YRD Region, we apply the WRF-CAMx modelling system together with monitoring data to investigate the impact of human activity pattern changes on air quality. Results show that human activities were lowered significantly during the period: industrial operations, VKT, constructions in operation, etc. were significantly reduced, leading to lowered SO2, NOx, PM2.5 and VOCs emissions by approximately 16-26%, 29-47%, 27-46% and 37-57% during the Level I and Level II response periods respectively. These emission reduction has played a significant role in the improvement of air quality. Concentrations of PM2.5, NO2 and SO2 decreased by 31.8%, 45.1% and 20.4% during the Level I period; and 33.2%, 27.2% and 7.6% during the Level II period compared with 2019. However, ozone did not show any reduction and increased greatly. Our results also show that even during the lockdown, with primary emissions reduction of 15%-61%, the daily average PM2.5 concentrations range between 15 and 79 μg m-3, which shows that background and residual pollutions are still high. Source apportionment results indicate that the residual pollution of PM2.5 comes from industry (32.2-61.1%), mobile (3.9-8.1%), dust (2.6-7.7%), residential sources (2.1-28.5%) in YRD and 14.0-28.6% contribution from long-range transport coming from northern China. This indicates that in spite of the extreme reductions in primary emissions, it cannot fully tackle the current air pollution. Re-organisation of the energy and industrial strategy together with trans-regional joint-control for a full long-term air pollution plan need to be further taken into account.
  10. An interdigitated aptasensor to detect interleukin-6 for diagnosing rheumatoid arthritis in serum
    Chen N, Yang H, Li Q, Song L, Gopinath SCB, Wu D
    Biotechnol Appl Biochem, 2021 Dec;68(6):1479-1485.
    PMID: 33244818 DOI: 10.1002/bab.2068
    Rheumatoid arthritis (RA) is an autoimmune disorder causing chronic inflammation in the small joints of the articular bone and destruction of articular cartilage. RA causes stiffness, pain, joint destruction, substantial comorbidity, and functional disability. Early-stage diagnosis of RA can help in the treatment of the disease and expand the patient life span. Interleukins are a group of inflammatory cytokines; in particular, an abundance of interleukin-6 (IL-6) was found in the synovial fluid and serum. In RA patients, the levels of IL-6 have been found to be correlated with the disease, and this work focused on detecting IL-6 by its aptamer with the help of a biotin-streptavidin strategy on an interdigitated electrode. A sensitivity of 1 fM (0.021 pg/mL) and a limit of detection of 10 fM (0.21 pg/mL) were found by a linear regression [y = 0.6413x - 0.6249; R² = 0.952] of the linear range from 1 fM to 100 pM. This method enhanced the immobilization of higher aptamer molecules for recognizing RA in serum-containing samples and is applicable to other diseases.
  11. An iron oxide nanoworm hybrid on an interdigitated microelectrode silica surface to detect abdominal aortic aneurysms
    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.
  12. Fulltext Author Correction: Dense sampling of bird diversity increases power of comparative genomics
    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
  13. Azimuthal Correlations within Exclusive Dijets with Large Momentum Transfer in Photon-Lead Collisions
    Tumasyan A, Adam W, Bergauer T, Dragicevic M, Del Valle AE, Frühwirth R, et al.
    Phys Rev Lett, 2023 Aug 04;131(5):051901.
    PMID: 37595238 DOI: 10.1103/PhysRevLett.131.051901
    The structure of nucleons is multidimensional and depends on the transverse momenta, spatial geometry, and polarization of the constituent partons. Such a structure can be studied using high-energy photons produced in ultraperipheral heavy-ion collisions. The first measurement of the azimuthal angular correlations of exclusively produced events with two jets in photon-lead interactions at large momentum transfer is presented, a process that is considered to be sensitive to the underlying nuclear gluon polarization. This study uses a data sample of ultraperipheral lead-lead collisions at sqrt[s_{NN}]=5.02  TeV, corresponding to an integrated luminosity of 0.38  nb^{-1}, collected with the CMS experiment at the LHC. The measured second harmonic of the correlation between the sum and difference of the two jet transverse momentum vectors is found to be positive, and rising, as the dijet transverse momentum increases. A well-tuned model that has been successful at describing a wide range of proton scattering data from the HERA experiments fails to describe the observed correlations, suggesting the presence of gluon polarization effects.
  14. Azimuthal correlations in Z +jets events in proton-proton collisions at s=13TeV
    Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, Damanakis K, et al.
    Eur Phys J C Part Fields, 2023;83(8):722.
    PMID: 37578844 DOI: 10.1140/epjc/s10052-023-11833-z
    The production of Z bosons associated with jets is measured in pp collisions at s=13TeV with data recorded with the CMS experiment at the LHC corresponding to an integrated luminosity of 36.3fb-1. The multiplicity of jets with transverse momentum pT>30GeV is measured for different regions of the Z boson's pT(Z), from lower than 10GeV to higher than 100GeV. The azimuthal correlation Δϕ between the Z boson and the leading jet, as well as the correlations between the two leading jets are measured in three regions of pT(Z). The measurements are compared with several predictions at leading and next-to-leading orders, interfaced with parton showers. Predictions based on transverse-momentum dependent parton distributions and corresponding parton showers give a good description of the measurement in the regions where multiple parton interactions and higher jet multiplicities are not important. The effects of multiple parton interactions are shown to be important to correctly describe the measured spectra in the low pT(Z) regions.
  15. Fulltext Azimuthal separation in nearly back-to-back jet topologies in inclusive 2- and 3-jet events in pp collisions at s = 13 Te
    Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2019;79(9):773.
    PMID: 31713548 DOI: 10.1140/epjc/s10052-019-7276-4
    A measurement for inclusive 2- and 3-jet events of the azimuthal correlation between the two jets with the largest transverse momenta, Δ ϕ 12 , is presented. The measurement considers events where the two leading jets are nearly collinear ("back-to-back") in the transverse plane and is performed for several ranges of the leading jet transverse momentum. Proton-proton collision data collected with the CMS experiment at a center-of-mass energy of 13 Te and corresponding to an integrated luminosity of 35.9 fb - 1 are used. Predictions based on calculations using matrix elements at leading-order and next-to-leading-order accuracy in perturbative quantum chromodynamics supplemented with leading-log parton showers and hadronization are generally in agreement with the measurements. Discrepancies between the measurement and theoretical predictions are as large as 15%, mainly in the region 177 ∘ < Δ ϕ 12 < 180 ∘ . The 2- and 3-jet measurements are not simultaneously described by any of models.
  16. Biochar-based solid acid accelerated carbon conversion by increasing the abundance of thermophilic bacteria in the cow manure composting process
    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.
  17. Fulltext Biomechanics of oral mucosa
    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.
  18. Burden and trends of iodine deficiency in Asia from 1990 to 2019
    Wei R, Wang Z, Zhang X, Wang X, Xu Y, Li Q
    Public Health, 2023 Sep;222:75-84.
    PMID: 37531713 DOI: 10.1016/j.puhe.2023.06.034
    OBJECTIVES: Understanding iodine deficiency (ID) burdens and trends in Asia can help guide effective intervention strategies. This study aims to report the incidence, prevalence, and disability-adjusted life years (DALYs) of ID in 48 Asian countries during the period 1990-2019.

    STUDY DESIGN: Data on ID were retrieved from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 and estimated by age, sex, geographical region, and sociodemographic index (SDI).

    METHODS: The estimated annual percentage change (EAPC) was calculated to evaluate the changing trend of age-standardized incidence rate (ASIR), age-standardized prevalence rate (ASPR), and age-standardized DALYs rate (ASDR) related to ID during the period 1990-2019.

    RESULTS: In Asia, there were 126,983,965.8 cases with 5,466,213.1 new incidence and 1,765,995.5 DALYs of ID in 2019. Between 1999 and 2019, the EAPC in ASIR, ASPR and ASDR were -0.6 (95% confidence interval [CI], -0.8 to -0.4), -0.9 (95% CI, -1.2 to -0.7), and -1.6 (95% CI, -1.8 to -1.5), respectively. Malaysia charted the largest decrease in ASIR, ASPR, and ASDR (82.4%, 85.3%, and 80.9% separately), whereas the Philippines and Pakistan were the only two countries that witnessed an increase in ASIR and ASPR. ID burdens were more pronounced in women, countries located to the south of the Himalayas, and low-middle SDI regions.

    CONCLUSIONS: The incidence, prevalence, and DALYs of ID in Asia substantially decreased from 1990 to 2019. Women and low-middle SDI countries have relatively high ID burdens. Governments need to pay constant attention to the implementation and monitoring of universal salt iodization.

  19. Fulltext CMS pythia  8 colour reconnection tunes based on underlying-event data
    Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, Damanakis K, et al.
    Eur Phys J C Part Fields, 2023;83(7):587.
    PMID: 37440247 DOI: 10.1140/epjc/s10052-023-11630-8
    New sets of parameter tunes for two of the colour reconnection models, quantum chromodynamics-inspired and gluon-move, implemented in the pythia  8 event generator, are obtained based on the default CMS pythia  8 underlying-event tune, CP5. Measurements sensitive to the underlying event performed by the CMS experiment at centre-of-mass energies s=7 and 13TeV, and by the CDF experiment at 1.96TeV are used to constrain the parameters of colour reconnection models and multiple-parton interactions simultaneously. The new colour reconnection tunes are compared with various measurements at 1.96, 7, 8, and 13TeV including measurements of the underlying-event, strange-particle multiplicities, jet substructure observables, jet shapes, and colour flow in top quark pair (tt¯) events. The new tunes are also used to estimate the uncertainty related to colour reconnection modelling in the top quark mass measurement using the decay products of tt¯ events in the semileptonic channel at 13TeV.
  20. Fulltext Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer
    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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