Displaying publications 41 - 60 of 74 in total

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  1. Sirunyan AM, Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, et al.
    Phys Rev Lett, 2021 Jun 25;126(25):252002.
    PMID: 34241533 DOI: 10.1103/PhysRevLett.126.252002
    A fiducial cross section for Wγ production in proton-proton collisions is measured at a center-of-mass energy of 13 TeV in 137  fb^{-1} of data collected using the CMS detector at the LHC. The W→eν and μν decay modes are used in a maximum-likelihood fit to the lepton-photon invariant mass distribution to extract the combined cross section. The measured cross section is compared with theoretical expectations at next-to-leading order in quantum chromodynamics. In addition, 95% confidence level intervals are reported for anomalous triple-gauge couplings within the framework of effective field theory.
  2. Sirunyan AM, Tumasyan A, Adam W, Bergauer T, Dragicevic M, Erö J, et al.
    Eur Phys J C Part Fields, 2021;81(4):378.
    PMID: 34727142 DOI: 10.1140/epjc/s10052-021-09014-x
    The rate for Higgs ( H ) bosons production in association with either one ( t H ) or two ( t t ¯ H ) top quarks is measured in final states containing multiple electrons, muons, or tau leptons decaying to hadrons and a neutrino, using proton-proton collisions recorded at a center-of-mass energy of 13 TeV by the CMS experiment. The analyzed data correspond to an integrated luminosity of 137 fb - 1 . The analysis is aimed at events that contain H → W W , H → τ τ , or H → Z Z decays and each of the top quark(s) decays either to lepton+jets or all-jet channels. Sensitivity to signal is maximized by including ten signatures in the analysis, depending on the lepton multiplicity. The separation among t H , t t ¯ H , and the backgrounds is enhanced through machine-learning techniques and matrix-element methods. The measured production rates for the t t ¯ H and t H signals correspond to 0.92 ± 0.19 (stat) - 0.13 + 0.17 (syst) and 5.7 ± 2.7 (stat) ± 3.0 (syst) of their respective standard model (SM) expectations. The corresponding observed (expected) significance amounts to 4.7 (5.2) standard deviations for t t ¯ H , and to 1.4 (0.3) for t H production. Assuming that the Higgs boson coupling to the tau lepton is equal in strength to its expectation in the SM, the coupling y t of the Higgs boson to the top quark divided by its SM expectation, κ t = y t / y t SM , is constrained to be within - 0.9 < κ t < - 0.7 or 0.7 < κ t < 1.1 , at 95% confidence level. This result is the most sensitive measurement of the t t ¯ H production rate to date.
  3. Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, Damanakis K, et al.
    Phys Rev Lett, 2023 Sep 22;131(12):121901.
    PMID: 37802954 DOI: 10.1103/PhysRevLett.131.121901
    The dependence of the ratio between the B_{s}^{0} and B^{+} hadron production fractions, f_{s}/f_{u}, on the transverse momentum (p_{T}) and rapidity of the B mesons is studied using the decay channels B_{s}^{0}→J/ψϕ and B^{+}→J/ψK^{+}. The analysis uses a data sample of proton-proton collisions at a center-of-mass energy of 13 TeV, collected by the CMS experiment in 2018 and corresponding to an integrated luminosity of 61.6  fb^{-1}. The f_{s}/f_{u} ratio is observed to depend on the B p_{T} and to be consistent with becoming asymptotically constant at large p_{T}. No rapidity dependence is observed. The ratio of the B^{0} to B^{+} meson production fractions, f_{d}/f_{u}, is also measured, for the first time in proton-proton collisions, using the B^{0}→J/ψK^{*0} decay channel. The result is found to be within 1 standard deviation of unity and independent of p_{T} and rapidity, as expected from isospin invariance.
  4. CMS Collaboration, Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Bergauer T, et al.
    Eur Phys J C Part Fields, 2021;81(7):629.
    PMID: 34727144 DOI: 10.1140/epjc/s10052-021-09236-z
    Results of the Model Unspecific Search in CMS (MUSiC), using proton-proton collision data recorded at the LHC at a centre-of-mass energy of 13 TeV , corresponding to an integrated luminosity of 35.9 fb - 1 , are presented. The MUSiC analysis searches for anomalies that could be signatures of physics beyond the standard model. The analysis is based on the comparison of observed data with the standard model prediction, as determined from simulation, in several hundred final states and multiple kinematic distributions. Events containing at least one electron or muon are classified based on their final state topology, and an automated search algorithm surveys the observed data for deviations from the prediction. The sensitivity of the search is validated using multiple methods. No significant deviations from the predictions have been observed. For a wide range of final state topologies, agreement is found between the data and the standard model simulation. This analysis complements dedicated search analyses by significantly expanding the range of final states covered using a model independent approach with the largest data set to date to probe phase space regions beyond the reach of previous general searches.
  5. Teng H, Chen Y, Lin X, Lv Q, Chai TT, Wong FC, et al.
    Food Chem Toxicol, 2019 Jul;129:138-143.
    PMID: 31034934 DOI: 10.1016/j.fct.2019.04.043
    The aim of this study was to assess the inhibitory effects of Sonchus olearleu extract on the generation of heterocyclic amines in roasted pork patties cooked by pan-frying. All samples were cooked for two different durations (45 min and 105 min) under 200 °C and 230 °C. 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), 2-ami- no-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), 2-amino-3,4,8-trimethylimidazo[4,5-f]quinox-aline (4,8-DiMeIQx), harman, and norharman were detected and quantified. In patties cooked at 230 °C for 105 min, S. olearleu extract (0.5%) significantly inhibited the formation of IQ, harman, and norharman by 39%, 67%, and 63%, respectively. In contrast to IQ, the levels of harman and norharman were significantly reduced by the extracts tested. However, no such effects were observed for MeIQx and 4, 8-DiMeIQx. Notably, the inhibitory effect on heterocyclic amines is significantly correlated with the antioxidant potential and total phenolic content of S. olearleu extract.
  6. Chai TT, Xiao J, Mohana Dass S, Teoh JY, Ee KY, Ng WJ, et al.
    Food Chem, 2021 Mar 15;340:127876.
    PMID: 32871354 DOI: 10.1016/j.foodchem.2020.127876
    Jackfruit is a sweet tropical fruit with very pleasant aroma, and the ripe seeds are edible. In this study, jackfruit seed proteins were isolated and subjected to trypsin digestion. The resultant protein hydrolysate was then subjected to antioxidant assay-guided purification, using centrifugal filtration, C18 reverse-phase and strong cation exchange (SCX) fractionations. The purified SCX fraction was further analyzed by de novo peptide sequencing, and two peptide sequences were identified and synthesized. Peptide JFS-2 (VGPWQK) was detected with antioxidant potential, with EC50 value comparable to that of commercial GSH antioxidant peptide. Additionally, the identified peptides were tested with protein protection potential, in an albumin protein denaturation inhibitory assay. Concurrently, we also investigated the pH, temperature, and gastrointestinal-digestion stability profiles for the identified peptide. With further research efforts, the identified peptides could potentially be developed into preservative agent for protein-rich food systems or as health-promoting diet supplements.
  7. Wong FC, Xiao J, Ong MG, Pang MJ, Wong SJ, Teh LK, et al.
    Food Chem, 2019 Jan 15;271:614-622.
    PMID: 30236723 DOI: 10.1016/j.foodchem.2018.07.206
    This study was conducted to identify and characterize antioxidant peptides from the alcalase hydrolysate of the blue-spotted stingray. Purification steps guided by ABTS cation radical (ABTS+) scavenging assay and de novo peptide sequencing produced two peptides, WAFAPA (661.3224 Da) and MYPGLA (650.3098 Da). WAFAPA (EC50 = 12.6 µM) had stronger antioxidant activity than glutathione (EC50 = 13.7 µM) and MYPGLA (EC50 = 19.8 µM). Synergism between WAFAPA and MYPGLA was detected. WAFAPA and MYPGLA surpassed carnosine in their ability to suppress H2O2-induced lipid oxidation. The peptides protected plasmid DNA and proteins from Fenton's reagent-induced oxidative damage. Thermal (25-100 °C) and pH 3-11 treatments did not alter antioxidant activity of the peptides. MYPGLA maintained its antioxidant activity after simulated gastrointestinal digestion, whereas WAFAPA showed a partial loss. The two peptides may have potential applications as functional food ingredients or nutraceuticals, whether used singly or in combination.
  8. Porwal P, Pachade S, Kokare M, Deshmukh G, Son J, Bae W, et al.
    Med Image Anal, 2020 01;59:101561.
    PMID: 31671320 DOI: 10.1016/j.media.2019.101561
    Diabetic Retinopathy (DR) is the most common cause of avoidable vision loss, predominantly affecting the working-age population across the globe. Screening for DR, coupled with timely consultation and treatment, is a globally trusted policy to avoid vision loss. However, implementation of DR screening programs is challenging due to the scarcity of medical professionals able to screen a growing global diabetic population at risk for DR. Computer-aided disease diagnosis in retinal image analysis could provide a sustainable approach for such large-scale screening effort. The recent scientific advances in computing capacity and machine learning approaches provide an avenue for biomedical scientists to reach this goal. Aiming to advance the state-of-the-art in automatic DR diagnosis, a grand challenge on "Diabetic Retinopathy - Segmentation and Grading" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2018). In this paper, we report the set-up and results of this challenge that is primarily based on Indian Diabetic Retinopathy Image Dataset (IDRiD). There were three principal sub-challenges: lesion segmentation, disease severity grading, and localization of retinal landmarks and segmentation. These multiple tasks in this challenge allow to test the generalizability of algorithms, and this is what makes it different from existing ones. It received a positive response from the scientific community with 148 submissions from 495 registrations effectively entered in this challenge. This paper outlines the challenge, its organization, the dataset used, evaluation methods and results of top-performing participating solutions. The top-performing approaches utilized a blend of clinical information, data augmentation, and an ensemble of models. These findings have the potential to enable new developments in retinal image analysis and image-based DR screening in particular.
  9. Xiao J, Ng CH, Chan KE, Fu C, Tay P, Yong JN, et al.
    J Clin Exp Hepatol, 2023;13(4):656-665.
    PMID: 37440949 DOI: 10.1016/j.jceh.2022.11.006
    BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver disease globally. While the prevalence, impact, and causes of mortality have been described in various meta-analyses, a systematic all-encompassing umbrella review has yet to be conducted to consolidate the evidence on outcomes associated with NAFLD.

    METHODS: Search was conducted on Medline and Embase for meta-analysis investigating associated complications and causes of mortality in NAFLD patients. Summary estimates were presented with original units, sample size, and I2 for heterogeneity. The Assessment of Multiple Systematic Reviews 2 was employed for article selection.

    RESULTS: 25 meta-analyses were included in the present review. NAFLD increased the risks of systemic complications, including cardiovascular diseases, systemic malignancies, diabetes, and chronic kidney disease. Regarding hepatic outcomes, the incidence of hepatocellular carcinoma in NAFLD was 2.39 per 100 person years (CI: 1.40 to 4.08). Individuals with NAFLD were also found to have an increased likelihood of cholangiocarcinoma (OR: 1.88, CI: 1.25 to 2.83) and gallstone disease (OR: 1.55, CI: 1.31 to 1.82) compared to individuals without NAFLD. NAFLD was associated with a higher risk of fatal and non-fatal CVD events (HR: 1.45, CI: 1.31 to 1.61) compared to individuals without NAFLD. Coronary heart disease and subclinical and clinical coronary heart disease were also significantly elevated in NAFLD individuals compared to individuals without NAFLD. Additionally, NAFLD was associated with an increased risk of all-cause mortality (HR: 1.34, CI: 1.17 to 1.54) and cardiovascular (HR: 1.30, CI: 1.08 to 1.56) but not cancer-related mortality.

    CONCLUSION: The study summarizes high-level evidence from published meta-analyses to provide a much-needed update on the outcomes in patients with NAFLD. The significant systemic burden associated with NAFLD and impending fatty liver epidemic requires prompt action from multidisciplinary providers, policy providers, and stakeholders to reduce the burden of NAFLD.

  10. Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.
    Autophagy, 2021 Jan;17(1):1-382.
    PMID: 33634751 DOI: 10.1080/15548627.2020.1797280
    In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
  11. Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.
    Autophagy, 2016;12(1):1-222.
    PMID: 26799652 DOI: 10.1080/15548627.2015.1100356
  12. Choo SW, Wee WY, Ngeow YF, Mitchell W, Tan JL, Wong GJ, et al.
    Sci Rep, 2014;4:4061.
    PMID: 24515248 DOI: 10.1038/srep04061
    Mycobacterium abscessus (Ma) is an emerging human pathogen that causes both soft tissue infections and systemic disease. We present the first comparative whole-genome study of Ma strains isolated from patients of wide geographical origin. We found a high proportion of accessory strain-specific genes indicating an open, non-conservative pan-genome structure, and clear evidence of rapid phage-mediated evolution. Although we found fewer virulence factors in Ma compared to M. tuberculosis, our data indicated that Ma evolves rapidly and therefore should be monitored closely for the acquisition of more pathogenic traits. This comparative study provides a better understanding of Ma and forms the basis for future functional work on this important pathogen.
  13. Yusof N, Hamid N, Ma ZF, Lawenko RM, Wan Mohammad WMZ, Collins DA, et al.
    Gut Pathog, 2017;9:75.
    PMID: 29255490 DOI: 10.1186/s13099-017-0224-7
    Background: After an environmental disaster, the affected community is at increased risk for persistent abdominal pain but mechanisms are unclear. Therefore, our study aimed to determine association between abdominal pain and poor water, sanitation and hygiene (WaSH) practices, and if small intestinal bacterial overgrowth (SIBO) and/or gut dysbiosis explain IBS, impaired quality of life (QOL), anxiety and/or depression after a major flood.

    Results: New onset abdominal pain, IBS based on the Rome III criteria, WaSH practices, QOL, anxiety and/or depression, SIBO (hydrogen breath testing) and stools for metagenomic sequencing were assessed in flood victims. Of 211 participants, 37.9% (n = 80) had abdominal pain and 17% (n = 36) with IBS subtyped diarrhea and/or mixed type (n = 27 or 12.8%) being the most common. Poor WaSH practices and impaired quality of life during flood were significantly associated with IBS. Using linear discriminant analysis effect size method, gut dysbiosis was observed in those with anxiety (Bacteroidetes and Proteobacteria, effect size 4.8), abdominal pain (Fusobacteria, Staphylococcus, Megamonas and Plesiomonas, effect size 4.0) and IBS (Plesiomonas and Trabulsiella, effect size 3.0).

    Conclusion: Disturbed gut microbiota because of environmentally-derived organisms may explain persistent abdominal pain and IBS after a major environmental disaster in the presence of poor WaSH practices.

  14. El-Seedi HR, Yosri N, Khalifa SAM, Guo Z, Musharraf SG, Xiao J, et al.
    J Ethnopharmacol, 2021 Apr 06;269:113626.
    PMID: 33248183 DOI: 10.1016/j.jep.2020.113626
    ETHNOPHARMACOLOGICAL RELEVANCE: Egyptian plants are a rich source of natural molecules, representing considerable biodiversity due to climate variations between the Northern, Southern, Eastern and Western regions of the country. Sinai is considered a precious nature reserves preserving flora, fauna, marine organisms, and historical habitats with ancient origins. Here, traditional medicinal approaches have been used for hundreds of years. Healthy lifestyles, low levels of stress and microbial infections, and a dependence on flora and herbal medicine might in combination explain why the burden of cancer is lower in some regions than in others.

    AIM OF THE STUDY: The primary aim of this review is to document the plants and natural products that are used as foods and medicines in Egypt, in general, and in Sinai, in particular, with a focus on those with demonstrated anticancer activities. The documented traditional uses of these plants are described, together with their chemical and pharmacological activities and the reported outcomes of clinical trials against cancer.

    MATERIALS AND METHODS: A literature search was performed to identify texts describing the medicinal plants that are cultivated and grown in Egypt, including information found in textbooks, published articles, the plant list website (http://www.theplantlist.org/), the medicinal plant names services website (http://mpns.kew.org/mpns-portal/), and web databases (PubMed, Science Direct, and Google Scholar).

    RESULTS AND DISCUSSION: We collected data for most of the plants cultivated or grown in Egypt that have been previously investigated for anticancer effects and reported their identified bioactive elements. Several plant species, belonging to different families and associated with 67 bioactive compounds, were investigated as potential anticancer agents (in vitro studies). The most potent cytotoxic activities were identified for the families Asteraceae, Lamiaceae, Chenopodiaceae, Apocynaceae, Asclepiadaceae, Euphorbiaceae, Gramineae, and Liliaceae. The anticancer activities of some species, such as Punica granatum L., Nerium oleander L., Olea europea L., Matricaria chamomilla L., Cassia acutifolia L., Nigella sativa L., Capsicum frutescens L., Withania somnifera L., and Zingiber officinale Roscoe, have been examined in clinical trials. Among the various Egyptian plant habitats, we found that most of these plants are grown in the North Sinai, New-Delta, and Giza Governorates.

    CONCLUSION: In this review, we highlight the role played by Egyptian flora in current medicinal therapies and the possibility that these plants may be examined in further studies for the development of anticancer drugs. These bioactive plant extracts form the basis for the isolation of phytochemicals with demonstrated anticancer activities. Some active components derived from these plants have been applied to preclinical and clinical settings, including resveratrol, quercetin, isoquercetin, and rutin.

  15. Aad G, Abbott B, Abeling K, Abicht NJ, Abidi SH, Aboulhorma A, et al.
    Phys Rev Lett, 2024 Jan 12;132(2):021803.
    PMID: 38277607 DOI: 10.1103/PhysRevLett.132.021803
    The first evidence for the Higgs boson decay to a Z boson and a photon is presented, with a statistical significance of 3.4 standard deviations. The result is derived from a combined analysis of the searches performed by the ATLAS and CMS Collaborations with proton-proton collision datasets collected at the CERN Large Hadron Collider (LHC) from 2015 to 2018. These correspond to integrated luminosities of around 140  fb^{-1} for each experiment, at a center-of-mass energy of 13 TeV. The measured signal yield is 2.2±0.7 times the standard model prediction, and agrees with the theoretical expectation within 1.9 standard deviations.
  16. Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Bergauer T, Dragicevic M, et al.
    Phys Rev Lett, 2020 Nov 27;125(22):222001.
    PMID: 33315428 DOI: 10.1103/PhysRevLett.125.222001
    Ultrarelativistic heavy ion collisions recreate in the laboratory the thermodynamical conditions prevailing in the early universe up to 10^{-6}  sec, thereby allowing the study of the quark-gluon plasma (QGP), a state of quantum chromodynamics (QCD) matter with deconfined partons. The top quark, the heaviest elementary particle known, is accessible in nucleus-nucleus collisions at the CERN LHC, and constitutes a novel probe of the QGP. Here, we report the first evidence for the production of top quarks in nucleus-nucleus collisions, using lead-lead collision data at a nucleon-nucleon center-of-mass energy of 5.02 TeV recorded by the CMS experiment. Two methods are used to measure the cross section for top quark pair production (σ_{tt[over ¯]}) via the selection of charged leptons (electrons or muons) and bottom quarks. One method relies on the leptonic information alone, and the second one exploits, in addition, the presence of bottom quarks. The measured cross sections, σ_{tt[over ¯]}=2.54_{-0.74}^{+0.84} and 2.03_{-0.64}^{+0.71}  μb, respectively, are compatible with expectations from scaled proton-proton data and QCD predictions.
  17. Lim WH, Ng CH, Tan DJH, Xiao J, Fu CE, Ong C, et al.
    Transplantation, 2024 Feb 01;108(2):473-482.
    PMID: 37439778 DOI: 10.1097/TP.0000000000004718
    BACKGROUND: Liver transplantation (LT) offers patients with decompensated cirrhosis the best chance at long-term survival. With the rising prevalence of diabetes, further clarity is needed on the impact of receiving a liver allograft from a donor with diabetes on post-LT outcomes. This study aims to evaluate the impact of donor diabetes on clinical outcomes after LT.

    METHODS: This is a retrospective analysis of the United Network for Organ Sharing registry data of LT recipients from January 1, 2000, to December 31, 2021. Outcomes analysis was performed using Cox proportional model for all-cause mortality and graft failure. Confounding was reduced by coarsened exact matching causal inference analysis.

    RESULTS: Of 66 960 donors identified, 7178 (10.7%) had diabetes. Trend analysis revealed a longitudinal increase in the prevalence of donor diabetes ( P  

  18. Zhao J, Xiao J, Lee ML, Ma Y
    Springerplus, 2016;5(1):1633.
    PMID: 27722051
    Slopes are subjected to stress redistributions during underground mining activities, and this may eventually cause deformation or landslide. This paper takes Madaling landslide in Guizhou Province, China as a case study to investigate the failure mechanism and its run-out behaviours by using discrete element method. Previous qualitative analysis indicated that the slope experienced four stages of failure mechanisms: (1) development of tension cracks, (2) development of stepped-like creep cracks, (3) development of potential rupture surfaces, and (4) occurrence of the landslide. PFC2D program was employed to model the pre-failure deformation characteristics in order to verify the failure mechanisms quantitatively. Subsequently, the run-out behaviours of the landslide were analyzed by PFC3D program. The results indicated that the movement could be summarized into four stages: acceleration stage, constant movement stage, rapid movement stage, and deceleration and deposition stage.
  19. Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Bergauer T, Dragicevic M, et al.
    Eur Phys J C Part Fields, 2021;81(4):312.
    PMID: 34727148 DOI: 10.1140/epjc/s10052-021-08949-5
    This paper presents new sets of parameters ("tunes") for the underlying-event model of the H E R W I G 7 event generator. These parameters control the description of multiple-parton interactions (MPI) and colour reconnection in H E R W I G 7 , and are obtained from a fit to minimum-bias data collected by the CMS experiment at s = 0.9 , 7, and 13 Te . The tunes are based on the NNPDF 3.1 next-to-next-to-leading-order parton distribution function (PDF) set for the parton shower, and either a leading-order or next-to-next-to-leading-order PDF set for the simulation of MPI and the beam remnants. Predictions utilizing the tunes are produced for event shape observables in electron-positron collisions, and for minimum-bias, inclusive jet, top quark pair, and Z and W boson events in proton-proton collisions, and are compared with data. Each of the new tunes describes the data at a reasonable level, and the tunes using a leading-order PDF for the simulation of MPI provide the best description of the data.
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