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Sökning: WFRF:(Li Xiangyu)

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1.
  • Zeng, Xiao, et al. (författare)
  • A scoping study on remelting process of a debris bed in the lower head of reactor pressure vessel
  • 2023
  • Ingår i: Annals of Nuclear Energy. - : Elsevier BV. - 0306-4549 .- 1873-2100. ; 189
  • Tidskriftsartikel (refereegranskat)abstract
    • Coolability and retention of core melt (corium) in the lower head of reactor pressure vessel (RPV) has been accepted as a severe accident management strategy to maintain the reactor pressure vessel (RPV) integrity of a light water reactor. To qualify the in-vessel melt retention strategy, lots of studies have been performed to investigate the natural convection heat transfer of a melt pool in the lower head. However, little work has been attributed to the precursory phase of the melt pool, i.e., the remelting process of a debris bed which is formed in the lower head at the very beginning of corium relocation from the core the lower head. The present study is motivated to conduct an experimental study on the debris remelting process. For this purpose, a dedicated test facility named COREM (COrium REMelting) is conceived and constructed, which features internal heating of electromagnetic induction and visualization of debris remelting dynamics. The test section is a semicircular vessel representing a slice of scaled-down RPV lower head, whose front and back walls are made of transparent tempered glass which facilitate visualization and induction heating of the debris bed. Fiber probes with multiple optical temperature sensors are mounted in the semicircular wall of the test section to measure its temperature distribution. In the scoping test, n-octanol and Wood's metal are selected as the simulant materials of metallic and oxidic components of corium, respectively, and their particles ware loaded in the test section to form a debris bed. This paper presents the first two scoping tests which have been performed with the COREM facility so far, under different mixing ratios of two debris materials. The measured data include the photography of debris remelting processes and the temperatures in the debris bed and the semicircular wall. Based on the temperature distributions, heat flux profile along the semicircular vessel wall is also estimated. The scoping tests well reproduce the dynamic process of debris remelting, with two distinct stages of fusion of n-octanol and Wood's metal, i.e., melting successively from low to high melting-point debris particles. During the remelting process, the vessel wall temperatures increase with the polar angle firstly and then decrease gradually, leading to the highest temperature appearing in the middle of the lower layer of the stratified molten pool which is finally formed.
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2.
  • Berntell, Ellen, et al. (författare)
  • Mid-Pliocene West African Monsoon rainfall as simulated in the PlioMIP2 ensemble
  • 2021
  • Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 17:4, s. 1777-1794
  • Tidskriftsartikel (refereegranskat)abstract
    • The mid-Pliocene warm period (mPWP; ∼3.2 million years ago) is seen as the most recent time period characterized by a warm climate state, with similar to modern geography and ∼400 ppmv atmospheric CO2 concentration, and is therefore often considered an interesting analogue for near-future climate projections. Paleoenvironmental reconstructions indicate higher surface temperatures, decreasing tropical deserts, and a more humid climate in West Africa characterized by a strengthened West African Monsoon (WAM). Using model results from the second phase of the Pliocene Modelling Intercomparison Project (PlioMIP2) ensemble, we analyse changes of the WAM rainfall during the mPWP by comparing them with the control simulations for the pre-industrial period. The ensemble shows a robust increase in the summer rainfall over West Africa and the Sahara region, with an average increase of 2.5 mm/d, contrasted by a rainfall decrease over the equatorial Atlantic. An anomalous warming of the Sahara and deepening of the Saharan Heat Low, seen in >90 % of the models, leads to a strengthening of the WAM and an increased monsoonal flow into the continent. A similar warming of the Sahara is seen in future projections using both phase 3 and 5 of the Coupled Model Intercomparison Project (CMIP3 and CMIP5). Though previous studies of future projections indicate a west–east drying–wetting contrast over the Sahel, PlioMIP2 simulations indicate a uniform rainfall increase in that region in warm climates characterized by increasing greenhouse gas forcing. We note that this effect will further depend on the long-term response of the vegetation to the CO2 forcing.
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3.
  • de Nooijer, Wesley, et al. (författare)
  • Evaluation of Arctic warming in mid-Pliocene climate simulations
  • 2020
  • Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 16:6, s. 2325-2341
  • Tidskriftsartikel (refereegranskat)abstract
    • Palaeoclimate simulations improve our understanding of the climate, inform us about the performance of climate models in a different climate scenario, and help to identify robust features of the climate system. Here, we analyse Arctic warming in an ensemble of 16 simulations of the mid-Pliocene Warm Period (mPWP), derived from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). The PlioMIP2 ensemble simulates Arctic (60-90 degrees N) annual mean surface air temperature (SAT) increases of 3.7 to 11.6 degrees C compared to the pre-industrial period, with a multimodel mean (MMM) increase of 7.2 degrees C. The Arctic warming amplification ratio relative to global SAT anomalies in the ensemble ranges from 1.8 to 3.1 (MMM is 2.3). Sea ice extent anomalies range from -3.0 to -10.4 x 10(6) km(2), with a MMM anomaly of -5.6 x 10 6 km(2), which constitutes a decrease of 53 % compared to the pre-industrial period. The majority (11 out of 16) of models simulate summer seaice-free conditions (<= 1 x 10(6) km(2)) in their mPWP simulation. The ensemble tends to underestimate SAT in the Arctic when compared to available reconstructions, although the degree of underestimation varies strongly between the simulations. The simulations with the highest Arctic SAT anomalies tend to match the proxy dataset in its current form better. The ensemble shows some agreement with reconstructions of sea ice, particularly with regard to seasonal sea ice. Large uncertainties limit the confidence that can be placed in the findings and the compatibility of the different proxy datasets. We show that while reducing uncertainties in the reconstructions could decrease the SAT data-model discord substantially, further improvements are likely to be found in enhanced boundary conditions or model physics. Lastly, we compare the Arctic warming in the mPWP to projections of future Arctic warming and find that the PlioMIP2 ensemble simulates greater Arctic amplification than CMIP5 future climate simulations and an increase instead of a decrease in Atlantic Meridional Overturning Circulation (AMOC) strength compared to pre-industrial period. The results highlight the importance of slow feedbacks in equilibrium climate simulations, and that caution must be taken when using simulations of the mPWP as an analogue for future climate change.
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4.
  • Han, Zixuan, et al. (författare)
  • Evaluating the large-scale hydrological cycle response within the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) ensemble
  • 2021
  • Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 17:6, s. 2537-2558
  • Tidskriftsartikel (refereegranskat)abstract
    • The mid-Pliocene (∼3 Ma) is one of the most recent warm periods with high CO2 concentrations in the atmosphere and resulting high temperatures, and it is often cited as an analog for near-term future climate change. Here, we apply a moisture budget analysis to investigate the response of the large-scale hydrological cycle at low latitudes within a 13-model ensemble from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). The results show that increased atmospheric moisture content within the mid-Pliocene ensemble (due to the thermodynamic effect) results in wetter conditions over the deep tropics, i.e., the Pacific intertropical convergence zone (ITCZ) and the Maritime Continent, and drier conditions over the subtropics. Note that the dynamic effect plays a more important role than the thermodynamic effect in regional precipitation minus evaporation (PmE) changes (i.e., northward ITCZ shift and wetter northern Indian Ocean). The thermodynamic effect is offset to some extent by a dynamic effect involving a northward shift of the Hadley circulation that dries the deep tropics and moistens the subtropics in the Northern Hemisphere (i.e., the subtropical Pacific). From the perspective of Earth's energy budget, the enhanced southward cross-equatorial atmospheric transport (0.22 PW), induced by the hemispheric asymmetries of the atmospheric energy, favors an approximately 1∘ northward shift of the ITCZ. The shift of the ITCZ reorganizes atmospheric circulation, favoring a northward shift of the Hadley circulation. In addition, the Walker circulation consistently shifts westward within PlioMIP2 models, leading to wetter conditions over the northern Indian Ocean. The PlioMIP2 ensemble highlights that an imbalance of interhemispheric atmospheric energy during the mid-Pliocene could have led to changes in the dynamic effect, offsetting the thermodynamic effect and, hence, altering mid-Pliocene hydroclimate.
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5.
  • Haywood, Alan M., et al. (författare)
  • The Pliocene Model Intercomparison Project Phase 2 : large-scale climate features and climate sensitivity
  • 2020
  • Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 16:6, s. 2095-2123
  • Tidskriftsartikel (refereegranskat)abstract
    • The Pliocene epoch has great potential to improve our understanding of the long-term climatic and environmental consequences of an atmospheric CO2 concentration near similar to 400 parts per million by volume. Here we present the large-scale features of Pliocene climate as simulated by a new ensemble of climate models of varying complexity and spatial resolution based on new reconstructions of boundary conditions (the Pliocene Model Intercomparison Project Phase 2; PlioMIP2). As a global annual average, modelled surface air temperatures increase by between 1.7 and 5.2 degrees C relative to the pre-industrial era with a multi-model mean value of 3.2 degrees C. Annual mean total precipitation rates increase by 7 % (range: 2 %-13 %). On average, surface air temperature (SAT) increases by 4.3 degrees C over land and 2.8 degrees C over the oceans. There is a clear pattern of polar amplification with warming polewards of 60 degrees N and 60 degrees S exceeding the global mean warming by a factor of 2.3. In the Atlantic and Pacific oceans, meridional temperature gradients are reduced, while tropical zonal gradients remain largely unchanged. There is a statistically significant relationship between a model's climate response associated with a doubling in CO2 (equilibrium climate sensitivity; ECS) and its simulated Pliocene surface temperature response. The mean ensemble Earth system response to a doubling of CO2 (including ice sheet feedbacks) is 67 % greater than ECS; this is larger than the increase of 47 % obtained from the PlioMIP1 ensemble. Proxy-derived estimates of Pliocene sea surface temperatures are used to assess model estimates of ECS and give an ECS range of 2.6-4.8 degrees C. This result is in general accord with the ECS range presented by previous Intergovernmental Panel on Climate Change (IPCC) Assessment Reports.
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6.
  • Li, Xiangyu, et al. (författare)
  • Identification of two-phase flow pattern in porous media based on signal feature extraction
  • 2022
  • Ingår i: Flow Measurement and Instrumentation. - : Elsevier BV. - 0955-5986 .- 1873-6998. ; 83
  • Tidskriftsartikel (refereegranskat)abstract
    • The statistical analysis methods based on differential pressure signals of two-phase flow are employed in the present study to identify the flow patterns in packed porous bed. The typical flow pattern images of two-phase flow in the packed porous beds are recognized and the corresponding differential pressure signals are recorded based on the visualization experiments. Then the statistical analysis methods, including probability density function (PDF), power spectral density (PSD), and wavelet energy spectrum (WES), are employed to extract the features of differential pressure signals in the time domain, frequency domain, and time-frequency domain respectively. The dimensionless parameters are proposed as the evaluation index to quantify the differences among flow patterns. The results show that the PDF, PSD, and WES methods can effectively characterize different flow patterns in the time, frequency, and time-frequency domain, respectively. The comprehensive recognition efficiency is about 88.5% using the introduced dimensionless parameters.
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7.
  • Li, Xiangyu, et al. (författare)
  • Two-phase flow patterns identification in porous media using feature extraction and SVM
  • 2022
  • Ingår i: International Journal of Multiphase Flow. - : Elsevier BV. - 0301-9322 .- 1879-3533. ; 156
  • Tidskriftsartikel (refereegranskat)abstract
    • Rapid and accurate identification of two-phase flow patterns in porous media is of great significance to the chemical industry, petroleum and nuclear engineering, etc. Based on the different pressure signals of gas-liquid two-phase flow in a porous bed, the present work proposes an intelligent recognition method to identify the two-phase flow patterns in porous media by the technologies of feature extraction and support vector machine (SVM). The analysis techniques, including time domain (PDF), frequency domain (PSD) and time-frequency domain (Wavelet), are employed to extract and summarize the corresponding characteristics of differential pressure signals of flow patterns. The intelligent recognition models are developed to identify the two-phase flow patterns in porous media by SVM. The models are trained respectively based on the characteristics of time domain + frequency domain (TF-SVM model), time domain + wavelet (TW-SVM model) and frequency domain + wavelet (FW-SVM model). The overall identification accuracy of the optimal model (TW-SVM model) reaches 96.08%.
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8.
  • Liu, Lihui, et al. (författare)
  • Ablation of ERO1A induces lethal endoplasmic reticulum stress responses and immunogenic cell death to activate anti-tumor immunity
  • 2023
  • Ingår i: Cell Reports Medicine. - : Cell Press. - 2666-3791. ; 4:10
  • Tidskriftsartikel (refereegranskat)abstract
    • Immunophenotyping of the tumor microenvironment (TME) is essential for enhancing immunotherapy effi-cacy. However, strategies for characterizing the TME exhibit significant heterogeneity. Here, we show that endoplasmic reticular oxidoreductase-1a (ERO1A) mediates an immune-suppressive TME and attenuates the response to PD-1 blockade. Ablation of ERO1A in tumor cells substantially incites anti-tumor T cell im-munity and promotes the efficacy of aPD-1 in therapeutic models. Single-cell RNA-sequencing analyses confirm that ERO1A correlates with immunosuppression and dysfunction of CD8+ T cells along anti-PD-1 treatment. In human lung cancer, high ERO1A expression is associated with a higher risk of recurrence following neoadjuvant immunotherapy. Mechanistically, ERO1A ablation impairs the balance between IRE1a and PERK signaling activities and induces lethal unfolded protein responses in tumor cells undergoing endoplasmic reticulum stress, thereby enhancing anti-tumor immunity via immunogenic cell death. These findings reveal how tumor ERO1A induces immunosuppression, highlighting its potential as a therapeutic target for cancer immunotherapy.
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9.
  • Luo, Yifei, et al. (författare)
  • Technology Roadmap for Flexible Sensors
  • 2023
  • Ingår i: ACS Nano. - : American Chemical Society. - 1936-0851 .- 1936-086X. ; 17:6, s. 5211-5295
  • Forskningsöversikt (refereegranskat)abstract
    • Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative efforts, scientific breakthroughs can be made sooner and capitalized for the betterment of humanity.
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10.
  • Oldeman, Arthur M., et al. (författare)
  • Reduced El Niño variability in the mid-Pliocene according to the PlioMIP2 ensemble
  • 2021
  • Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 17:6, s. 2427-2450
  • Tidskriftsartikel (refereegranskat)abstract
    • The mid-Pliocene warm period (3.264–3.025 Ma) is the most recent geological period during which atmospheric CO2 levels were similar to recent historical values (∼400 ppm). Several proxy reconstructions for the mid-Pliocene show highly reduced zonal sea surface temperature (SST) gradients in the tropical Pacific Ocean, indicating an El Niño-like mean state. However, past modelling studies do not show these highly reduced gradients. Efforts to understand mid-Pliocene climate dynamics have led to the Pliocene Model Intercomparison Project (PlioMIP). Results from the first phase (PlioMIP1) showed clear El Niño variability (albeit significantly reduced) and did not show the greatly reduced time-mean zonal SST gradient suggested by some of the proxies.In this work, we study El Niño–Southern Oscillation (ENSO) variability in the PlioMIP2 ensemble, which consists of additional global coupled climate models and updated boundary conditions compared to PlioMIP1. We quantify ENSO amplitude, period, spatial structure and “flavour”, as well as the tropical Pacific annual mean state in mid-Pliocene and pre-industrial simulations. Results show a reduced ENSO amplitude in the model-ensemble mean (−24 %) with respect to the pre-industrial, with 15 out of 17 individual models showing such a reduction. Furthermore, the spectral power of this variability considerably decreases in the 3–4-year band. The spatial structure of the dominant empirical orthogonal function shows no particular change in the patterns of tropical Pacific variability in the model-ensemble mean, compared to the pre-industrial. Although the time-mean zonal SST gradient in the equatorial Pacific decreases for 14 out of 17 models (0.2 ∘C reduction in the ensemble mean), there does not seem to be a correlation with the decrease in ENSO amplitude. The models showing the most “El Niño-like” mean state changes show a similar ENSO amplitude to that in the pre-industrial reference, while models showing more “La Niña-like” mean state changes generally show a large reduction in ENSO variability. The PlioMIP2 results show a reasonable agreement with both time-mean proxies indicating a reduced zonal SST gradient and reconstructions indicating a reduced, or similar, ENSO variability.
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11.
  • Weiffenbach, Julia E., et al. (författare)
  • Unraveling the mechanisms and implications of a stronger mid-Pliocene Atlantic Meridional Overturning Circulation (AMOC) in PlioMIP2
  • 2023
  • Ingår i: Climate of the Past. - : COPERNICUS GESELLSCHAFT MBH. - 1814-9324 .- 1814-9332. ; 19:1, s. 61-85
  • Tidskriftsartikel (refereegranskat)abstract
    • The mid-Pliocene warm period (3.264-3.025 Ma) is the most recent geological period in which the atmospheric CO2 concentration was approximately equal to the concentration we measure today (ca. 400 ppm). Sea surface temperature (SST) proxies indicate above-average warming over the North Atlantic in the mid-Pliocene with respect to the pre-industrial period, which may be linked to an intensified Atlantic Meridional Overturning Circulation (AMOC). Earlier results from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) show that the ensemble simulates a stronger AMOC in the mid-Pliocene than in the pre-industrial. However, no consistent relationship between the stronger mid-Pliocene AMOC and either the Atlantic northward ocean heat transport (OHT) or average North Atlantic SSTs has been found. In this study, we look further into the drivers and consequences of a stronger AMOC in mid-Pliocene compared to pre-industrial simulations in PlioMIP2. We find that all model simulations with a closed Bering Strait and Canadian Archipelago show reduced freshwater transport from the Arctic Ocean into the North Atlantic. This contributes to an increase in salinity in the subpolar North Atlantic and Labrador Sea that can be linked to the stronger AMOC in the mid-Pliocene. To investigate the dynamics behind the ensembles variable response of the total Atlantic OHT to the stronger AMOC, we separate the Atlantic OHT into two components associated with either the overturning circulation or the wind-driven gyre circulation. While the ensemble mean of the overturning component is increased significantly in magnitude in the mid-Pliocene, it is partly compensated by a reduction in the gyre component in the northern subtropical gyre region. This indicates that the lack of relationship between the total OHT and AMOC is due to changes in OHT by the subtropical gyre. The overturning and gyre components should therefore be considered separately to gain a more complete understanding of the OHT response to a stronger mid-Pliocene AMOC. In addition, we show that the AMOC exerts a stronger influence on North Atlantic SSTs in the mid-Pliocene than in the pre-industrial, providing a possible explanation for the improved agreement of the PlioMIP2 ensemble mean SSTs with reconstructions in the North Atlantic.
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12.
  • Yao, Xiangyu, et al. (författare)
  • A highly sensitive bead-based flow cytometric competitive binding assay to detect SARS-CoV-2 neutralizing antibody activity
  • 2022
  • Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Accurate detection of SARS-CoV-2 neutralizing antibody (nAb) is critical for assessing the immunity levels after virus infection or vaccination. As fast, cost-effective alternatives to viral infection-based assays, competitive binding (CB) assays were developed to quantitate nAb by monitoring the ability of sera to inhibit the binding of viral spike (S) protein to the angiotensin converting enzyme 2 (ACE2) receptor. Herein, we established a bead-based flow cytometric CB assay and tested the detection performance of six combination models, i.e. immobilized ACE2 and soluble Fc-tagged S1 subunit of S protein (iACE2/S1-Fc), immobilized ACE2 and soluble Fc-tagged receptor binding domain (RBD) of S protein (iACE2/RBD-Fc), immobilized S1 and soluble Fc-tagged ACE2 (iS1/ACE2-Fc), immobilized S1 and soluble His-tagged ACE2 (iS1/ACE2-His), immobilized RBD and soluble Fc-tagged ACE2 (iRBD/ACE2-Fc), and immobilized RBD and soluble His-tagged ACE2 (iRBD/ACE2-His). Using SARS-CoV-2 monoclonal antibodies and sera of convalescent COVID-19 patients and vaccinated subjects, the combination models iACE2/RBD-Fc, iACE2/S1-Fc and iS1/ACE2-His were identified to be able to specifically detect SARS-CoV-2 nAb, among which iACE2/RBD-Fc model showed the highest sensitivity, superior to a commercial SARS-CoV-2 surrogate virus neutralization test (sVNT) ELISA kit. Further studies demonstrated that the sensitivity and specificity of CB assays were affected by the tag of ACE2, type of spike and method of measuring binding rate between ACE2 and spike. Moreover, the iACE2/RBD-Fc model showed good performance in detecting kinetic development of nAb against both the prototype SARS-CoV-2 strain and an omicron variant of SARS-CoV-2 in people immunized by an inactivated SARS-CoV-2 vaccine, and the results of iACE2/RBD-Fc model are correlated well with those of live virus-based and pseudovirus-based neutralization tests, demonstrating the potential to be developed into a highly sensitive, specific, versatile and high-throughput method for detecting SARS-CoV-2 nAb in clinical practice.
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13.
  • Zhang, Zhongshi, et al. (författare)
  • Mid-Pliocene Atlantic Meridional Overturning Circulation simulated in PlioMIP2
  • 2021
  • Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 17:1, s. 529-543
  • Tidskriftsartikel (refereegranskat)abstract
    • In the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2), coupled climate models have been used to simulate an interglacial climate during the mid-Piacenzian warm period (mPWP; 3.264 to 3.025 Ma). Here, we compare the Atlantic Meridional Overturning Circulation (AMOC), poleward ocean heat transport and sea surface warming in the Atlantic simulated with these models. In PlioMIP2, all models simulate an intensified mid-Pliocene AMOC. How- ever, there is no consistent response in the simulated Atlantic ocean heat transport nor in the depth of the Atlantic overturning cell. The models show a large spread in the simulated AMOC maximum, the Atlantic ocean heat transport and the surface warming in the North Atlantic. Although a few models simulate a surface warming of similar to 8-12 degrees C in the North Atlantic, similar to the reconstruction from Pliocene Research, Interpretation and Synoptic Mapping (PRISM) version 4, most models appear to underestimate this warming. The large model spread and model-data discrepancies in the PlioMIP2 ensemble do not support the hypothesis that an intensification of the AMOC, together with an increase in northward ocean heat transport, is the dominant mechanism for the mid-Pliocene warm climate over the North Atlantic.
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14.
  • Altay, Özlem, et al. (författare)
  • Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19
  • 2021
  • Ingår i: Advanced Science. - : Wiley. - 2198-3844. ; 8:17
  • Tidskriftsartikel (refereegranskat)abstract
    • COVID-19 is associated with mitochondrial dysfunction and metabolic abnormalities, including the deficiencies in nicotinamide adenine dinucleotide (NAD+) and glutathione metabolism. Here it is investigated if administration of a mixture of combined metabolic activators (CMAs) consisting of glutathione and NAD+ precursors can restore metabolic function and thus aid the recovery of COVID-19 patients. CMAs include l-serine, N-acetyl-l-cysteine, nicotinamide riboside, and l-carnitine tartrate, salt form of l-carnitine. Placebo-controlled, open-label phase 2 study and double-blinded phase 3 clinical trials are conducted to investigate the time of symptom-free recovery on ambulatory patients using CMAs. The results of both studies show that the time to complete recovery is significantly shorter in the CMA group (6.6 vs 9.3 d) in phase 2 and (5.7 vs 9.2 d) in phase 3 trials compared to placebo group. A comprehensive analysis of the plasma metabolome and proteome reveals major metabolic changes. Plasma levels of proteins and metabolites associated with inflammation and antioxidant metabolism are significantly improved in patients treated with CMAs as compared to placebo. The results show that treating patients infected with COVID-19 with CMAs lead to a more rapid symptom-free recovery, suggesting a role for such a therapeutic regime in the treatment of infections leading to respiratory problems.
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15.
  • Arif, Muhammad, et al. (författare)
  • INetModels 2.0: An interactive visualization and database of multi-omics data
  • 2021
  • Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 49:W1, s. W271-W276
  • Tidskriftsartikel (refereegranskat)abstract
    • It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.
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16.
  • Baboota, Ritesh, et al. (författare)
  • BMP4 and Gremlin 1 regulate hepatic cell senescence during clinical progression of NAFLD/NASH
  • 2022
  • Ingår i: Nature Metabolism. - : Springer Science and Business Media LLC. - 2522-5812. ; 4:8, s. 1007-21
  • Tidskriftsartikel (refereegranskat)abstract
    • The role of hepatic cell senescence in human non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) is not well understood. To examine this, we performed liver biopsies and extensive characterization of 58 individuals with or without NAFLD/NASH. Here, we show that hepatic cell senescence is strongly related to NAFLD/NASH severity, and machine learning analysis identified senescence markers, the BMP4 inhibitor Gremlin 1 in liver and visceral fat, and the amount of visceral adipose tissue as strong predictors. Studies in liver cell spheroids made from human stellate and hepatocyte cells show BMP4 to be anti-senescent, anti-steatotic, anti-inflammatory and anti-fibrotic, whereas Gremlin 1, which is particularly highly expressed in visceral fat in humans, is pro-senescent and antagonistic to BMP4. Both senescence and anti-senescence factors target the YAP/TAZ pathway, making this a likely regulator of senescence and its effects. We conclude that senescence is an important driver of human NAFLD/NASH and that BMP4 and Gremlin 1 are novel therapeutic targets. Baboota et al. investigate senescence as a driver of human NAFLD/NASH and show the roles of BMP4 and its antagonist Gremlin 1 as anti-senescent and pro-senescent molecules, respectively.
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17.
  • Bai, Pu, et al. (författare)
  • A Layered Cationic Aluminum Oxyhydroxide as a Highly Efficient and Selective Trap for Heavy Metal Oxyanions
  • 2020
  • Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 59:44, s. 19539-19544
  • Tidskriftsartikel (refereegranskat)abstract
    • Cationic framework materials, especially pure inorganic cationic frameworks that can efficiently and selectively capture harmful heavy metal oxyanions from aqueous solution are highly desired yet scarcely reported. Herein, we report the discovery of a 2D cationic aluminum oxyhydroxide, JU-111, which sets a new benchmark for heavy metal oxyanion sorbents, especially for Cr-VI. Its structure was solved based on 3D electron diffraction tomography data. JU-111 shows fast sorption kinetics (ca. 20 min), high capture capacity (105.4 mg g(-1)), and broad working pH range (3-10) toward Cr(VI)oxyanions. Unlike layered double hydroxides (LDHs), which are poorly selective in the presence of CO32-, JU-111 retains excellent selectivity for Cr(VI)even under a large excess of CO32-. These superior features coupled with the ultra-low cost and environmentally benign nature make JU-111 a promising candidate for toxic metal oxyanion remediation as well as other potential applications.
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18.
  • Bayraktar, Abdulahad, et al. (författare)
  • Drug repositioning targeting glutaminase reveals drug candidates for the treatment of Alzheimer's disease patients
  • 2023
  • Ingår i: Journal of Translational Medicine. - : BMC. - 1479-5876. ; 21:1
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundDespite numerous clinical trials and decades of endeavour, there is still no effective cure for Alzheimer's disease. Computational drug repositioning approaches may be employed for the development of new treatment strategies for Alzheimer's patients since an extensive amount of omics data has been generated during pre-clinical and clinical studies. However, targeting the most critical pathophysiological mechanisms and determining drugs with proper pharmacodynamics and good efficacy are equally crucial in drug repurposing and often imbalanced in Alzheimer's studies.MethodsHere, we investigated central co-expressed genes upregulated in Alzheimer's disease to determine a proper therapeutic target. We backed our reasoning by checking the target gene's estimated non-essentiality for survival in multiple human tissues. We screened transcriptome profiles of various human cell lines perturbed by drug induction (for 6798 compounds) and gene knockout using data available in the Connectivity Map database. Then, we applied a profile-based drug repositioning approach to discover drugs targeting the target gene based on the correlations between these transcriptome profiles. We evaluated the bioavailability, functional enrichment profiles and drug-protein interactions of these repurposed agents and evidenced their cellular viability and efficacy in glial cell culture by experimental assays and Western blotting. Finally, we evaluated their pharmacokinetics to anticipate to which degree their efficacy can be improved.ResultsWe identified glutaminase as a promising drug target. Glutaminase overexpression may fuel the glutamate excitotoxicity in neurons, leading to mitochondrial dysfunction and other neurodegeneration hallmark processes. The computational drug repurposing revealed eight drugs: mitoxantrone, bortezomib, parbendazole, crizotinib, withaferin-a, SA-25547 and two unstudied compounds. We demonstrated that the proposed drugs could effectively suppress glutaminase and reduce glutamate production in the diseased brain through multiple neurodegeneration-associated mechanisms, including cytoskeleton and proteostasis. We also estimated the human blood-brain barrier permeability of parbendazole and SA-25547 using the SwissADME tool.ConclusionsThis study method effectively identified an Alzheimer's disease marker and compounds targeting the marker and interconnected biological processes by use of multiple computational approaches. Our results highlight the importance of synaptic glutamate signalling in Alzheimer's disease progression. We suggest repurposable drugs (like parbendazole) with well-evidenced activities that we linked to glutamate synthesis hereby and novel molecules (SA-25547) with estimated mechanisms for the treatment of Alzheimer's patients.
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19.
  • Bayraktar, Abdulahad, et al. (författare)
  • Revealing the Molecular Mechanisms of Alzheimer's Disease Based on Network Analysis
  • 2021
  • Ingår i: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 22:21
  • Tidskriftsartikel (refereegranskat)abstract
    • The complex pathology of Alzheimer's disease (AD) emphasises the need for comprehensive modelling of the disease, which may lead to the development of efficient treatment strategies. To address this challenge, we analysed transcriptome data of post-mortem human brain samples of healthy elders and individuals with late-onset AD from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) and Mayo Clinic (MayoRNAseq) studies in the AMP-AD consortium. In this context, we conducted several bioinformatics and systems medicine analyses including the construction of AD-specific co-expression networks and genome-scale metabolic modelling of the brain in AD patients to identify key genes, metabolites and pathways involved in the progression of AD. We identified AMIGO1 and GRPRASP2 as examples of commonly altered marker genes in AD patients. Moreover, we found alterations in energy metabolism, represented by reduced oxidative phosphorylation and ATPase activity, as well as the depletion of hexanoyl-CoA, pentanoyl-CoA, (2E)-hexenoyl-CoA and numerous other unsaturated fatty acids in the brain. We also observed that neuroprotective metabolites (e.g., vitamins, retinoids and unsaturated fatty acids) tend to be depleted in the AD brain, while neurotoxic metabolites (e.g., beta-alanine, bilirubin) were more abundant. In summary, we systematically revealed the key genes and pathways related to the progression of AD, gained insight into the crucial mechanisms of AD and identified some possible targets that could be used in the treatment of AD.
  •  
20.
  • Ceyhan, Atakan Burak, et al. (författare)
  • Novel drug targets and molecular mechanisms for sarcopenia based on systems biology
  • 2024
  • Ingår i: Biomedicine and Pharmacotherapy. - : Elsevier BV. - 0753-3322 .- 1950-6007. ; 176
  • Tidskriftsartikel (refereegranskat)abstract
    • Sarcopenia is a major public health concern among older adults, leading to disabilities, falls, fractures, and mortality. This study aimed to elucidate the pathophysiological mechanisms of sarcopenia and identify potential therapeutic targets using systems biology approaches. RNA-seq data from muscle biopsies of 24 sarcopenic and 29 healthy individuals from a previous cohort were analysed. Differential expression, gene set enrichment, gene co-expression network, and topology analyses were conducted to identify target genes implicated in sarcopenia pathogenesis, resulting in the selection of 6 hub genes (PDHX, AGL, SEMA6C, CASQ1, MYORG, and CCDC69). A drug repurposing approach was then employed to identify new pharmacological treatment options for sarcopenia (clofibric-acid, troglitazone, withaferin-a, palbociclib, MG-132, bortezomib). Finally, validation experiments in muscle cell line (C2C12) revealed MG-132 and troglitazone as promising candidates for sarcopenia treatment. Our approach, based on systems biology and drug repositioning, provides insight into the molecular mechanisms of sarcopenia and offers potential new treatment options using existing drugs.
  •  
21.
  • Feng, Ran, et al. (författare)
  • Past terrestrial hydroclimate sensitivity controlled by Earth system feedbacks
  • 2022
  • Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Despite tectonic conditions and atmospheric CO2 levels (pCO2) similar to those of present-day, geological reconstructions from the mid-Pliocene (3.3-3.0 Ma) document high lake levels in the Sahel and mesic conditions in subtropical Eurasia, suggesting drastic reorganizations of subtropical terrestrial hydroclimate during this interval. Here, using a compilation of proxy data and multi-model paleoclimate simulations, we show that the mid-Pliocene hydroclimate state is not driven by direct CO2 radiative forcing but by a loss of northern high-latitude ice sheets and continental greening. These ice sheet and vegetation changes are long-term Earth system feedbacks to elevated pCO2. Further, the moist conditions in the Sahel and subtropical Eurasia during the mid-Pliocene are a product of enhanced tropospheric humidity and a stationary wave response to the surface warming pattern, which varies strongly with land cover changes. These findings highlight the potential for amplified terrestrial hydroclimate responses over long timescales to a sustained CO2 forcing.
  •  
22.
  • Graves, Occam Kelly, et al. (författare)
  • Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma
  • 2023
  • Ingår i: Biomedicine and Pharmacotherapy. - : Elsevier BV. - 0753-3322 .- 1950-6007. ; 161
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Lung adenocarcinoma (LUAD) is the one of the most common subtypes in lung cancer. Although various targeted therapies have been used in the clinical practice, the 5-year overall survival rate of patients is still low. Thus, it is urgent to identify new therapeutic targets and develop new drugs for the treatment of the LUAD patients. Methods: Survival analysis was used to identify the prognostic genes. Gene co-expression network analysis was used to identify the hub genes driving the tumor development. A profile-based drug repositioning approach was used to repurpose the potentially useful drugs for targeting the hub genes. MTT and LDH assay were used to measure the cell viability and drug cytotoxicity, respectively. Western blot was used to detect the expression of the proteins. Findings: We identified 341 consistent prognostic genes from two independent LUAD cohorts, whose high expression was associated with poor survival outcomes of patients. Among them, eight genes were identified as hub genes due to their high centrality in the key functional modules in the gene-co-expression network analysis and these genes were associated with the various hallmarks of cancer (e.g., DNA replication and cell cycle). We performed drug repositioning analysis for three of the eight genes (CDCA8, MCM6, and TTK) based on our drug repositioning approach. Finally, we repurposed five drugs for inhibiting the protein expression level of each target gene and validated the drug efficacy by performing in vitro experiments. Interpretation: We found the consensus targetable genes for the treatment of LUAD patients with different races and geographic characteristics. We also proved the feasibility of our drug repositioning approach for the development of new drugs for disease treatment.
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23.
  • Guo, Donglin, et al. (författare)
  • Highly restricted near-surface permafrost extent during the mid-Pliocene warm period
  • 2023
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 120:36
  • Tidskriftsartikel (refereegranskat)abstract
    • Accurate understanding of permafrost dynamics is critical for evaluating and mitigating impacts that may arise as permafrost degrades in the future; however, existing projections have large uncertainties. Studies of how permafrost responded historically during Earth's past warm periods are helpful in exploring potential future permafrost behavior and to evaluate the uncertainty of future permafrost change projections. Here, we combine a surface frost index model with outputs from the second phase of the Pliocene Model Intercomparison Project to simulate the near-surface (similar to 3 to 4 m depth) permafrost state in the Northern Hemisphere during the mid-Pliocene warm period (mPWP, similar to 3.264 to 3.025 Ma). This period shares similarities with the projected future climate. Constrained by proxy-based surface air temperature records, our simulations demonstrate that near-surface permafrost was highly spatially restricted during the mPWP and was 93 +/- 3% smaller than the preindustrial extent. Near-surface permafrost was present only in the eastern Siberian uplands, Canadian high Arctic Archipelago, and northernmost Greenland. The simulations are similar to near-surface permafrost changes projected for the end of this century under the SSP5-8.5 scenario and provide a perspective on the potential permafrost behavior that may be expected in a warmer world.
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24.
  • Jin, Han, et al. (författare)
  • Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation
  • 2023
  • Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1, s. 5417-
  • Tidskriftsartikel (refereegranskat)abstract
    • Cell lines are valuable resources as model for human biology and translational medicine. It is thus important to explore the concordance between the expression in various cell lines vis-à-vis human native and disease tissues. In this study, we investigate the expression of all human protein-coding genes in more than 1,000 human cell lines representing 27 cancer types by a genome-wide transcriptomics analysis. The cell line gene expression is compared with the corresponding profiles in various tissues, organs, single-cell types and cancers. Here, we present the expression for each cell line and give guidance for the most appropriate cell line for a given experimental study. In addition, we explore the cancer-related pathway and cytokine activity of the cell lines to aid human biology studies and drug development projects. All data are presented in an open access cell line section of the Human Protein Atlas to facilitate the exploration of all human protein-coding genes across these cell lines.
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25.
  • Karlsson, Max, et al. (författare)
  • A single-cell type transcriptomics map of human tissues
  • 2021
  • Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:31
  • Tidskriftsartikel (refereegranskat)abstract
    • Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.
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26.
  • Karlsson, Max, et al. (författare)
  • Genome-wide annotation of protein-coding genes in pig
  • 2022
  • Ingår i: BMC Biology. - : Springer Nature. - 1741-7007. ; 20:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: There is a need for functional genome-wide annotation of the protein-coding genes to get a deeper understanding of mammalian biology. Here, a new annotation strategy is introduced based on dimensionality reduction and density-based clustering of whole-body co-expression patterns. This strategy has been used to explore the gene expression landscape in pig, and we present a whole-body map of all protein-coding genes in all major pig tissues and organs. Results: An open-access pig expression map (www.rnaatlas.org ) is presented based on the expression of 350 samples across 98 well-defined pig tissues divided into 44 tissue groups. A new UMAP-based classification scheme is introduced, in which all protein-coding genes are stratified into tissue expression clusters based on body-wide expression profiles. The distribution and tissue specificity of all 22,342 protein-coding pig genes are presented. Conclusions: Here, we present a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering. A genome-wide resource of the transcriptome map across all major tissues and organs in pig is presented, and the data is available as an open-access resource (www.rnaatlas.org), including a comparison to the expression of human orthologs.
  •  
27.
  • Kaynar, Ali, et al. (författare)
  • Systems Biology Approaches to Decipher the Underlying Molecular Mechanisms of Glioblastoma Multiforme
  • 2021
  • Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 22:24, s. 13213-
  • Tidskriftsartikel (refereegranskat)abstract
    • Glioblastoma multiforme (GBM) is one of the most malignant central nervous system tumors, showing a poor prognosis and low survival rate. Therefore, deciphering the underlying molecular mechanisms involved in the progression of the GBM and identifying the key driver genes responsible for the disease progression is crucial for discovering potential diagnostic markers and therapeutic targets. In this context, access to various biological data, development of new methodologies, and generation of biological networks for the integration of multi-omics data are necessary for gaining insights into the appearance and progression of GBM. Systems biology approaches have become indispensable in analyzing heterogeneous high-throughput omics data, extracting essential information, and generating new hypotheses from biomedical data. This review provides current knowledge regarding GBM and discusses the multi-omics data and recent systems analysis in GBM to identify key biological functions and genes. This knowledge can be used to develop efficient diagnostic and treatment strategies and can also be used to achieve personalized medicine for GBM.
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28.
  • Li, Xiangyu, et al. (författare)
  • Classification of clear cell renal cell carcinoma based on PKM alternative splicing
  • 2020
  • Ingår i: Heliyon. - : Elsevier BV. - 2405-8440. ; 6:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Clear cell renal cell carcinoma (ccRCC) accounts for 70-80% of kidney cancer diagnoses and displays high molecular and histologic heterogeneity. Hence, it is necessary to reveal the underlying molecular mechanisms involved in progression of ccRCC to better stratify the patients and design effective treatment strategies. Here, we analyzed the survival outcome of ccRCC patients as a consequence of the differential expression of four transcript isoforms of the pyruvate kinase muscle type (PKM). We first extracted a classification biomarker consisting of eight gene pairs whose within-sample relative expression orderings (REOs) could be used to robustly classify the patients into two groups with distinct molecular characteristics and survival outcomes. Next, we validated our findings in a validation cohort and an independent Japanese ccRCC cohort. We finally performed drug repositioning analysis based on transcriptomic expression profiles of drug-perturbed cancer cell lines and proposed that paracetamol, nizatidine, dimethadione and conessine can be repurposed to treat the patients in one of the subtype of ccRCC whereas chenodeoxycholic acid, fenoterol and hexylcaine can be repurposed to treat the patients in the other subtype.
  •  
29.
  • Li, Xiangyu, et al. (författare)
  • Discovery of Functional Alternatively Spliced PKM Transcripts in Human Cancers
  • 2021
  • Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 13:2, s. 1-23
  • Tidskriftsartikel (refereegranskat)abstract
    • Simple Summary Pyruvate kinase muscle type (PKM) is a key enzyme in glycolysis and is a mediator of the Warburg effect in tumors. The association of PKM with survival of cancer patients is controversial. In this study, we investigated the associations of the alternatively spliced transcripts of PKM with cancer patients' survival outcomes and explained the conflicts in previous studies. We discovered three poorly studied alternatively spliced PKM transcripts that exhibited opposite prognostic indications in different human cancers based on integrative systems analysis. We also detected their protein products and explored their potential biological functions based on in-vitro experiments. Our analysis demonstrated that alternatively spliced transcripts of not only PKM but also other genes should be considered in cancer studies, since it may enable the discovery and targeting of the right protein product for development of the efficient treatment strategies. Pyruvate kinase muscle type (PKM) is a key enzyme in glycolysis and plays an important oncological role in cancer. However, the association of PKM expression and the survival outcome of patients with different cancers is controversial. We employed systems biology methods to reveal prognostic value and potential biological functions of PKM transcripts in different human cancers. Protein products of transcripts were shown and detected by western blot and mass spectrometry analysis. We focused on different transcripts of PKM and investigated the associations between their mRNA expression and the clinical survival of the patients in 25 different cancers. We find that the transcripts encoding PKM2 and three previously unstudied transcripts, namely ENST00000389093, ENST00000568883, and ENST00000561609, exhibited opposite prognostic indications in different cancers. Moreover, we validated the prognostic effect of these transcripts in an independent kidney cancer cohort. Finally, we revealed that ENST00000389093 and ENST00000568883 possess pyruvate kinase enzymatic activity and may have functional roles in metabolism, cell invasion, and hypoxia response in cancer cells. Our study provided a potential explanation to the controversial prognostic indication of PKM, and could invoke future studies focusing on revealing the biological and oncological roles of these alternative spliced variants of PKM.
  •  
30.
  • Li, Xiangyu, et al. (författare)
  • Prediction of drug candidates for clear cell renal cell carcinoma using a systems biology-based drug repositioning approach
  • 2022
  • Ingår i: EBioMedicine. - : Elsevier BV. - 2352-3964. ; 78, s. 103963-
  • Tidskriftsartikel (refereegranskat)abstract
    • SummaryBackground: The response rates of the clinical chemotherapies are still low in clear cell renal cell carcinoma (ccRCC). Computational drug repositioning is a promising strategy to discover new uses for existing drugs to treat patients who cannot get benefits from clinical drugs.Methods: We proposed a systematic approach which included the target prediction based on the co-expression network analysis of transcriptomics profiles of ccRCC patients and drug repositioning for cancer treatment based on the analysis of shRNA-and drug-perturbed signature profiles of human kidney cell line.Findings: First, based on the gene co-expression network analysis, we identified two types of gene modules in ccRCC, which significantly enriched with unfavorable and favorable signatures indicating poor and good survival outcomes of patients, respectively. Then, we selected four genes, BUB1B, RRM2, ASF1B and CCNB2, as the potential drug targets based on the topology analysis of modules. Further, we repurposed three most effective drugs for each target by applying the proposed drug repositioning approach. Finally, we evaluated the effects of repurposed drugs using an in vitro model and observed that these drugs inhibited the protein levels of their corresponding target genes and cell viability.Interpretation: These findings proved the usefulness and efficiency of our approach to improve the drug repositioning researches for cancer treatment and precision medicine.Funding: This study was funded by Knut and Alice Wallenberg Foundation and Bash Biotech Inc., San Diego, CA, USA. 
  •  
31.
  • Li, Xiangyu, et al. (författare)
  • Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning
  • 2021
  • Ingår i: iScience. - : Elsevier BV. - 2589-0042. ; 24:7
  • Tidskriftsartikel (refereegranskat)abstract
    • Clear cell renal cell carcinoma (ccRCC) is the most common histological type of kidney cancer and has high heterogeneity. Stratification of ccRCC is important since distinct subtypes differ in prognosis and treatment. Here, we applied a systems biology approach to stratify ccRCC into three molecular subtypes with different mRNA expression patterns and prognosis of patients. Further, we developed a set of biomarkers that could robustly classify the patients into each of the three subtypes and predict the prognosis of patients. Then, we reconstructed subtype-specific metabolic models and performed essential gene analysis to identify the potential drug targets. We identified four drug targets, including SOAT1, CRLS1, and ACACB, essential in all the three subtypes and GPD2, exclusively essential to subtype 1. Finally, we repositioned mitotane, an FDA-approved SOAT1 inhibitor, to treat ccRCC and showed that it decreased tumor cell viability and inhibited tumor cell growth based on in vitro experiments.
  •  
32.
  • Li, Xiangyu, et al. (författare)
  • The acute effect of different NAD+ precursors included in the combined metabolic activators
  • 2023
  • Ingår i: Free Radical Biology & Medicine. - : Elsevier BV. - 0891-5849 .- 1873-4596. ; 205, s. 77-89
  • Tidskriftsartikel (refereegranskat)abstract
    • NAD+ and glutathione precursors are currently used as metabolic modulators for improving the metabolic conditions associated with various human diseases, including non-alcoholic fatty liver disease, neurodegenerative diseases, mitochondrial myopathy, and age-induced diabetes. Here, we performed a one-day double blinded, placebo-controlled human clinical study to assess the safety and acute effects of six different Combined Metabolic Activators (CMAs) with 1 g of different NAD+ precursors based on global metabolomics analysis. Our integrative analysis showed that the NAD+ salvage pathway is the main source for boosting the NAD+ levels with the administration of CMAs without NAD+ precursors. We observed that incorporation of nicotinamide (Nam) in the CMAs can boost the NAD+ products, followed by niacin (NA), nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN), but not flush free niacin (FFN). In addition, the NA administration led to a flushing reaction, accompanied by decreased phospholipids and increased bilirubin and bilirubin derivatives, which could be potentially risky. In conclusion, this study provided a plasma metabolomic landscape of different CMA formulations, and proposed that CMAs with Nam, NMN as well as NR can be administered for boosting NAD+ levels to improve altered metabolic conditions.
  •  
33.
  • Liao, Xinmeng, et al. (författare)
  • Open MoA : revealing the mechanism of action (MoA) based on network topology and hierarchy
  • 2023
  • Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 39:11
  • Tidskriftsartikel (refereegranskat)abstract
    • MOTIVATION: Many approaches in systems biology have been applied in drug repositioning due to the increased availability of the omics data and computational biology tools. Using a multi-omics integrated network, which contains information of various biological interactions, could offer a more comprehensive inspective and interpretation for the drug mechanism of action (MoA). RESULTS: We developed a computational pipeline for dissecting the hidden MoAs of drugs (Open MoA). Our pipeline computes confidence scores to edges that represent connections between genes/proteins in the integrated network. The interactions showing the highest confidence score could indicate potential drug targets and infer the underlying molecular MoAs. Open MoA was also validated by testing some well-established targets. Additionally, we applied Open MoA to reveal the MoA of a repositioned drug (JNK-IN-5A) that modulates the PKLR expression in HepG2 cells and found STAT1 is the key transcription factor. Overall, Open MoA represents a first-generation tool that could be utilized for predicting the potential MoA of repurposed drugs and dissecting de novo targets for developing effective treatments. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/XinmengLiao/Open_MoA.
  •  
34.
  • Liu, Xiangyu, et al. (författare)
  • Correlation-Based Calibration for Nonlinearity Mismatches in Dual-Channel TIADCs
  • 2020
  • Ingår i: IEEE Transactions on Circuits and Systems - II - Express Briefs. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 1549-7747 .- 1558-3791. ; 67:3, s. 585-589
  • Tidskriftsartikel (refereegranskat)abstract
    • Mismatches affect the dynamic performance of time-interleaved analog-to-digital converters (TIADCs). Linear mismatches can be calibrated by many mature methods, but if higher performance is required, nonlinearity mismatches have to be suppressed. The background calibration method based on input-free band (IFB) functions poorly for narrow-band signals. This brief proposes a correlation-based calibration method for nonlinearity mismatches in dual-channel TIADCs which behaves well for both wide-band and narrow-band signals. The output samples are calibrated by reducing the residual distortions which are approximated by multiplying the pseudo distortions and the estimated mismatch coefficients. The pseudo distortions are acquired by using a frequency-shifter, a differentiator, and multipliers. The coefficients which indicate the mismatch strength are estimated by eliminating the cross-correlation of the calibrated output samples and the calibrated pseudo distortions at zero lag. Simulations show that the proposed method can improve the SFDR by dozens of dBc for narrow-band input signals, compared with the IFB method. For the 16-QAM signal, the error vector magnitude improvement over the IFB method is 35.48 dB.
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35.
  •  
36.
  • Ren, Xin, et al. (författare)
  • The hydrological cycle and ocean circulation of the Maritime Continent in the Pliocene : results from PlioMIP2
  • 2023
  • Ingår i: Climate of the Past. - 1814-9324 .- 1814-9332. ; 19:10, s. 2053-2077
  • Tidskriftsartikel (refereegranskat)abstract
    • The Maritime Continent (MC) forms the western boundary of the tropical Pacific Ocean, and relatively small changes in this region can impact the climate locally and remotely. In the mid-Piacenzian warm period of the Pliocene (mPWP; 3.264 to 3.025 Ma) atmospheric CO2 concentrations were ∼ 400 ppm, and the subaerial Sunda and Sahul shelves made the land–sea distribution of the MC different to today. Topographic changes and elevated levels of CO2, combined with other forcings, are therefore expected to have driven a substantial climate signal in the MC region at this time. By using the results from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2), we study the mean climatic features of the MC in the mPWP and changes in Indonesian Throughflow (ITF) with respect to the preindustrial. Results show a warmer and wetter mPWP climate of the MC and lower sea surface salinity in the surrounding ocean compared with the preindustrial. Furthermore, we quantify the volume transfer through the ITF; although the ITF may be expected to be hindered by the subaerial shelves, 10 out of 15 models show an increased volume transport compared with the preindustrial.In order to avoid undue influence from closely related models that are present in the PlioMIP2 ensemble, we introduce a new metric, the multi-cluster mean (MCM), which is based on cluster analysis of the individual models. We study the effect that the choice of MCM versus the more traditional analysis of multi-model mean (MMM) and individual models has on the discrepancy between model results and data. We find that models, which reproduce modern MC climate well, are not always good at simulating the mPWP climate anomaly of the MC. By comparing with individual models, the MMM and MCM reproduce the preindustrial sea surface temperature (SST) of the reanalysis better than most individual models and produce less discrepancy with reconstructed sea surface temperature anomalies (SSTA) than most individual models in the MC. In addition, the clusters reveal spatial signals that are not captured by the MMM, so that the MCM provides us with a new way to explore the results from model ensembles that include similar models.
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37.
  • Song, Yubao, et al. (författare)
  • Vibration and sound properties of metamaterial sandwich panels with periodically attached resonators : Simulation and experiment study
  • 2020
  • Ingår i: Journal of Sound and Vibration. - : Academic Press. - 0022-460X .- 1095-8568. ; 489
  • Tidskriftsartikel (refereegranskat)abstract
    • The vibration and sound properties of a type of metamaterial sandwich panels are investigated in this paper. The metamaterial sandwich panels consisting of a host sandwich panel and periodically attached resonant units are designed. Both the panels with and without damping are considered. Via the comparison of metamaterial and bare panels, the effects of the periodic design on wave propagation, vibration, sound radiation and sound transmission properties are analysed and compared numerically. The reduction on the vibration and sound is studied. The numerical results indicate that the vibration, sound radiation and sound transmission are significantly reduced over a wide frequency range. The reduction is obviously larger than that obtained only by increasing the mass. In addition, the experiment specimens of bare and metamaterial sandwich panels are designed. The vibration and sound properties of them are tested and compared. According to the experimental results, the reduction is also observed in a wide frequency range. The simulation results and corresponding analysis are verified. Further, the effects of structural parameters of sandwich panels on the reduction of vibration and sound properties from periodic design are investigated. Several typical cases are analysed concretely. The reasons for the reduction and other effects on the vibration and sound properties from periodic design are analysed. For the panels with various parameter settings, a nice reduction of vibration and sound is generated also form periodic design; on the other hand, the reduction characteristics are changed.
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38.
  • Sun, Wei, et al. (författare)
  • Molecular and Biochemical Analysis of Chalcone Synthase from Freesia hybrid in Flavonoid Biosynthetic Pathway
  • 2015
  • Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:3
  • Tidskriftsartikel (refereegranskat)abstract
    • Chalcone synthase (CHS) catalyzes the first committed step in the flavonoid biosynthetic pathway. In this study, the cDNA (FhCHS1) encoding CHS from Freesia hybrida was successfully isolated and analyzed. Multiple sequence alignments showed that both the conserved CHS active site residues and CHS signature sequence were found in the deduced amino acid sequence of FhCHS1. Meanwhile, crystallographic analysis revealed that protein structure of FhCHS1 is highly similar to that of alfalfa CHS2, and the biochemical analysis results indicated that it has an enzymatic role in naringenin biosynthesis. Moreover, quantitative real-time PCR was performed to detect the transcript levels of FhCHS1 in flowers and different tissues, and patterns of FhCHS1 expression in flowers showed significant correlation to the accumulation patterns of anthocyanin during flower development. To further characterize the functionality of FhCHS1, its ectopic expression in Arabidopsis thaliana tt4 mutants and Petunia hybrida was performed. The results showed that overexpression of FhCHS1 in tt4 mutants fully restored the pigmentation phenotype of the seed coats, cotyledons and hypocotyls, while transgenic petunia expressing FhCHS1 showed flower color alteration from white to pink. In summary, these results suggest that FhCHS1 plays an essential role in the biosynthesis of flavonoid in Freesia hybrida and may be used to modify the components of flavonoids in other plants.
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39.
  • Yang, Hong, et al. (författare)
  • A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic liver disease
  • 2021
  • Ingår i: Iscience. - : Elsevier BV. - 2589-0042. ; 24:11
  • Tidskriftsartikel (refereegranskat)abstract
    • Non-alcoholic fatty liver disease (NAFLD) is a leading cause of chronic liver disease worldwide. We performed network analysis to investigate the dysregulated biological processes in the disease progression and revealed the molecular mechanism underlying NAFLD. Based on network analysis, we identified a highly conserved disease-associated gene module across three different NAFLD cohorts and highlighted the predominant role of key transcriptional regulators associated with lipid and cholesterol metabolism. In addition, we revealed the detailed metabolic differences between heterogeneous NAFLD patients through integrative systems analysis of transcriptomic data and liver-specific genomescale metabolic model. Furthermore, we identified transcription factors (TFs), including SREBF2, HNF4A, SREBF1, YY1, and KLF13, showing regulation of hepatic expression of genes in the NAFLD-associated modules and validated the TFs using data generated from a mouse NAFLD model. In conclusion, our integrative analysis facilitates the understanding of the regulatory mechanism of these perturbed TFs and their associated biological processes.
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40.
  • Yang, Hong, et al. (författare)
  • Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators
  • 2023
  • Ingår i: Free Radical Biology and Medicine. - : Elsevier BV. - 0891-5849 .- 1873-4596. ; 204, s. 347-358
  • Tidskriftsartikel (refereegranskat)abstract
    • Growing evidence suggests that the depletion of plasma NAD+ and glutathione (GSH) may play an important role in the development of metabolic disorders. The administration of Combined Metabolic Activators (CMA), con-sisting of GSH and NAD+ precursors, has been explored as a promising therapeutic strategy to target multiple altered pathways associated with the pathogenesis of the diseases. Although studies have examined the thera-peutic effect of CMA that contains N-acetyl-L-cysteine (NAC) as a metabolic activator, a system-wide comparison of the metabolic response to the administration of CMA with NAC and cysteine remains lacking. In this placebo-controlled study, we studied the acute effect of the CMA administration with different metabolic activators, including NAC or cysteine with/without nicotinamide or flush free niacin, and performed longitudinal untargeted-metabolomics profiling of plasma obtained from 70 well-characterized healthy volunteers. The time-series metabolomics data revealed the metabolic pathways affected after the administration of CMAs showed high similarity between CMA containing nicotinamide and NAC or cysteine as metabolic activators. Our analysis also showed that CMA with cysteine is well-tolerated and safe in healthy individuals throughout the study. Last, our study systematically provided insights into a complex and dynamics landscape involved in amino acid, lipid and nicotinamide metabolism, reflecting the metabolic responses to CMA administration containing different metabolic activators.
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41.
  • Yuan, Meng, et al. (författare)
  • A Gene Co-Expression Network-Based Drug Repositioning Approach Identifies Candidates for Treatment of Hepatocellular Carcinoma
  • 2022
  • Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 14:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Hepatocellular carcinoma (HCC) is a malignant liver cancer that continues to increase deaths worldwide owing to limited therapies and treatments. Computational drug repurposing is a promising strategy to discover potential indications of existing drugs. In this study, we present a systematic drug repositioning method based on comprehensive integration of molecular signatures in liver cancer tissue and cell lines. First, we identify robust prognostic genes and two gene co-expression modules enriched in unfavorable prognostic genes based on two independent HCC cohorts, which showed great consistency in functional and network topology. Then, we screen 10 genes as potential target genes for HCC on the bias of network topology analysis in these two modules. Further, we perform a drug repositioning method by integrating the shRNA and drug perturbation of liver cancer cell lines and identifying potential drugs for every target gene. Finally, we evaluate the effects of the candidate drugs through an in vitro model and observe that two identified drugs inhibited the protein levels of their corresponding target genes and cell migration, also showing great binding affinity in protein docking analysis. Our study demonstrates the usefulness and efficiency of network-based drug repositioning approach to discover potential drugs for cancer treatment and precision medicine approach.
  •  
42.
  • Yulug, B., et al. (författare)
  • Combined metabolic activators improve cognitive functions in Alzheimer's disease patients: a randomised, double-blinded, placebo-controlled phase-II trial
  • 2023
  • Ingår i: Translational Neurodegeneration. - : Springer Science and Business Media LLC. - 2047-9158. ; 12:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Alzheimer's disease (AD) is associated with metabolic abnormalities linked to critical elements of neurodegeneration. We recently administered combined metabolic activators (CMA) to the AD rat model and observed that CMA improves the AD-associated histological parameters in the animals. CMA promotes mitochondrial fatty acid uptake from the cytosol, facilitates fatty acid oxidation in the mitochondria, and alleviates oxidative stress.Methods Here, we designed a randomised, double-blinded, placebo-controlled phase-II clinical trial and studied the effect of CMA administration on the global metabolism of AD patients. One-dose CMA included 12.35 g L-serine (61.75%), 1 g nicotinamide riboside (5%), 2.55 g N-acetyl-L-cysteine (12.75%), and 3.73 g L-carnitine tartrate (18.65%). AD patients received one dose of CMA or placebo daily during the first 28 days and twice daily between day 28 and day 84. The primary endpoint was the difference in the cognitive function and daily living activity scores between the placebo and the treatment arms. The secondary aim of this study was to evaluate the safety and tolerability of CMA. A comprehensive plasma metabolome and proteome analysis was also performed to evaluate the efficacy of the CMA in AD patients.Results We showed a significant decrease of AD Assessment Scale-cognitive subscale (ADAS-Cog) score on day 84 vs day 0 (P = 0.00001, 29% improvement) in the CMA group. Moreover, there was a significant decline (P = 0.0073) in ADAS-Cog scores (improvement of cognitive functions) in the CMA compared to the placebo group in patients with higher ADAS-Cog scores. Improved cognitive functions in AD patients were supported by the relevant alterations in the hippocampal volumes and cortical thickness based on imaging analysis. Moreover, the plasma levels of proteins and metabolites associated with NAD + and glutathione metabolism were significantly improved after CMA treatment.Conclusion Our results indicate that treatment of AD patients with CMA can lead to enhanced cognitive functions and improved clinical parameters associated with phenomics, metabolomics, proteomics and imaging analysis.
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43.
  • Zeybel, M., et al. (författare)
  • Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients
  • 2021
  • Ingår i: Molecular Systems Biology. - : EMBO. - 1744-4292. ; 17:10
  • Tidskriftsartikel (refereegranskat)abstract
    • Nonalcoholic fatty liver disease (NAFLD) refers to excess fat accumulation in the liver. In animal experiments and human kinetic study, we found that administration of combined metabolic activators (CMAs) promotes the oxidation of fat, attenuates the resulting oxidative stress, activates mitochondria, and eventually removes excess fat from the liver. Here, we tested the safety and efficacy of CMA in NAFLD patients in a placebo-controlled 10-week study. We found that CMA significantly decreased hepatic steatosis and levels of aspartate aminotransferase, alanine aminotransferase, uric acid, and creatinine, whereas found no differences on these variables in the placebo group after adjustment for weight loss. By integrating clinical data with plasma metabolomics and inflammatory proteomics as well as oral and gut metagenomic data, we revealed the underlying molecular mechanisms associated with the reduced hepatic fat and inflammation in NAFLD patients and identified the key players involved in the host-microbiome interactions. In conclusion, we showed that CMA can be used to develop a pharmacological treatment strategy in NAFLD patients.
  •  
44.
  • Zeybel, Mujdat, et al. (författare)
  • Multi-omics analysis reveals the influence of the oral and gut microbiome on host metabolism in non-alcoholic fatty liver disease
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Non-alcoholic fatty liver disease (NAFLD) is a complex disease involving alterations in multiple biological processes regulated by the interactions between obesity, genetic background and environmental factors including the microbiome. To decipher hepatic steatosis (HS) pathogenesis by excluding critical confounding factors including genetic variants, obesity and diabetes, we characterized 56 heterogeneous NAFLD patients by generating multi-omics data including oral and gut metagenomics as well as plasma metabolomics and inflammatory proteomics data. We explored the dysbiosis in the oral and gut microbiome and revealed host-microbiome interactions based on global metabolic and inflammatory processes. We integrated this multi-omics data using the biological network and identified HS's key features using multi-omics data. We finally predicted HS using these key features and validated our findings in a validation dataset, where we characterized 22 subjects with varying degree of HS 
  •  
45.
  • Zeybel, M., et al. (författare)
  • Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis
  • 2022
  • Ingår i: Advanced Science. - : Wiley. - 2198-3844. ; 9:11, s. 2104373-
  • Tidskriftsartikel (refereegranskat)abstract
    • Metabolic dysfunction-associated fatty liver disease (MAFLD) is a complex disease involving alterations in multiple biological processes regulated by the interactions between obesity, genetic background, and environmental factors including the microbiome. To decipher hepatic steatosis (HS) pathogenesis by excluding critical confounding factors including genetic variants and diabetes, 56 heterogenous MAFLD patients are characterized by generating multiomics data including oral and gut metagenomics as well as plasma metabolomics and inflammatory proteomics data. The dysbiosis in the oral and gut microbiome is explored and the host–microbiome interactions based on global metabolic and inflammatory processes are revealed. These multiomics data are integrated using the biological network and HS's key features are identified using multiomics data. HS is finally predicted using these key features and findings are validated in a follow-up cohort, where 22 subjects with varying degree of HS are characterized.
  •  
46.
  • Zhang, Cheng, et al. (författare)
  • Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning
  • 2022
  • Ingår i: eBioMedicine. - : Elsevier BV. - 2352-3964. ; 83
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Non-alcoholic fatty liver disease (NAFLD) encompasses a wide spectrum of liver pathologies. However, no medical treatment has been approved for the treatment of NAFLD. In our previous study, we found that PKLR could be a potential target for treatment of NALFD. Here, we investigated the effect of PKLR in in vivo model and performed drug repositioning to identify a drug candidate for treatment of NAFLD. Methods Tissue samples from liver, muscle, white adipose and heart were obtained from control and PKLR knock-out mice fed with chow and high sucrose diets. Lipidomics as well as transcriptomics analyses were conducted using these tissue samples. In addition, a computational drug repositioning analysis was performed and drug candidates were identified. The drug candidates were both tested in in vitro and in vivo models to evaluate their toxicity and efficacy. Findings The Pklr KO reversed the increased hepatic triglyceride level in mice fed with high sucrose diet and partly recovered the transcriptomic changes in the liver as well as in other three tissues. Both liver and white adipose tissues exhibited dysregulated circadian transcriptomic profiles, and these dysregulations were reversed by hepatic knockout of Pklr. In addition, 10 small molecule drug candidates were identified as potential inhibitor of PKLR using our drug repositioning pipeline, and two of them significantly inhibited both the PKLR expression and triglyceride level in in vitro model. Finally, the two selected small molecule drugs were evaluated in in vivo rat models and we found that these drugs attenuate the hepatic steatosis without side effect on other tissues. Interpretation In conclusion, our study provided biological insights about the critical role of PKLR in NAFLD progression and proposed a treatment strategy for NAFLD patients, which has been validated in preclinical studies. Copyright (C) 2022 The Authors. Published by Elsevier B.V.
  •  
47.
  • Zhang, Cheng, et al. (författare)
  • Elucidating the Reprograming of Colorectal Cancer Metabolism Using Genome-Scale Metabolic Modeling
  • 2019
  • Ingår i: Frontiers in Oncology. - : Frontiers Media SA. - 2234-943X. ; 9
  • Tidskriftsartikel (refereegranskat)abstract
    • Colorectal cancer is the third most incidental cancer worldwide, and the response rate of current treatment for colorectal cancer is very low. Genome-scale metabolic models (GEMs) are systems biology platforms, and they had been used to assist researchers in understanding the metabolic alterations in different types of cancer. Here, we reconstructed a generic colorectal cancer GEM by merging 374 personalized GEMs from the Human Pathology Atlas and used it as a platform for systematic investigation of the difference between tumor and normal samples. The reconstructed model revealed the metabolic reprogramming in glutathione as well as the arginine and proline metabolism in response to tumor occurrence. In addition, six genes including ODC1, SMS, SRM, RRM2, SMOX, and SAT1 associated with arginine and proline metabolism were found to be key players in this metabolic alteration. We also investigated these genes in independent colorectal cancer patients and cell lines and found that many of these genes showed elevated level in colorectal cancer and exhibited adverse effect in patients. Therefore, these genes could be promising therapeutic targets for treatment of a specific colon cancer patient group.
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