bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting densities and elastic moduli of SiO2-based glasses by machine learning
Authors: Hu Yong-Jie , Zhao Ge , Zhang Mingfei , Bin Bin , Del Rose Tyler , Zhao Qian , Zu Qun , Chen Yang , Sun Xuekun , de Jong Maarten , Qi Liang 
Published: March 2020

AbstractChemical design of SiO2-based glasses with high elastic moduli and low weight is of great interest. However, it is difficult to find a universal expression to predict the elastic moduli according to the glass composition before synthesis since the elastic moduli are a complex function of interatomic bonds and their ordering at different length scales. Here we show that the densities and elastic moduli of SiO2-based glasses can be efficiently predicted by machine learning (ML) techniques across a complex compositional space with multiple (>10) types of additive oxides besides SiO2. Our machine learning approach relies on a training set generated by high-throughput molecular dynamic (MD) simulations, a set of elaborately constructed descriptors that bridges the empirical statistical modeling with the fundamental physics of interatomic bonding, and a statistical learning/predicting model developed by implementing least absolute shrinkage and selection operator with a gradient boost machine (GBM-LASSO). The predictions of the ML model are comprehensively compared and validated with a large amount of both simulation and experimental data. By just training with a dataset only composed of binary and ternary glass samples, our model shows very promising capabilities to predict the density and elastic moduli for k-nary SiO2-based glasses beyond the training set. As an example of its potential applications, our GBM-LASSO model was used to perform a rapid and low-cost screening of many (~105) compositions of a multicomponent glass system to construct a compositional-property database that allows for a fruitful overview on the glass density and elastic properties.
The Impact of PPARD and PPARG Polymorphisms on Glioma Risk and Prognosis
Authors: Ding Xiaoying , Han Xinsheng , Yuan Haozheng , Zhang Yong , Gao Ya 
Published: March 2020

AbstractRecent studies showed that peroxisome proliferator-activated receptors (PPARs) had effects on the progression of multiple tumors, but the role of PPARD and PPARG in glioma remains poorly understand. We conducted a case-control study to investigate the association of polymorphisms in PPARD and PPARG with glioma risk and prognosis in the Chinese Han population. Seven polymorphisms (PPARD: rs2016520, rs67056409, rs1053049 and rs2206030; PPARG: rs2920503, rs4073770 and rs1151988) were genotyped using the Agena MassARRAY system in 568 glioma patients and 509 healthy controls. The odd ratios (OR) and 95% confidence interval (CI) were calculated to assess the association of PPARD and PPARG polymorphisms with glioma risk. The Multifactor dimensionality reduction (MDR) method was used to analysis interactions of genetic polymorphisms on glioma risk. Then, we conducted log-rank test, Kaplan-Meier analysis and Cox regression model to evaluate the relationship of PPARD and PPARG polymorphisms with glioma prognosis. We found PPARD polymorphisms (rs2016520, rs67056409, rs1053049) were significantly associated with glioma risk in multiple models (P < 0.05). Stratified analysis showed rs2016520, rs67056409, rs1053049 of PPARD significantly decreased risk of glioma in the subgroup of age > 40 and astrocytoma (P < 0.05). For male, PPARD rs1053049 had a strong relationship with glioma risk in allele (P = 0.041), dominant (P = 0.040) and additive (P = 0.040) models. The effect of PPARG rs2920503 on glioma risk was related to glioma grade (P < 0.05). MDR showed that a seven-locus model was the best polymorphisms interaction pattern. Moreover, surgery and chemotherapy had strongly impact on overall survival and progression free survival of glioma patients. Our findings suggested that PPARD and PPARG polymorphisms were associated with glioma risk and prognosis in the Chinese Han population, and further studies are need to confirm our results.
Quantitative real-time imaging of intracellular FRET biosensor dynamics using rapid multi-beam confocal FLIM
Authors: Levitt James A. , Poland Simon P. , Krstajic Nikola , Pfisterer Karin , Erdogan Ahmet , Barber Paul R. , Parsons Maddy , Henderson Robert K. , Ameer-Beg Simon M. 
Published: March 2020

AbstractFluorescence lifetime imaging (FLIM) is a quantitative, intensity-independent microscopical method for measurement of diverse biochemical and physical properties in cell biology. It is a highly effective method for measurements of Förster resonance energy transfer (FRET), and for quantification of protein-protein interactions in cells. Time-domain FLIM-FRET measurements of these dynamic interactions are particularly challenging, since the technique requires excellent photon statistics to derive experimental parameters from the complex decay kinetics often observed from fluorophores in living cells. Here we present a new time-domain multi-confocal FLIM instrument with an array of 64 visible beamlets to achieve parallelised excitation and detection with average excitation powers of ~ 1–2 μW per beamlet. We exemplify this instrument with up to 0.5 frames per second time-lapse FLIM measurements of cAMP levels using an Epac-based fluorescent biosensor in live HeLa cells with nanometer spatial and picosecond temporal resolution. We demonstrate the use of time-dependent phasor plots to determine parameterisation for multi-exponential decay fitting to monitor the fractional contribution of the activated conformation of the biosensor. Our parallelised confocal approach avoids having to compromise on speed, noise, accuracy in lifetime measurements and provides powerful means to quantify biochemical dynamics in living cells.
Floods and rivers: a circular causality perspective
Authors: Sofia G. , Nikolopoulos E. I. 
Published: March 2020

AbstractAn improved understanding of changes in flood hazard and the underlying driving mechanisms is critical for predicting future changes for better adaptation strategies. While recent increases in flooding across the world have been partly attributed to a range of atmospheric or landscape drivers, one often-forgotten driver of changes in flood properties is the variability of river conveyance capacity. This paper proposes a new framework for connecting flood changes to longitudinal variability in river conveyance, precipitation climatology, flows and sediment connectivity. We present a first step, based on a regional analysis, towards a longer-term research effort that is required to decipher the circular causality between floods and rivers. The results show how this system of interacting units in the atmospheric, hydrologic and geomorphological realm function as a nonlinear filter that fundamentally alters the frequency of flood events. To revise and refine our estimation of future flood risk, this work highlights that multidriver attribution studies are needed, that include boundary conditions such as underlying climate, water and sediment connectivity, and explicit estimations of river conveyance properties.
Glioblastoma infiltration of both tumor- and virus-antigen specific cytotoxic T cells correlates with experimental virotherapy responses
Authors: Alayo Quazim A. , Ito Hirotaka , Passaro Carmela , Zdioruk Mykola , Mahmoud Ahmad Bakur , Grauwet Korneel , Zhang Xiaoli , Lawler Sean E. , Reardon David A. , Goins William F. , Fernandez Soledad , Chiocca E. Antonio , Nakashima Hiroshi 
Published: March 2020

AbstractThe mode of action for oncolytic viruses (OVs) in cancer treatment is thought to depend on a direct initial cytotoxic effect against infected tumor cells and subsequent activation of immune cell responses directed against the neoplasm. To study both of these effects in a mouse model of glioblastoma (GBM), we employed murine GBM cells engineered to constitutively express the type I Herpes Simplex Virus (HSV1) HSV-1 receptor, nectin-1, to allow for more efficient infection and replication by oncolytic HSV (oHSV). These cells were further engineered with a surrogate tumor antigen to facilitate assays of T cell activity. We utilized MRI-based volumetrics to measure GBM responses after injection with the oHSV and bioluminescent imaging (BLI) to determine oHSV replicative kinetics in the injected tumor mass. We found increased infiltration of both surrogate tumor antigen- and oHSV antigen-specific CD8+ T cells within 7 days after oHSV injection. There was no increase in tumor infiltrating CD8+ T cells expressing “exhaustion” markers, yet oHSV infection led to a reduction in PD-1+ CD8+ T cells in injected GBMs and an increase in IFNγ+ CD8+ T cells. There was a significant direct correlation between oHSV-mediated reduction in GBM volume and increased infiltration of both viral and tumor antigen-specific CD8+ T cells, as well as oHSV intratumoral gene activity. These findings imply that CD8+ T cell cytotoxicity against both tumor and viral antigens as well as intratumoral oHSV gene expression are important in oHSV-mediated GBM therapy.
The unprecedented membrane deformation of the human nuclear envelope, in a magnetic field, indicates formation of nuclear membrane invaginations
Authors: Dazzoni Régine , Grélard Axelle , Morvan Estelle , Bouter Anthony , Applebee Christopher J. , Loquet Antoine , Larijani Banafshé , Dufourc Erick J. 
Published: March 2020

AbstractHuman nuclear membrane (hNM) invaginations are thought to be crucial in fusion, fission and remodeling of cells and present in many human diseases. There is however little knowledge, if any, about their lipid composition and dynamics. We therefore isolated nuclear envelope lipids from human kidney cells, analyzed their composition and determined the membrane dynamics after resuspension in buffer. The hNM lipid extract was composed of a complex mixture of phospholipids, with high amounts of phosphatidylcholines, phosphatidylinositols (PI) and cholesterol. hNM dynamics was determined by solid-state NMR and revealed that the lamellar gel-to-fluid phase transition occurs below 0 °C, reflecting the presence of elevated amounts of unsaturated fatty acid chains. Fluidity was higher than the plasma membrane, illustrating the dual action of Cholesterol (ordering) and PI lipids (disordering). The most striking result was the large magnetic field-induced membrane deformation allowing to determine the membrane bending elasticity, a property related to hydrodynamics of cells and organelles. Human Nuclear Lipid Membranes were at least two orders of magnitude more elastic than the classical plasma membrane suggesting a physical explanation for the formation of nuclear membrane invaginations.
Resistance of seagrass habitats to ocean acidification via altered interactions in a tri-trophic chain
Authors: Martínez-Crego Begoña , Vizzini Salvatrice , Califano Gianmaria , Massa-Gallucci Alexia , Andolina Cristina , Gambi Maria Cristina , Santos Rui 
Published: March 2020

AbstractDespite the wide knowledge about prevalent effects of ocean acidification on single species, the consequences on species interactions that may promote or prevent habitat shifts are still poorly understood. Using natural CO2vents, we investigated changes in a key tri-trophic chain embedded within all its natural complexity in seagrass systems. We found that seagrass habitats remain stable at vents despite the changes in their tri-trophic components. Under highpCO2, the feeding of a key herbivore (sea urchin) on a less palatable seagrass and its associated epiphytes decreased, whereas the feeding on higher-palatable green algae increased. We also observed a doubled density of a predatory wrasse under acidified conditions. Bottom-up CO2effects interact with top-down control by predators to maintain the abundance of sea urchin populations under ambient and acidified conditions. The weakened urchin herbivory on a seagrass that was subjected to an intense fish herbivory at vents compensates the overall herbivory pressure on the habitat-forming seagrass. Overall plasticity of the studied system components may contribute to prevent habitat loss and to stabilize the system under acidified conditions. Thus, preserving the network of species interactions in seagrass ecosystems may help to minimize the impacts of ocean acidification in near-future oceans.
Insulin activates hepatic Wnt/β-catenin signaling through stearoyl-CoA desaturase 1 and Porcupine
Authors: Cabrae Régine , Dubuquoy Céline , Caüzac Michèle , Morzyglod Lucille , Guilmeau Sandra , Noblet Bénédicte , Fève Bruno , Postic Catherine , Burnol Anne-Françoise , Moldes Marthe 
Published: March 2020

AbstractThe Wnt/β-catenin pathway plays a pivotal role in liver structural and metabolic homeostasis. Wnt activity is tightly regulated by the acyltransferase Porcupine through the addition of palmitoleate. Interestingly palmitoleate can be endogenously produced by the stearoyl-CoA desaturase 1 (SCD1), a lipogenic enzyme transcriptionally regulated by insulin. This study aimed to determine whether nutritional conditions, and insulin, regulate Wnt pathway activity in liver. An adenoviral TRE-Luciferase reporter was used as a readout of Wnt/β-catenin pathway activity, in vivo in mouse liver and in vitro in primary hepatocytes. Refeeding enhanced TRE-Luciferase activity and expression of Wnt target genes in mice liver, revealing a nutritional regulation of the Wnt/β-catenin pathway. This effect was inhibited in liver specific insulin receptor KO (iLIRKO) mice and upon wortmannin or rapamycin treatment. Overexpression or inhibition of SCD1 expression regulated Wnt/β-catenin activity in primary hepatocytes. Similarly, palmitoleate added exogenously or produced by SCD1-mediated desaturation of palmitate, induced Wnt signaling activity. Interestingly, this effect was abolished in the absence of Porcupine, suggesting that both SCD1 and Porcupine are key mediators of insulin-induced Wnt/β-catenin activity in hepatocytes. Altogether, our findings suggest that insulin and lipogenesis act as potential novel physiological inducers of hepatic Wnt/β-catenin pathway.
Current era outcomes of pulmonary atresia with ventricular septal defect: A single center cohort in Thailand
Authors: Lertsakulpiriya Kanthalas , Vijarnsorn Chodchanok , Chanthong Prakul , Chungsomprasong Paweena , Kanjanauthai Supaluck , Durongpisitkul Kritvikrom , Soongswang Jarupim , Subtaweesin Thaworn , Sriyoschati Somchai 
Published: March 2020

AbstractPulmonary atresia with ventricular septal defect (PA/VSD) is a complex cyanotic congenital heart disease with a wide-range of presentations and treatment strategies, depending on the source of pulmonary circulation, anatomy of pulmonary arteries (PAs), and major aortopulmonary collateral arteries (MAPCAs). Data about the outcomes in developing countries is scarce. We therefore conducted a retrospective study to assess survival rates and mortality risks of 90 children with PA/VSD at Siriraj Hospital, Thailand during 2005–2016. Patients with single ventricle were excluded. Survival and mortality risks were analyzed at the end of 2018. The median age of diagnosis was 0.5 (0–13.8) years. The patients’ PAs were categorized into four groups: 1) PA/VSD with confluent PAs (n = 40), 2) PA/VSD with confluent PAs and MAPCAs (n = 21), 3) PA/VSD with non-confluent PAs and MAPCAs (n = 12), and 4) PA/VSD with small native PAs and MAPCAs (n = 17). Of the 88 patients who underwent operations, 32 patients had complete repair at 8.4 ± 4.6 years old. During the follow-up [median time of 5.7 years (7 days-13.6 years)], 17 patients (18.9%) died. The survival rates at 1, 5, and 10 years of age were 95%, 83.7%, and 79.6%, respectively. Significant mortality risks were the presence of associated anomalies and non-confluent PAs.
Dynamic changes of innate lymphoid cells in acute ST-segment elevation myocardial infarction and its association with clinical outcomes
Authors: Li Jing , Wu Jing , Zhang Mingyou , Zheng Yang 
Published: March 2020

AbstractAn increasing body of evidence has implicated the innate immune system in the causation of acute ST-segment elevation myocardial infarction (STEMI). Innate lymphoid cells (ILCs) are newly identified members of the lymphoid lineage that are important effectors of innate immunity. The role of ILCs in STEMI has not been explored. We characterized the ILCs present in peripheral blood of 176 STEMI patients and 52 controls. Patients were followed up for up to 23 months. Flow cytometry showed that the proportion of total ILCs and ILC1s were significantly increased compared with controls; contrary to ILC1s, the proportion of ILC2s among total ILCs decreased significantly during the acute phase of STEMI. ILC1s percentage was an independent predictor of major adverse cardiovascular events (MACE). On multivariate Cox regression, the 3rd tertile of ILC1s was associated with a higher MACE rate compared with the 1st tertile (hazard ratio: 2.26; 95% confidence interval 1.56–3.27; P = 0.014). RNA-sequencing (RNA-Seq) revealed increased expressions of interferon-γ, tumor necrosis factor-α, vascular cell adhesion molecule 1 (VCAM1), and matrix metallopeptidase 9. Moreover, as active factors secreted by ILC1s, levels of interleukin (IL)−12 and IL-18 were significantly increased in STEMI patients. Increased ILC1s in patients with STEMI was associated with poor outcomes. Our findings suggest that ILC1s may play an important role in STEMI.
Fungal secretome profile categorization of CAZymes by function and family corresponds to fungal phylogeny and taxonomy: Example Aspergillus and Penicillium
Authors: Barrett Kristian , Jensen Kristian , Meyer Anne S. , Frisvad Jens C. , Lange Lene 
Published: March 2020

AbstractFungi secrete an array of carbohydrate-active enzymes (CAZymes), reflecting their specialized habitat-related substrate utilization. Despite its importance for fitness, enzyme secretome composition is not used in fungal classification, since an overarching relationship between CAZyme profiles and fungal phylogeny/taxonomy has not been established. For 465 Ascomycota and Basidiomycota genomes, we predicted CAZyme-secretomes, using a new peptide-based annotation method, Conserved-Unique-Peptide-Patterns, enabling functional prediction directly from sequence. We categorized each enzyme according to CAZy-family and predicted molecular function, hereby obtaining a list of “EC-Function;CAZy-Family” observations. These “Function;Family”-based secretome profiles were compared, using a Yule-dissimilarity scoring algorithm, giving equal consideration to the presence and absence of individual observations. Assessment of “Function;Family” enzyme profile relatedness (EPR) across 465 genomes partitioned Ascomycota from Basidiomycota placing Aspergillus and Penicillium among the Ascomycota. Analogously, we calculated CAZyme “Function;Family” profile-similarities among 95 Aspergillus and Penicillium species to form an alignment-free, EPR-based dendrogram. This revealed a stunning congruence between EPR categorization and phylogenetic/taxonomic grouping of the Aspergilli and Penicillia. Our analysis suggests EPR grouping of fungi to be defined both by “shared presence“ and “shared absence” of CAZyme “Function;Family” observations. This finding indicates that CAZymes-secretome evolution is an integral part of fungal speciation, supporting integration of cladogenesis and anagenesis.
Tenascin-C inactivation impacts lung structure and function beyond lung development
Authors: Gremlich Sandrine , Roth-Kleiner Matthias , Equey Lucile , Fytianos Kleanthis , Schittny Johannes C. , Cremona Tiziana P. 
Published: March 2020

AbstractTenascin-C (TNC) is an extracellular matrix protein expressed at high levels during lung organogenesis. Later, TNC is only transiently de novo expressed to orchestrate tissue repair in pathological situations. We previously showed that TNC inactivation affects lung development and thus evaluated here the implications on lung function in newborn/adult mice. Respiratory function parameters were measured in anesthetized and mechanically ventilated wild-type (WT) and TNC-deficient mice at 5 (P5) and 90 (P90) days of age under basal conditions, as well as following high tidal volume (HTV) ventilation. At P5, TNC-deficient mice showed an increased static compliance (Cst) and inspiratory capacity (IC) relative to WT at baseline and throughout HTV. At P90, however, Cst and IC were only elevated at baseline. Control non-ventilated newborn and adult TNC-deficient mice showed similar lung morphology, but less alpha smooth muscle actin (α-SMA) around small airways. SMA + cells were decreased by 50% in adult TNC-deficient lungs and collagen layer thickened around small airways. Increased surfactant protein C (SP-C) and altered TGFβ and TLR4 signaling pathways were also detected. Thus, TNC inactivation-related defects during organogenesis led to persisting functional impairment in adulthood. This might be of interest in the context of pulmonary diseases with thickened airway smooth muscle layer or ventilation heterogeneity, like asthma and COPD.
Preparation of graphene nanocomposites from aqueous silver nitrate using graphene oxide’s peroxidase-like and carbocatalytic properties
Authors: Garg Kunal , Papponen Petri , Johansson Andreas , Puttaraksa Nitipon , Gilbert Leona 
Published: March 2020

AbstractThe present study evaluates the role of graphene oxide’s (GO’s) peroxidase-like and inherent/carbocatalytic properties in oxidising silver nitrate (AgNO3) to create graphene nanocomposites with silver nanoparticles (GO/Ag nanocomposite). Activation of peroxidase-like catalytic function of GO required hydrogen peroxide (H2O2) and ammonia (NH3) in pH 4.0 disodium hydrogen phosphate (Na2HPO4). Carbocatalytic abilities of GO were triggered in pH 4.0 deionised distilled water (ddH2O). Transmission electron microscope (TEM), scanning electron microscope (SEM), cyclic voltammetry (CV) and UV-Vis spectroscopy aided in qualitatively and quantitatively assessing GO/Ag nanocomposites. TEM and SEM analysis demonstrated the successful use of GO’s peroxidase-like and carbocatalytic properties to produce GO/Ag nanocomposite. UV-Vis analysis indicated a higher yield in optical density values for GO/Ag nanocomposites created using GO’s carbocatalytic ability rather than its peroxidase-like counterpart. Additionally, CV demonstrated that GO/Ag nanocomposite fabricated here is a product of an irreversible electrochemical reaction. Our study outcomes show new opportunities for GO as a standalone catalyst in biosensing. We demonstrate a sustainable approach to obtain graphene nanocomposites exclusive of harmful chemicals or physical methods.
Optical Fredkin gate assisted by quantum dot within optical cavity under vacuum noise and sideband leakage
Authors: Kang Min-Sung , Heo Jino , Choi Seong-Gon , Moon Sung , Han Sang-Wook 
Published: March 2020

AbstractWe propose a deterministic Fredkin gate which can accomplish controlled-swap operation between three-qubit states. The proposed Fredkin gate consists of a photonic system (single photon) and quantum dots (QDs) confined in single-sided cavities (two electron spin states). In our scheme, the control qubit is the polarization state of the single photon, and two electron spin states in QDs play the role of target qubits (swapped states by control qubit). The interaction between a photon and an electron of QD within the cavity (QD-cavity system) significantly affects the performance of Fredkin gate. Thus, through the analysis of the QD-cavity system under vacuum noise and sideband leakage, we demonstrate that reliable interaction and performance of the QD-cavity system with photonic state (photon) can be acquired in our scheme. Consequently, the Fredkin gate proposed in this paper can be experimentally implemented with high feasibility and efficiency.