bluuebunny/crossref_metadata_2025_split huggingface dataset:
PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys
Authors: Yaghoobi Mohammadreza , Stopka Krzysztof S. , Lakshmanan Aaditya , Sundararaghavan Veera , Allison John E. , McDowell David L. 
Published: March 2021

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.
Structural and biochemical mechanisms of NLRP1 inhibition by DPP9
Authors: Huang Menghang , Zhang Xiaoxiao , Toh Gee Ann , Gong Qin , Wang Jia , Han Zhifu , Wu Bin , Zhong Franklin , Chai Jijie 
Published: March 2021

AbstractNucleotide-binding domain, leucine-rich repeat receptors (NLRs) mediate innate immunity by forming inflammasomes. Activation of the NLR protein NLRP1 requires autocleavage within its function-to-find domain (FIIND)1–7. In resting cells, the dipeptidyl peptidases DPP8 and DPP9 interact with the FIIND of NLRP1 and suppress spontaneous NLRP1 activation8,9; however, the mechanisms through which this occurs remain unknown. Here we present structural and biochemical evidence that full-length rat NLRP1 (rNLRP1) and rat DPP9 (rDPP9) form a 2:1 complex that contains an autoinhibited rNLRP1 molecule and an active UPA–CARD fragment of rNLRP1. The ZU5 domain is required not only for autoinhibition of rNLRP1 but also for assembly of the 2:1 complex. Formation of the complex prevents UPA-mediated higher-order oligomerization of UPA–CARD fragments and strengthens ZU5-mediated NLRP1 autoinhibition. Structure-guided biochemical and functional assays show that both NLRP1 binding and enzymatic activity are required for DPP9 to suppress NLRP1 in human cells. Together, our data reveal the mechanism of DPP9-mediated inhibition of NLRP1 and shed light on the activation of the NLRP1 inflammasome.
Identification of nodes influence based on global structure model in complex networks
Authors: Ullah Aman , Wang Bin , Sheng JinFang , Long Jun , Khan Nasrullah , Sun ZeJun 
Published: March 2021

AbstractIdentification of Influential nodes in complex networks is challenging due to the largely scaled data and network sizes, and frequently changing behaviors of the current topologies. Various application scenarios like disease transmission and immunization, software virus infection and disinfection, increased product exposure and rumor suppression, etc., are applicable domains in the corresponding networks where identification of influential nodes is crucial. Though a lot of approaches are proposed to address the challenges, most of the relevant research concentrates only on single and limited aspects of the problem. Therefore, we propose Global Structure Model (GSM) for influential nodes identification that considers self-influence as well as emphasizes on global influence of the node in the network. We applied GSM and utilized Susceptible Infected Recovered model to evaluate its efficiency. Moreover, various standard algorithms such as Betweenness Centrality, Profit Leader, H-Index, Closeness Centrality, Hyperlink Induced Topic Search, Improved K-shell Hybrid, Density Centrality, Extended Cluster Coefficient Ranking Measure, and Gravity Index Centrality are employed as baseline benchmarks to evaluate the performance of GSM. Similarly, we used seven real-world and two synthetic multi-typed complex networks along-with different well-known datasets for experiments. Results analysis indicates that GSM outperformed the baseline algorithms in identification of influential node(s).
Measurement of the sound velocity of shock compressed water
Authors: Shu Hua , Li Jiangtao , Tu Yucheng , Ye Junjian , Wang Junyue , Zhang Qili , Tian Huiru , Jia Guo , He Zhiyu , Zhang Fan , Xie Zhiyong , Huang Xiuguang , Pei Wenbin , Fu Sizu 
Published: March 2021

AbstractThe sound velocities of water in the Hugoniot states are investigated by laser shock compression of precompressed water in a diamond anvil cell. The obtained sound velocities in the off-Hugoniot region of liquid water at precompressed conditions are used to test the predictions of quantum molecular dynamics (QMD) simulations and the SESAME equation-of-state (EOS) library. It is found that the prediction of QMD simulations agrees with the experimental data while the prediction of SESAME EOS library underestimates the sound velocities probably due to its improper accounting for the ionization processes.
Catalytic hydrotreating of bio-oil and evaluation of main noxious emissions of gaseous phase
Authors: Doukeh Rami , Bombos Dorin , Bombos Mihaela , Oprescu Elena-Emilia , Dumitrascu Gheorghe , Vasilievici Gabriel , Calin Catalina 
Published: March 2021

AbstractBio-oil produced from biomass pyrolysis has the potential to become an alternative renewable fuel. However due to the high content of oxygenated compounds is unsuitable as transportation fuel. The objective of this work is to evaluate the catalytic activity of CoMo /γ-Al2O3-HMS in the hydrotreating process of biomass pyrolysis bio-oil. The prepared catalyst was characterized by different techniques (X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy (XPS)) analysis. The experiments were carried out in a flow fixed-bed reactor at the temperature range of 250–320 °C, pressure between 20–40 bar, and LHSV of 3 h-1. The results showed that at mild conditions of 320 °C and 40 bar, the catalyst is very active in the hydrotreating process leading to a decrease of total acid number of hydrotreated bio-oil with almost 89% and bio-oil conversion of 87.23%. In addition, in order to evaluate the harmful emissions resulted from combustion of gaseous phase obtained in the hydrotreating process a chemical modelling algorithm was developed.
MgO surface lattice phonons observation during interstellar ice transition
Authors: Chavarría-Sibaja A. , Marín-Sosa S. , Bolaños-Jiménez E. , Hernández-Calderón M. , Herrera-Sancho O. A. 
Published: March 2021

AbstractRelevant information on the origins of the solar system and the early evolution of life itself can be derive from systematic and controlled exploration of water ice here on Earth. Therefore, over the last decades, a huge effort on experimental methodologies has been made to study the multiple crystal ice phases, which are observed outside our home–gravitational–potential. By employing (100)–oriented MgO lattice surface as a microcantilever sensor, we conducted the first ever study on the dynamics of the Structural Phase Transition at 185 K in water ice by means of coherent elastic scattering of electron diffraction. We estimate the amount of phonons caused by this transition applying precise quantum computing key tools, and resulting in a maximum value of 1.23 ± 0.02. Further applications of our microcantilever sensor were assessed using unambiguous mapping of the surface stress induced by the c($$4 \times 2$$

4
×
2

) → p($$3 \times 2$$

3
×
2

) Structural Phase Transition of the interstellar ice formulated on the Williamsom–Hall model. This development paves the way and thus establishes an efficient characterization tool of the surface mechanical strains of materials with potential applications arising from interstellar ice inclusive glaciers to the wide spectrum of solid–state physics.
IgGFc-binding protein in pregnancies complicated by spontaneous preterm delivery: a retrospective cohort study
Authors: Stranik Jaroslav , Kacerovsky Marian , Soucek Ondrej , Kolackova Martina , Musilova Ivana , Pliskova Lenka , Bolehovska Radka , Bostik Pavel , Matulova Jana , Jacobsson Bo , Andrys Ctirad 
Published: March 2021

AbstractTo determine the IgGFc-binding protein (FcgammaBP) concentration in amniotic and cervical fluids in preterm prelabor rupture of membranes (PPROM) and preterm labor with intact membranes (PTL) and to assess the diagnostic indices of FcgammaBP to predict intra-amniotic infection (the presence of both microbial invasion of the amniotic cavity and intra-amniotic inflammation). In this study, we included 170 and 79 women with PPROM and PTL, respectively. Paired cervical and amniotic fluid samples were obtained using a Dacron polyester swab and transabdominal amniocentesis, respectively. The FcgammaBP concentrations in the samples were assessed using an enzyme-linked immunosorbent assay. The presence of intra-amniotic infection was associated with elevated FcgammaBP concentrations in pregnancies with PPROM and PTL [PPROM—presence: 86 ng/mL vs. absence: 13 ng/mL,p < 0.0001, area under receiver operating characteristic curve (AUC) = 0.94; PTL—presence: 140 ng/mL vs. absence: 22 ng/mL,p < 0.0001, AUC = 0.86]. In cervical fluid, the concentrations of FcgammaBP were elevated in the presence of intra-amniotic infection in pregnancies with PPROM only (presence: 345 ng/mL vs. absence: 60 ng/mL,p < 0.0001, AUC = 0.93). FcgammaBP in amniotic fluid might be a marker of intra-amniotic infection in women with both PPROM and PTL However, in cervical fluid, it is only observed in women with PPROM.
Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli
Authors: Deter Heather S. , Hossain Tahmina , Butzin Nicholas C. 
Published: March 2021

AbstractAntibiotic treatment kills a large portion of a population, while a small, tolerant subpopulation survives. Tolerant bacteria disrupt antibiotic efficacy and increase the likelihood that a population gains antibiotic resistance, a growing health concern. We examined how E. coli transcriptional networks changed in response to lethal ampicillin concentrations. We are the first to apply transcriptional regulatory network (TRN) analysis to antibiotic tolerance by leveraging existing knowledge and our transcriptional data. TRN analysis shows that gene expression changes specific to ampicillin treatment are likely caused by specific sigma and transcription factors typically regulated by proteolysis. These results demonstrate that to survive lethal concentration of ampicillin specific regulatory proteins change activity and cause a coordinated transcriptional response that leverages multiple gene systems.
Systematic differences in effect estimates between observational studies and randomized control trials in meta-analyses in nephrology
Authors: Kimachi Miho , Onishi Akira , Tajika Aran , Kimachi Kimihiko , Furukawa Toshi A. 
Published: March 2021

AbstractThe limited availability of randomized controlled trials (RCTs) in nephrology undermines causal inferences in meta-analyses. Systematic reviews of observational studies have grown more common under such circumstances. We conducted systematic reviews of all comparative observational studies in nephrology from 2006 to 2016 to assess the trends in the past decade. We then focused on the meta-analyses combining observational studies and RCTs to evaluate the systematic differences in effect estimates between study designs using two statistical methods: by estimating the ratio of odds ratios (ROR) of the pooled OR obtained from observational studies versus those from RCTs and by examining the discrepancies in their statistical significance. The number of systematic reviews of observational studies in nephrology had grown by 11.7-fold in the past decade. Among 56 records combining observational studies and RCTs, ROR suggested that the estimates between study designs agreed well (ROR 1.05, 95% confidence interval 0.90–1.23). However, almost half of the reviews led to discrepant interpretations in terms of statistical significance. In conclusion, the findings based on ROR might encourage researchers to justify the inclusion of observational studies in meta-analyses. However, caution is needed, as the interpretations based on statistical significance were less concordant than those based on ROR.
Extracellular vesicles from human airway basal cells respond to cigarette smoke extract and affect vascular endothelial cells
Authors: Saxena Ashish , Walters Matthew S. , Shieh Jae-Hung , Shen Ling-Bo , Gomi Kazunori , Downey Robert J. , Crystal Ronald G. , Moore Malcolm A. S. 
Published: March 2021

AbstractThe human airway epithelium lining the bronchial tree contains basal cells that proliferate, differentiate, and communicate with other components of their microenvironment. One method that cells use for intercellular communication involves the secretion of exosomes and other extracellular vesicles (EVs). We isolated exosome-enriched EVs that were produced from an immortalized human airway basal cell line (BCi-NS1.1) and found that their secretion is increased by exposure to cigarette smoke extract, suggesting that this stress stimulates release of EVs which could affect signaling to other cells. We have previously shown that primary human airway basal cells secrete vascular endothelial growth factor A (VEGFA) which can activate MAPK signaling cascades in endothelial cells via VEGF receptor–2 (VEGFR2). Here, we show that exposure of endothelial cells to exosome-enriched airway basal cell EVs promotes the survival of these cells and that this effect also involves VEGFR2 activation and is, at least in part, mediated by VEGFA present in the EVs. These observations demonstrate that EVs are involved in the intercellular signaling between airway basal cells and the endothelium which we previously reported. The downstream signaling pathways involved may be distinct and specific to the EVs, however, as increased phosphorylation of Akt, STAT3, p44/42 MAPK, and p38 MAPK was not seen following exposure of endothelial cells to airway basal cell EVs.
Potential drug-drug interactions of antiretrovirals and antimicrobials detected by three databases
Authors: Vivithanaporn Pornpun , Kongratanapasert Teetat , Suriyapakorn Bovornpat , Songkunlertchai Pichayut , Mongkonariyawong Patpicha , Limpikirati Patanachai K. , Khemawoot Phisit 
Published: March 2021

AbstractStandard treatment for HIV infection involves a combination of antiretrovirals. Additionally, opportunistic infections in HIV infected patients require further antimicrobial medications that might cause drug-drug interactions (DDIs). The objective of this study was to to compare the recognition of DDIs between antiretrovirals and antimicrobials by three proprietary databases and evaluate their concordance. 114 items of antiretrovirals and antimicrobials from the National List of Essential Medicines of Thailand 2018 were used in the study. However, 21 items were not recognised by Micromedex, Drugs.com, and Liverpool HIV interactions. Only 93 items were available for the detection of potential DDIs by the three databases. Potential DDIs detected from the three databases included 292 pairs. Liverpool showed the highest number of DDIs with 285 pairs compared with 259 pairs by drugs.com and 133 pairs by Micromedex. Regarding the severity classifications, Liverpool reported 10% Contraindicated; Micromedex reported 14% contraindicated and 59% major; Drugs.com reported 21% major. The Fleiss’ kappa agreements were fair to poor among the three databases, higher agreement was observed for DDIs classified as severe. This study highlights the need to harmonize the evaluation and interpretation of DDI risk in order to produce standardized information to support prescribers.
Bioprospecting of Sechium spp. varieties for the selection of characters with pharmacological activity
Authors: Iñiguez-Luna María Isabel , Cadena-Iñiguez Jorge , Soto-Hernández Ramón Marcos , Morales-Flores Francisco Javier , Cortes-Cruz Moisés , Watanabe Kazuo N. , Machida-Hirano Ryoko , Cadena-Zamudio Jorge David 
Published: March 2021

AbstractBioprospecting identifies new sources of compounds with actual or potential economic value that come from biodiversity. An analysis was performed regarding bioprospecting purposes in ten genotypes of Sechium spp., through a meta-analysis of 20 information sources considering different variables: five morphological, 19 biochemical, anti-proliferative activity of extracts on five malignant cell lines, and 188 polymorphic bands of amplified fragment length polymorphisms, were used in order to identify the most relevant variables for the design of genetic interbreeding. Significant relationships between morphological and biochemical characters and anti-proliferative activity in cell lines were obtained, with five principal components for principal component analysis (SAS/ETS); variables were identified with a statistical significance (< 0.7 and Pearson values ≥ 0.7), with 80.81% of the accumulation of genetic variation and 110 genetic bands. Thirty-nine (39) variables were recovered using NTSYSpc software where 30 showed a Pearson correlation (> 0.5) and nine variables (< 0.05), Finally, using a cladistics analysis approach highlighted 65 genetic bands, in addition to color of the fruit, presence of thorns, bitter flavor, piriform and oblong shape, and also content of chlorophylls a and b, presence of cucurbitacins, and the IC50 effect of chayote extracts on the four cell lines.
Buspirone alleviates anxiety, depression, and colitis; and modulates gut microbiota in mice
Authors: Kim Jeon-Kyung , Han Sang-Kap , Joo Min-Kyung , Kim Dong-Hyun 
Published: March 2021

AbstractGut microbiota regulate the neurodevelopmental processes and brain functions through the regulation of the microbiota–gut interaction and gut–brain communication. Buspirone, an agonist for serotonin 5-HT1A receptors, is used for the treatment of anxiety/depression. Therefore, to understand the gut microbiota-mediated mechanism of buspirone on anxiety/depression, we examined its effect on the immobilization stress (IS) or Escherichia coli K1 (EC)-induced anxiety/depression in mice. Oral or intraperitoneal administration of buspirone significantly suppressed stressor-induced anxiety/depression-like behaviors in the elevated plus maze, light/dark transition, tail suspension, and forced swimming tasks. Their treatments also reduced TNF-α expression and NF-κB+/Iba1+ cell population in the hippocampus and myeloperoxidase activity and NF-κB+/CD11c+ cell population in the colon. Buspirone treatments partially restored IS- or EC-induced gut microbiota perturbation such as β-diversity to those of normal control mice: they reduced the IS- or EC-induced gut Proteobacteria population. In particular, the anxiolytic activity of buspirone was positively correlated with the populations of Bacteroides and PAC001066_g in EC- or IS-exposed mice, while the populations of Lachnospiraceae, KE159660_g, LLKB_g, Helicobacter, and PAC001228_g were negatively correlated. The anti-depressant effect of buspirone was positively correlated with the Roseburia population. The fecal microbiota transplantations from buspirone-treated mice with IS-induced anxiety/depression or normal control mice suppressed IS-induced anxiety/depression-like behaviors and reduced hippocampal NF-κB+/Iba1+ and colonic NF-κB+/CD11c+ cell populations in the transplanted mice. Furthermore, they modified IS-induced perturbation of gut microbiota composition, particularly Proteobacteria, in the transplanted mice. In conclusion, buspirone alleviates IS as well as EC-induced anxiety/depression and colitis. It also suppresses associated neuroinflammation and modulates gut microbiota. Future studies can help to explain the relationship, if any, in the central and peripheral effects of buspirone.
Stroke prediction in patients presenting with isolated dizziness in the emergency department
Authors: Kim June-sung , Bae Hong Jun , Kim Muyeol , Ahn Shin , Sohn Chang Hwan , Seo Dong Woo , Kim Won Young 
Published: March 2021

AbstractDiagnosing stroke in patients experiencing dizziness without neurological deficits is challenging for physicians. The aim of this study was to evaluate the prevalence of acute stroke in patients who presented with isolated dizziness without neurological deficits at the emergency department (ED), and determine the relevant stroke predictors in this population. This was an observational, retrospective record review of consecutive 2215 adult patients presenting with dizziness at the ED between August 2019 and February 2020. Multivariate analysis was performed to identify risk factors for acute stroke. 1239 patients were enrolled and analyzed. Acute stroke was identified in 55 of 1239 patients (4.5%); most cases (96.3%) presented as ischemic stroke with frequent involvement (29.1%) of the cerebellum. In the multivariate analysis, the history of cerebrovascular injury (odds ratio [OR] 3.08 [95% confidence interval {CI} 1.24 to 7.67]) and an age of > 65 years (OR 3.01 [95% CI 1.33 to 6.83]) were the independent risk factors for predicting acute stroke. The combination of these two risks showed a higher specificity (94.26%) than that of each factor alone. High-risk patients, such as those aged over 65 years or with a history of cerebrovascular injury, may require further neuroimaging workup in the ED to rule out stroke.
Efficiency of nilotinib to target chronic phase-chronic myeloid leukaemia primary mature CD34− and immature CD34+ cells
Authors: Berger Marc G. , Lebecque Benjamin , Tassin Thomas , Dannus Louis-Thomas , Berger Juliette , Soucal Mélanie , Guerci Agnès , Cony-Makhoul Pascale , Johnson Hyacinthe , Etienne Gabriel , Guyotat Denis , Gagnieu Marie-Claude , Pereira Bruno , Saugues Sandrine , Tournilhac Olivier , Hermet Eric , Bourgne Céline 
Published: March 2021

AbstractAccumulation in target cells is an essential pharmacokinetic step of targeted therapies. Tyrosine Kinase Inhibitors (TKI) against the BCR-ABL fusion protein in Chronic Phase-Chronic Myeloid Leukaemia (CP-CML) cells constitute a unique model in terms of efficacy, specificity, and in vivo demonstration of response heterogeneity by target cells. The overall therapeutic response to nilotinib is heterogeneous with no satisfactory explanation. To better understand the patients’ response heterogeneity, we quantified nilotinib uptake by primary CP-CML cells in standardized conditions using flow cytometry, which allowed also distinguishing mature (polymorphonuclear cells) from immature (CD34+) cells. Nilotinib was undetectable in 13.3% of PMN and 40% of CD34+ cells. Moreover, in CD34+ cells, intracellular nilotinib did not completely abolish BCR-ABL activity (monitored by CrkL phosphorylation inhibition), although nilotinib accumulated well in most CD34+ cell samples. Intracellular nilotinib concentration was inversely correlated with disease burden parameters, Sokal score, and early haematologic response at day 6 ± 1 only in PMN, suggesting an intrinsic ability to limit nilotinib entry in the forms with higher tumor cell burdenat diagnosis. These findings suggest that nilotinib accumulation in CP-CML cells is influenced by individual characteristics and intra-clonal heterogeneity, and might be used for pharmacokinetic studies and to assess the therapeutic response.