bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting dwell fatigue life in titanium alloys using modelling and experiment
Authors: Xu Yilun , Joseph Sudha , Karamched Phani , Fox Kate , Rugg David , Dunne Fionn P. E. , Dye David 
Published: November 2020

AbstractFatigue is a difficult multi-scale modelling problem nucleating from localised plasticity at the scale of dislocations and microstructure with significant engineering safety implications. Cold dwell fatigue is a phenomenon in titanium where stress holds at moderate temperatures lead to substantial reductions in cyclic life, and has been implicated in service failures. Using discrete dislocation plasticity modelling complemented by transmission electron microscopy, we successfully predict lifetimes for ‘worst case’ microstructures representative of jet engine spin tests. Fatigue loading above a threshold stress is found to produce slip in soft grains, leading to strong dislocation pile-ups at boundaries with hard grains. Pile-up stresses generated are high enough to nucleate hard grain basal dislocations, as observed experimentally. Reduction of applied cyclic load alongside a temperature excursion during the cycle lead to much lower densities of prism dislocations in soft grains and, sometimes, the elimination of basal dislocations in hard grains altogether.
Long non-coding RNA Gm15441 attenuates hepatic inflammasome activation in response to PPARA agonism and fasting
Authors: Brocker Chad N. , Kim Donghwan , Melia Tisha , Karri Kritika , Velenosi Thomas J. , Takahashi Shogo , Aibara Daisuke , Bonzo Jessica A. , Levi Moshe , Waxman David J. , Gonzalez Frank J. 
Published: November 2020

AbstractExploring the molecular mechanisms that prevent inflammation during caloric restriction may yield promising therapeutic targets. During fasting, activation of the nuclear receptor peroxisome proliferator-activated receptor α (PPARα) promotes the utilization of lipids as an energy source. Herein, we show that ligand activation of PPARα directly upregulates the long non-coding RNA gene Gm15441 through PPARα binding sites within its promoter. Gm15441 expression suppresses its antisense transcript, encoding thioredoxin interacting protein (TXNIP). This, in turn, decreases TXNIP-stimulated NLR family pyrin domain containing 3 (NLRP3) inflammasome activation, caspase-1 (CASP1) cleavage, and proinflammatory interleukin 1β (IL1B) maturation. Gm15441-null mice were developed and shown to be more susceptible to NLRP3 inflammasome activation and to exhibit elevated CASP1 and IL1B cleavage in response to PPARα agonism and fasting. These findings provide evidence for a mechanism by which PPARα attenuates hepatic inflammasome activation in response to metabolic stress through induction of lncRNA Gm15441.
Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning
Authors: Li Jieming , Zhang Leyou , Johnson-Buck Alexander , Walter Nils G. 
Published: November 2020

AbstractTraces from single-molecule fluorescence microscopy (SMFM) experiments exhibit photophysical artifacts that typically necessitate human expert screening, which is time-consuming and introduces potential for user-dependent expectation bias. Here, we use deep learning to develop a rapid, automatic SMFM trace selector, termed AutoSiM, that improves the sensitivity and specificity of an assay for a DNA point mutation based on single-molecule recognition through equilibrium Poisson sampling (SiMREPS). The improved performance of AutoSiM is based on accepting both more true positives and fewer false positives than the conventional approach of hidden Markov modeling (HMM) followed by hard thresholding. As a second application, the selector is used for automated screening of single-molecule Förster resonance energy transfer (smFRET) data to identify high-quality traces for further analysis, and achieves ~90% concordance with manual selection while requiring less processing time. Finally, we show that AutoSiM can be adapted readily to novel datasets, requiring only modest Transfer Learning.
Immune suppression in the early stage of COVID-19 disease
Authors: Tian Wenmin , Zhang Nan , Jin Ronghua , Feng Yingmei , Wang Siyuan , Gao Shuaixin , Gao Ruqin , Wu Guizhen , Tian Di , Tan Wenjie , Chen Yang , Gao George Fu , Wong Catherine C. L. 
Published: November 2020

AbstractThe outbreak of COVID-19 has become a worldwide pandemic. The pathogenesis of this infectious disease and how it differs from other drivers of pneumonia is unclear. Here we analyze urine samples from COVID-19 infection cases, healthy donors and non-COVID-19 pneumonia cases using quantitative proteomics. The molecular changes suggest that immunosuppression and tight junction impairment occur in the early stage of COVID-19 infection. Further subgrouping of COVID-19 patients into moderate and severe types shows that an activated immune response emerges in severely affected patients. We propose a two-stage mechanism of pathogenesis for this unusual viral infection. Our data advance our understanding of the clinical features of COVID-19 infections and provide a resource for future mechanistic and therapeutics studies.
Nutritional and bioactive constituents and scavenging capacity of radicals in Amaranthus hypochondriacus
Authors: Sarker Umakanta , Oba Shinya 
Published: November 2020

AbstractA. hypochondriacus leaves contained ample phytopigments including betalain, anthocyanin, β-xanthin, β-cyanin, and bioactive phytochemicals of interest in the industry of food. We have been evaluating the possibility of utilizing phytopigments of amaranth and bioactive constituents for making drinks. Therefore, we evaluated bioactive phytopigments and compounds including the potentiality of antioxidants in A. hypochondriacus leaves. A. hypochondriacus leaves have abundant protein, carbohydrates, and dietary fiber. We found considerable levels of inorganic minerals including magnesium, calcium, potassium (3.88, 3.01, 8.56 mg g−1), zinc, manganese, copper, iron (16.23, 15.51, 2.26, 20.57 µg g−1), chlorophyll b, chlorophyll ab chlorophyll a (271.08, 905.21, 636.87 μg g−1), scavenging capacity of radicals (DPPH, ABTS+) (33.46, 62.92 TEAC μg g−1 DW), total polyphenols (29.34 GAE μg g−1 FW), β-xanthin, betalain, β-cyanin (584.71, 1,121.93, 537.21 ng g−1), total flavonoids (170.97 RE μg g−1 DW), vitamin C, β-carotene, carotenoids (184.77, 82.34, 105.08 mg 100 g−1) in A. hypochondriacus leaves. The genotypes AHC6, AHC4, AHC11, AHC5, and AHC10 had a good scavenging capacity of radicals. Polyphenols, phytopigments, flavonoids, and β-carotene of A. hypochondriacus had potential antioxidant activity. Extracted juice of A. hypochondriacus can be an ample source of phytopigments and compounds for detoxification of reactive oxygen species (ROS) and attaining nutritional and antioxidant sufficiency.
FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins
Authors: Lagardère Matthieu , Chamma Ingrid , Bouilhol Emmanuel , Nikolski Macha , Thoumine Olivier 
Published: November 2020

AbstractFluorescence live-cell and super-resolution microscopy methods have considerably advanced our understanding of the dynamics and mesoscale organization of macro-molecular complexes that drive cellular functions. However, different imaging techniques can provide quite disparate information about protein motion and organization, owing to their respective experimental ranges and limitations. To address these issues, we present here a robust computer program, called FluoSim, which is an interactive simulator of membrane protein dynamics for live-cell imaging methods including SPT, FRAP, PAF, and FCS, and super-resolution imaging techniques such as PALM, dSTORM, and uPAINT. FluoSim integrates diffusion coefficients, binding rates, and fluorophore photo-physics to calculate in real time the localization and intensity of thousands of independent molecules in 2D cellular geometries, providing simulated data directly comparable to actual experiments. FluoSim was thoroughly validated against experimental data obtained on the canonical neurexin-neuroligin adhesion complex at cell–cell contacts. This unified software allows one to model and predict membrane protein dynamics and localization at the ensemble and single molecule level, so as to reconcile imaging paradigms and quantitatively characterize protein behavior in complex cellular environments.
Pirfenidone regulates LPS mediated activation of neutrophils
Authors: Evani Shankar J. , Karna S. L. Rajasekhar , Seshu Janakiram , Leung Kai P. 
Published: November 2020

AbstractExcessive inflammation or its absence may result in impaired wound healing. Neutrophils are among the first innate immune cells to arrive at the injury site. They participate in infection control and debris removal to initiate healing. If not timely resolved, neutrophils can cause excessive tissue inflammation and damage. Drugs with anti-inflammatory and anti-fibrotic effects are of promise for improving healing by balancing the primary defensive functions and excessive tissue damage actions. Of interest, pirfenidone (Pf), an FDA approved anti-fibrotic drug to treat idiopathic pulmonary fibrosis, has been shown to ameliorate inflammation in several animal models including mouse deep partial-thickness burn wounds. However, there is a lack of mechanistic insights into Pf drug action on inflammatory cells such as neutrophils. Here, we examined the treatment effects of Pf on LPS-stimulated neutrophils as a model of non-sterile inflammation. Firstly, Pf reduced chemotaxis and production of pro-inflammatory ROS, cytokines, and chemokines by LPS-activated neutrophils. Secondly, Pf increased anti-inflammatory IL-1RA and reduced neutrophil degranulation, phagocytosis, and NETosis. Thirdly, Pf affected downstream signaling kinases which might directly or indirectly influence neutrophil responses to LPS. In conclusion, the results suggest that Pf lessens the inflammatory phenotypes of LPS-activated neutrophils.
Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203
Authors: Ren Juansheng , Zhang Fan , Gao Fangyuan , Zeng Lihua , Lu Xianjun , Zhao Xiuqin , Lv Jianqun , Su Xiangwen , Liu Liping , Dai Mingli , Xu Jianlong , Ren Guangjun 
Published: November 2020

AbstractThe yield heterosis of rice is sought by farmers and strong contributes to food safety, but the quality of hybrid rice may be reduced. Therefore, developing new varieties with both high yield and good quality is a heavily researched topic in hybrid rice breeding. However, the molecular mechanism governing yield heterosis and high rice quality has not been elucidated to date. In this study, a comparative transcriptomics and genomic analysis was performed on a hybrid rice variety, Chuanyou6203 (CY6203), and its parents to investigate the molecular mechanism and gene regulation network governing the formation of yield and quality stages. A total of 66,319 SNPs and InDels between CH3203 and C106B were detected in the 5′-UTR, exon, intronic, and 3′-UTR regions according to the reference genome annotation, which involved 7473 genes. A total of 436, 70, 551, 993, and 1216 common DEGs between CY6203 and both of its parents were identified at the same stage in panicles and flag leaves. Of the common DEGs, the numbers of upregulated DEGs between CY6203 and CH3203 were all greater than those of upregulated DEGs between CY6203 and C106B in panicles and flag leaves at the booting, flowering, and middle filling stages. Approximately 40.61% of mRNA editing ratios were between 0.4 and 0.6, and 1.68% of mRNA editing events (editing ratio ≥ 0.8) in CY6203 favored one of its parents at three stages or a particular stage, suggesting that the hypothetical heterosis mechanism of CY6203 might involve dominance or epistasis. Also 15,934 DEGs were classified into 19 distinct modules that were classified into three groups by the weighted gene coexpression network analysis. Through transcriptome analysis of panicles and flag leaves in the yield and quality stages, the DEGs in the green-yellow module primarily contributed to the increase in the source of CY6203 due to an in increase in photosynthetic efficiency and nitrogen utilization efficiency, and a small number of DEGs related to the grain number added spikelet number per panicle amplified its sink. The balanced expression of the major high-quality alleles of C106B and CH3203 in CY6203 contributed to the outstanding quality of CY6203. Our transcriptome and genome analyses offer a new data set that may help to elucidate the molecular mechanism governing the yield heterosis and high quality of a hybrid rice variety.
Multi-phase-field simulation of microstructure evolution in metallic foams
Authors: Vakili Samad , Steinbach Ingo , Varnik Fathollah 
Published: November 2020

AbstractThis paper represents a model for microstructure formation in metallic foams based on the multi-phase-field approach. The model allows to naturally account for the effect of additives which prevent two gas bubbles from coalescence. By applying a non-merging criterion to the phase fields and at the same time raising the free energy penalty associated with additives, it is possible to completely prevent coalescence of bubbles in the time window of interest and thus focus on the formation of a closed porous microstructure. On the other hand, using a modification of this criterion along with lower free energy barriers we investigate with this model initiation of coalescence and the evolution of open structures. The method is validated and used to simulate foam structure formation both in two and three dimensions.
Energy depletion and opportunistic microbial colonisation in white syndrome lesions from corals across the Indo-Pacific
Authors: Smith Hillary A. , Conlan Jessica A. , Pollock F. Joseph , Wada Naohisa , Shore Amanda , Hung Julia Yun-Hsuan , Aeby Greta S. , Willis Bette L. , Francis David S. , Bourne David G. 
Published: November 2020

AbstractCorals are dependent upon lipids as energy reserves to mount a metabolic response to biotic and abiotic challenges. This study profiled lipids, fatty acids, and microbial communities of healthy and white syndrome (WS) diseased colonies of Acropora hyacinthus sampled from reefs in Western Australia, the Great Barrier Reef, and Palmyra Atoll. Total lipid levels varied significantly among locations, though a consistent stepwise decrease from healthy tissues from healthy colonies (HH) to healthy tissue on WS-diseased colonies (HD; i.e. preceding the lesion boundary) to diseased tissue on diseased colonies (DD; i.e. lesion front) was observed, demonstrating a reduction in energy reserves. Lipids in HH tissues were comprised of high energy lipid classes, while HD and DD tissues contained greater proportions of structural lipids. Bacterial profiling through 16S rRNA gene sequencing and histology showed no bacterial taxa linked to WS causation. However, the relative abundance of Rhodobacteraceae-affiliated sequences increased in DD tissues, suggesting opportunistic proliferation of these taxa. While the cause of WS remains inconclusive, this study demonstrates that the lipid profiles of HD tissues was more similar to DD tissues than to HH tissues, reflecting a colony-wide systemic effect and provides insight into the metabolic immune response of WS-infected Indo-Pacific corals.
Two-stage fluid pathways generated by volume expansion reactions: insights from the replacement of pyrite by chalcopyrite
Authors: Zhang Yang , Cai Yuanfeng , Qu Yang , Wang Qin , Gu Lixin , Li Gaojun 
Published: November 2020

AbstractVolume expansion reactions involved in mineral–fluid interactions are linked to a number of geological processes, including silicate weathering, retrograde metamorphism, and mineralization. However, the effect of volume expansion on replacement reactions remains unclear. Here, we demonstrate that reactions associated with volume expansion during the replacement of pyrite by chalcopyrite involve two competing processes. The reaction is initially augmented because of the development of reaction-induced fractures in the pyrite. However, these fractures are subsequently filled by compacted products, which ultimately disrupts the contact and interaction between bulk fluids and the pristine pyrite surface. These competing processes indicate that replacement reactions are both augmented and inhibited by volume expansion reactions during pyrite replacement.
Identification of synthetic chemosensitivity genes paired with BRAF for BRAF/MAPK inhibitors
Authors: Lee Kye Hwa , Goh Jinmin , Kim Yi-Jun , Kim Kwangsoo 
Published: November 2020

AbstractMolecular-targeted approaches are important for personalised cancer treatment, which requires knowledge regarding drug target specificity. Here, we used the synthetic lethality concept to identify candidate gene pairs with synergistic effects on drug responses. A synergistic chemo-sensitivity response was identified if a drug had a significantly lower half-maximal inhibitory concentration (IC50) in cell lines with a pair of mutated genes compared with those in other cell lines (wild-type or one mutated gene). Among significantly damaging mutations in the Genomics of Drug Sensitivity in Cancer database, we found 580 candidate synergistic chemo-sensitivity interaction sets for 456 genes and 54 commercial drugs. Clustering analyses according to drug/gene and drug/tissue interactions showed that BRAF/MAPK inhibitors clustered together; 11 partner genes for BRAF were identified. The combined effects of these partners on IC50 values were significant for both drug-specific and drug-combined comparisons. Survival analysis using The Cancer Genome Atlas data showed that patients who had mutated gene pairs in synergistic interaction sets had longer overall survival compared with that in patients with other mutation profiles. Overall, this analysis demonstrated that synergistic drug-responsive gene pairs could be successfully used as predictive markers of drug sensitivity and patient survival, offering new targets for personalised medicine.
Prediction improvement of potential PV production pattern, imagery satellite-based
Authors: Ben Othman A. , Belkilani K. , Besbes M. 
Published: November 2020

AbstractThe results obtained by using an existing model to estimate global solar radiation (GHI) in three different locations in Tunisia. These data are compared with GHI meteorological measurements and PV_Gis satellite imagery estimation. Some statistical indicators (R, R2, MPE, AMPE, MBE, AMBE and RMSE) have been used to measure the performance of the used model. Correlation coefficient for the different stations was close to 1.0. The meteorology and satellite determination coefficient (R2) were also near 1.0 except in the case of Nabeul station in which the meteorology measurements (R) were equals to 0.5848 because of the loss of data in this location due to meteorological conditions. This numerical model provides the best performance according to statistical results in different locations; therefore, this model can be used to estimate global solar radiation in Tunisia. The R square values are used as a statistical indicator to demonstrate that the model’s results are compatible with those of meteorology with a percentage of error less than 10%.
Risk factors for post-bronchoscopy pneumonia: a case–control study
Authors: Sato Yu , Murata Kengo , Yamamoto Miake , Ishiwata Tsukasa , Kitazono-Saitoh Miyako , Wada Akihiko , Takamori Mikio 
Published: November 2020

AbstractThe bronchoscopy, though usually safe, is occasionally associated with complications, such as pneumonia. However, the use of prophylactic antibiotics is not recommended by the guidelines of the British Thoracic Society. Thus far there are few reports of the risk factors for post-bronchoscopy pneumonia; the purpose of this study was to evaluate these risk factors. We retrospectively collected data on patients in whom post-bronchoscopy pneumonia developed from the medical records of 2,265 patients who received 2666 diagnostic bronchoscopies at our institution between April 2006 and November 2011. Twice as many patients were enrolled in the control group as in the pneumonia group. The patients were matched for age and sex. In total, 37 patients (1.4%) had post-bronchoscopy pneumonia. Univariate analysis showed that a significantly larger proportion of patients in the pneumonia group had tracheobronchial stenosis (75.7% vs 18.9%, p < 0.01) and a final diagnosis of primary lung cancer (75.7% vs 43.2%, p < 0.01) than in the control group. The pneumonia group tended to have more patients with a history of smoking (83.8% vs 67.1%, p = 0.06) or bronchoalveolar lavage (BAL) (4.3% vs 14.9%, p = 0.14) than the control group. In multivariate analysis, we found that tracheobronchial stenosis remained an independent risk factor for post-bronchoscopy pneumonia (odds ratio: 7.8, 95%CI: 2.5–24.2). In conclusion, tracheobronchial stenosis was identified as an independent risk factor for post-bronchoscopy pneumonia by multivariate analysis in this age- and sex- matched case control study.
High-content screening of Thai medicinal plants reveals Boesenbergia rotunda extract and its component Panduratin A as anti-SARS-CoV-2 agents
Authors: Kanjanasirirat Phongthon , Suksatu Ampa , Manopwisedjaroen Suwimon , Munyoo Bamroong , Tuchinda Patoomratana , Jearawuttanakul Kedchin , Seemakhan Sawinee , Charoensutthivarakul Sitthivut , Wongtrakoongate Patompon , Rangkasenee Noppawan , Pitiporn Supaporn , Waranuch Neti , Chabang Napason , Khemawoot Phisit , Sa-ngiamsuntorn Khanit , Pewkliang Yongyut , Thongsri Piyanoot , Chutipongtanate Somchai , Hongeng Suradej , Borwornpinyo Suparerk , Thitithanyanont Arunee 
Published: November 2020

AbstractSince December 2019, the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused severe pneumonia, a disease named COVID-19, that became pandemic and created an acute threat to public health. The effective therapeutics are in urgent need. Here, we developed a high-content screening for the antiviral candidates using fluorescence-based SARS-CoV-2 nucleoprotein detection in Vero E6 cells coupled with plaque reduction assay. Among 122 Thai natural products, we found that Boesenbergia rotunda extract and its phytochemical compound, panduratin A, exhibited the potent anti-SARS-CoV-2 activity. Treatment with B. rotunda extract and panduratin A after viral infection drastically suppressed SARS-CoV-2 infectivity in Vero E6 cells with IC50 of 3.62 μg/mL (CC50 = 28.06 µg/mL) and 0.81 μΜ (CC50 = 14.71 µM), respectively. Also, the treatment of panduratin A at the pre-entry phase inhibited SARS-CoV-2 infection with IC50 of 5.30 µM (CC50 = 43.47 µM). Our study demonstrated, for the first time, that panduratin A exerts the inhibitory effect against SARS-CoV-2 infection at both pre-entry and post-infection phases. Apart from Vero E6 cells, treatment with this compound was able to suppress viral infectivity in human airway epithelial cells. This result confirmed the potential of panduratin A as the anti-SARS-CoV-2 agent in the major target cells in human. Since B. rotunda is a culinary herb generally grown in China and Southeast Asia, its extract and the purified panduratin A may serve as the promising candidates for therapeutic purposes with economic advantage during COVID-19 situation.