bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Classification of Blood-Brain-Barrier Drugs Using Deep Learning
Authors: Miao Rui , Xia Liang-Yong , Chen Hao-Heng , Huang Hai-Hui , Liang Yong 
Published: June 2019

AbstractBlood-Brain-Barrier (BBB) is a strict permeability barrier for maintaining the Central Nervous System (CNS) homeostasis. One of the most important conditions to judge a CNS drug is to figure out whether it has BBB permeability or not. In the past 20 years, the existing prediction approaches are usually based on the data of the physical characteristics and chemical structure of drugs. However, these methods are usually only applicable to small molecule compounds based on passive diffusion through BBB. To deal this problem, one of the most famous methods is multi-core SVM method, which is based on clinical phenotypes about Drug Side Effects and Drug Indications to predict drug penetration of BBB. This paper proposed a Deep Learning method to predict the Blood-Brain-Barrier permeability based on the clinical phenotypes data. The validation result on three datasets proved that Deep Learning method achieves better performance than the other existing methods. The average accuracy of our method reaches 0.97, AUC reaches 0.98, and the F1 score is 0.92. The results proved that Deep Learning methods can significantly improve the prediction accuracy of drug BBB permeability and it can help researchers to reduce clinical trials and find new CNS drugs.
Working memory capacity affects trade-off between quality and quantity only when stimulus exposure duration is sufficient: Evidence for the two-phase model
Authors: Ye Chaoxiong , Sun Hong-Jin , Xu Qianru , Liang Tengfei , Zhang Yin , Liu Qiang 
Published: June 2019

AbstractThe relation between visual working memory (VWM) capacity and attention has attracted much interest. In this study, we investigated the correlation between the participants’ VWM capacity and their ability to voluntarily trade off the precision and number of items remembered. The two-phase resource allocation model proposed by Ye et al. (2017) suggests that for a given set size, it takes a certain amount of consolidation time for an individual to control attention to adjust the VWM resources to trade off the precision and number. To verify whether trade-off ability varies across VWM capacity, we measured each individual’s VWM capacity and then conducted a colour recall task to examine their trade-off ability. By manipulating the task requirement, participants were instructed to memorise either more colours in a low-precision way or fewer colours in a high-precision way. We conducted two experiments by adjusting stimulus duration to be longer than predicted critical value (Experiment 1) and duration shorter than predicted critical value (Experiment 2). While the results of Experiment 1 showed a positive correlation between the VWM capacity and trade-off ability, the results of Experiment 2 showed a lack of such correlation. These results are consistent with the prediction from the two-phase model.
Unconventional Magnetization below 25 K in Nitrogen-doped Diamond provides hints for the existence of Superconductivity and Superparamagnetism
Authors: Barzola-Quiquia J. , Stiller M. , Esquinazi P. D. , Molle A. , Wunderlich R. , Pezzagna S. , Meijer J. , Kossack W. , Buga S. 
Published: June 2019

AbstractThe magnetization of nitrogen-doped single crystalline diamond bulk samples shows unconventional field and temperature hysteresis loops at T $${\boldsymbol{\lesssim }}$$
≲
25 K. The results suggest the existence of superparamagnetic and superconducting regions in samples with nitrogen concentration <200 ppm. Both phases vanish at temperatures above 25 K where the samples show diamagnetic behavior similar to undoped diamond. The observation of superparamagnetism and superconductivity is attributed to the nitrogen doping and to the existence of defective regions. From particle-induced X-ray emission with ppm resolution we rule out that the main observations below 25 K are due to magnetic impurities. We investigated also the magnetic properties of ferromagnetic/high-temperature superconducting oxide bilayers. The magnetization results obtained from those bilayers show remarkable similarities to the ones in nitrogen-doped diamond.
Environmental microcystin targets the microbiome and increases the risk of intestinal inflammatory pathology via NOX2 in underlying murine model of Nonalcoholic Fatty Liver Disease
Authors: Sarkar Sutapa , Kimono Diana , Albadrani Muayad , Seth Ratanesh K. , Busbee Philip , Alghetaa Hasan , Porter Dwayne E. , Scott Geoff I. , Brooks Bryan , Nagarkatti Mitzi , Nagarkatti Prakash , Chatterjee Saurabh 
Published: June 2019

AbstractWith increased climate change pressures likely to influence harmful algal blooms, exposure to microcystin, a known hepatotoxin and a byproduct of cyanobacterial blooms can be a risk factor for NAFLD associated comorbidities. Using both in vivo and in vitro experiments we show that microcystin exposure in NAFLD mice cause rapid alteration of gut microbiome, rise in bacterial genus known for mediating gut inflammation and lactate production. Changes in the microbiome were strongly associated with inflammatory pathology in the intestine, gut leaching, tight junction protein alterations and increased oxidative tyrosyl radicals. Increased lactate producing bacteria from the altered microbiome was associated with increased NOX-2, an NADPH oxidase isoform. Activationof NOX2 caused inflammasome activation as shown by NLRP3/ASCII and NLRP3/Casp-1 colocalizations in these cells while use of mice lacking a crucial NOX2 component attenuated inflammatory pathology and redox changes. Mechanistically, NOX2 mediated peroxynitrite species were primary to inflammasome activation and release of inflammatory mediators. Thus, in conclusion, microcystin exposure in NAFLD could significantly alter intestinal pathology especially by the effects on microbiome and resultant redox status thus advancing our understanding of the co-existence of NAFLD-linked inflammatory bowel disease phenotypes in the clinic.
Energetic, Structural and Dynamic Properties of Nucleobase-Urea Interactions that Aid in Urea Assisted RNA Unfolding
Authors: Jaganade Tanashree , Chattopadhyay Aditya , Pazhayam Nila M. , Priyakumar U. Deva 
Published: June 2019

AbstractUnderstanding the structure-function relationships of RNA has become increasingly important given the realization of its functional role in various cellular processes. Chemical denaturation of RNA by urea has been shown to be beneficial in investigating RNA stability and folding. Elucidation of the mechanism of unfolding of RNA by urea is important for understanding the folding pathways. In addition to studying denaturation of RNA in aqueous urea, it is important to understand the nature and strength of interactions of the building blocks of RNA. In this study, a systematic examination of the structural features and energetic factors involving interactions between nucleobases and urea is presented. Results from molecular dynamics (MD) simulations on each of the five DNA/RNA bases in water and eight different concentrations of aqueous urea, and free energy calculations using the thermodynamic integration method are presented. The interaction energies between all the nucleobases with the solvent environment and the transfer free energies become more favorable with respect to increase in the concentration of urea. Preferential interactions of urea versus water molecules with all model systems determined using Kirkwood-Buff integrals and two-domain models indicate preference of urea by nucleobases in comparison to water. The modes of interaction between urea and the nucleobases were analyzed in detail. In addition to the previously identified hydrogen bonding and stacking interactions between urea and nucleobases that stabilize the unfolded states of RNA in aqueous solution, NH-π interactions are proposed to be important. Dynamic properties of each of these three modes of interactions have been presented. The study provides fundamental insights into the nature of interaction of urea molecules with nucleobases and how it disrupts nucleic acids.
Management of ecosystems alters vector dynamics and haemosporidian infections
Authors: van Hoesel Willem , Marzal Alfonso , Magallanes Sergio , Santiago-Alarcon Diego , Ibáñez-Bernal Sergio , Renner Swen C. 
Published: June 2019

AbstractThe presence of insect vectors is a key prerequisite for transmission of vector-borne disease such as avian haemosporidians. In general, the effects of land use change on Diptera vectors are not well studied; the response of vectors to forest management depends on vector species, as has been shown previously for the birds. We tested if abundance of insects from different Diptera families and haemosporidian infection are affected through alteration of habitat structural variables (measured by LiDAR) and forest management intensities. We identified higher large-scale variation of female insect abundance in northeastern than in southwestern Germany. Unmanaged forest stands had higher Diptera insect abundances. We found that abundance of female Diptera increased with the amount of forest gaps but decreased in forest plots with more south facing aspect, higher habitat structural heterogeneity, temperature and humidity. We found that haemosporidian infections in Diptera insects increased with increased management intensity and more canopy structural diversity (e.g., amount of edge habitat), but decreased with a denser shrub layer, deeper leaf litter and higher humidity (characteristics for unmanaged forest stands). Although higher forest management intensity decreased vector abundance, the haemosporidian infections in the vectors increased, indicating a significant effect of forest management on disease dynamics.
Hydrogen peroxide signaling integrates with phytohormones during the germination of magnetoprimed tomato seeds
Authors: Anand Anjali , Kumari Archana , Thakur Meenakshi , Koul Archana 
Published: June 2019

AbstractSeeds of tomato were magnetoprimed at 100 mT for 30 min followed by imbibition for 12 and 24 h, respectively, at 20 °C, to examine the biochemical and molecular changes involved in homeostasis of hydrogen peroxide (H2O2) and its signaling associated with hormone interactions for promoting vigor. The relative transcript profiles of genes involved in the synthesis of H2O2 like Cu-amine oxidase (AO), receptor for activated C kinase 1 (RACK1) homologue (ArcA2) and superoxide dismutase (SOD1 and SOD9) increased in magnetoprimed tomato seeds as compared to unprimed ones with a major contribution (21.7-fold) from Cu-amine oxidase. Amongst the genes involved in the scavenging of H2O2 i.e, metallothionein (MT1, MT3 and MT4), catalase (CAT1) and ascorbate peroxidase (APX1 and APX2), MT1 and MT4 exhibited 14.4- and 15.4-fold increase respectively, in the transcript abundance, in primed seeds compared to the control. We report in our study that metallothionein and RACK1 play a vital role in the reactive oxygen species mediated signal transduction pathway to enhance the speed of germination in magnetoprimed tomato seeds. Increased enzymatic activities of catalase and ascorbate peroxidase were observed at 12 h of imbibition in the magnetoprimed seeds indicating their roles in maintaining H2O2 levels in the primed seeds. The upregulation of ABA 8′-hydroxylase and GA3 oxidase1 genes eventually, lead to the decreased abscisic acid/gibberellic acid (ABA/GA3) ratio in the primed seeds, suggesting the key role of H2O2 in enhancing the germination capacity of magnetoprimed tomato seeds.
Prognostic Impact of Longitudinal Monitoring of Radiomic Features in Patients with Advanced Non-Small Cell Lung Cancer
Authors: Bak So Hyeon , Park Hyunjin , Sohn Insuk , Lee Seung Hak , Ahn Myung-Ju , Lee Ho Yun 
Published: June 2019

AbstractTumor growth dynamics vary substantially in non-small cell lung cancer (NSCLC). We aimed to develop biomarkers reflecting longitudinal change of radiomic features in NSCLC and evaluate their prognostic power. Fifty-three patients with advanced NSCLC were included. Three primary variables reflecting patterns of longitudinal change were extracted: area under the curve of longitudinal change (AUC1), beta value reflecting slope over time, and AUC2, a value obtained by considering the slope and area over the longitudinal change of features. We constructed models for predicting survival with multivariate cox regression, and identified the performance of these models. AUC2 exhibited an excellent correlation between patterns of longitudinal volume change and a significant difference in overall survival time. Multivariate regression analysis based on cut-off values of radiomic features extracted from baseline CT and AUC2 showed that kurtosis of positive pixel values and surface area from baseline CT, AUC2 of density, skewness of positive pixel values, and entropy at inner portion were associated with overall survival. For the prediction model, the areas under the receiver operating characteristic curve (AUROC) were 0.948 and 0.862 at 1 and 3 years of follow-up, respectively. Longitudinal change of radiomic tumor features may serve as prognostic biomarkers in patients with advanced NSCLC.
Modeling sensitivity and uncertainties in platelet activation models applied on centrifugal pumps for extracorporeal life support
Authors: Fuchs Gabriel , Berg Niclas , Broman L. Mikael , Prahl Wittberg Lisa 
Published: June 2019

AbstractTwo platelet activation models were studied with respect to uncertainties of model parameters and variables. The sensitivity was assessed using two direct/deterministic approaches as well as the statistical Monte Carlo method. The first two, are linear in character whereas the latter is non-linear. The platelet activation models were applied on platelets moving within an extracorporeal centrifugal blood pump. The phenomenological, Lagrangian stress- and time-based power law-based models under consideration, have experimentally calibrated parameters and the stress expressed in a scalar form. The sensitivity of the model with respect to model parameters and the expression of the scalar stress was examined focusing on a smaller group of platelets associated with an elevated risk of activation. The results showed a high disparity between the models in terms of platelet activation state, found to depend on the platelets’ trajectory in the pump and the expression used for the scalar stress. Monte Carlo statistics was applied to the platelets at risk for activation and not to the entire platelet population. The method reveals the non-linear sensitivity of the activation models. The results imply that power-law based models have a restricted range of validity. The conclusions of this study apply to both platelet activation and hemolysis models.
Pseudomonas donghuensis HYS virulence towards Caenorhabditis elegans is regulated by the Cbr/Crc system
Authors: Xie Guanfang , Zeng Man , You Jia , Xie Zhixiong 
Published: June 2019

AbstractPseudomonas donghuensis HYS is the type strain of a recently identified species, P. donghuensis, which has pathogenic potential with an unclear virulence mechanism. In this study, we used Caenorhabditis elegans as a host to explore the virulence mechanism of P. donghuensis HYS. Based on a correlation between P. donghuensis HYS virulence and its repellence property, we identified 68 potential virulence-related genes, among them the Cbr/Crc system, which regulates the virulence of prokaryotic microorganisms. Slow-killing assays indicated that cbrA, cbrB, or specific sRNA-encoding genes all affected P. donghuensis virulence positively, whereas crc affected it negatively. Transcriptome analyses demonstrated that the Cbr/Crc system played an important role in the pathogenesis of P. donghuensis. In addition, experiments using the worm mutant KU25 pmk-1(km25) showed a correlation between P. donghuensis HYS virulence and the PMK-1/p38 MAPK pathway in C. elegans. In conclusion, our data show that Crc plays a novel role in the Cbr/Crc system, and the P. donghuensis virulence phenotype therefore differs from that of P. aeruginosa. This process also involves C. elegans innate immunity. These findings significantly increase the available information about Cbr/Crc-based virulence mechanisms in the genus Pseudomonas.
Label-free neuroblastoma cell separation from hematopoietic progenitor cell products using acoustophoresis - towards cell processing of complex biological samples
Authors: Olm Franziska , Urbansky Anke , Dykes Josefina H. , Laurell Thomas , Scheding Stefan 
Published: June 2019

AbstractProcessing of complex cell preparations such as blood and peripheral blood progenitor cell (PBPC) transplants using label-free technologies is challenging. Transplant-contaminating neuroblastoma cells (NBCs) can contribute to relapse, and we therefore aimed to provide proof-of-principle evidence that label-free acoustophoretic separation can be applied for diagnostic NBC enrichment and removal (“purging”) from human blood and PBPC products. Neuroblastoma cells spiked into blood and PBPC preparations served as model systems. Acoustophoresis enabled to enrich NBCs from mononuclear peripheral blood cells and PBPC samples with recovery rates of up to 60–97%. When aiming at high purity, NBC purities of up to 90% were realized, however, compromising recovery. Acoustophoretic purging of PBPC products allowed substantial tumour cell depletion of 1.5–2.3 log. PBPC loss under these conditions was considerable (>43%) but could be decreased to less than 10% while still achieving NBC depletion rates of 60–80%. Proliferation of cells was not affected by acoustic separation. These results provide first evidence that NBCs can be acoustically separated from blood and stem cell preparations with high recovery and purity, thus indicating that acoustophoresis is a promising technology for the development of future label-free, non-contact cell processing of complex cell products.
Experimental test of fine-grained entropic uncertainty relation in the presence of quantum memory
Authors: Lv Wei-Min , Zhang Chao , Hu Xiao-Min , Huang Yun-Feng , Cao Huan , Wang Jian , Hou Zhi-Bo , Liu Bi-Heng , Li Chuan-Feng , Guo Guang-Can 
Published: June 2019

AbstractThe uncertainty principle, which gives the constraints on obtaining precise outcomes for incompatible measurements, provides a new vision of the real world that we are not able to realize from the classical knowledge. In recent years, numerous theoretical and experimental developments about the new forms of the uncertainty principle have been achieved. Among these efforts, one attractive goal is to find tighter bounds of the uncertainty relation. Here, using an all optical setup, we experimentally investigate a most recently proposed form of uncertainty principle—the fine-grained uncertainty relation assisted by a quantum memory. The experimental results on the case of two-qubit state with maximally mixed marginal demonstrate that the fine-graining method can help to get a tighter bound of the uncertainty relation. Our results might contribute to further understanding and utilizing of the uncertainty principle.
Modified expression of ZmMYB167 in Brachypodium distachyon and Zea mays leads to increased cell wall lignin and phenolic content
Authors: Bhatia Rakesh , Dalton Sue , Roberts Luned A. , Moron-Garcia Odin M. , Iacono Rosario , Kosik Ondrej , Gallagher Joe A. , Bosch Maurice 
Published: June 2019

AbstractOne of the challenges to enable targeted modification of lignocellulosic biomass from grasses for improved biofuel and biochemical production lies within our limited understanding of the transcriptional control of secondary cell wall biosynthesis. Here, we investigated the role of the maize MYB transcription factor ZmMYB167 in secondary cell wall biosynthesis and how modified ZmMYB167 expression in two distinct grass model species affects plant biomass and growth phenotypes. Heterologous expression of ZmMYB167 in the C3 model system Brachypodium led to mild dwarf phenotypes, increased lignin (~7% to 13%) and S-lignin monomer (~11% to 16%) content, elevated concentrations of cell wall-bound p-coumaric acid (~15% to 24%) and reduced biomass sugar release (~20%) compared to controls. Overexpression of ZmMYB167 in the C4 model system Zea mays increased lignin (~4% to 13%), p-coumaric acid (~8% to 52%) and ferulic acid (~13% to 38%) content but did not affect plant growth and development nor biomass recalcitrance. Taken together, modifying ZmMYB167 expression represents a target to alter lignin and phenolic content in grasses. The ZmMYB167 expression-induced discrepancies in plant phenotypic and biomass properties between the two grass model systems highlight the challenges and opportunities for MYB transcription factor-based genetic engineering approaches of grass biomass.
Gold (III) adsorption from dilute waste solutions onto Amberlite XAD7 resin modified with L-glutamic acid
Authors: Mihăilescu Maria , Negrea Adina , Ciopec Mihaela , Davidescu Corneliu Mircea , Negrea Petru , Duţeanu Narcis , Rusu Gerlinde 
Published: June 2019

AbstractThe main purpose of this paper was to obtain a material with efficient adsorbing properties and selectivity, to recover the gold (III) from residual diluted solutions resulted from the electroplating process. In this regard, a material was obtained by physico-chemical functionalization of a chemically inert support with functional groups of nitrogen and carboxyl. As a source of functional groups glutamic acid was used, and Amberlite XAD7 type acrylic resin was used as solid support. In order to establish the mechanism of the adsorption process, kinetic, thermodynamic and equilibrium studies were performed. The maximum adsorption capacity of the material has been established, and a gold (III) recovery process has been proposed using thermal decomposition of the exhausted adsorbed material. Main objective of this study was to evaluate an environmental friendly adsorbent material to recover gold from secondary industrial sources.
Relationship Analysis of Central Venous-to-arterial Carbon Dioxide Difference and Cardiac Index for Septic Shock
Authors: Guo Zhiqiang , Yin Ming , Kong Jichang , Wang Bin , Dai Kunpeng , Zuo Tian , Yu Guangyan , Bao Yong 
Published: June 2019

AbstractTo analyze the relationship of the central venous-to-arterial carbon dioxide difference (p(cv-a)CO2) and cardiac index (CI) in patients with septic shock, an observational study was conducted in intensive care unit (ICU). 66 consecutive patients with septic shock and central venous oxygen saturation (ScvO2) ≥ 70% were included after early fluid resuscitation. Measurements were taken at a 6 h interval (T0, T6, T12, T18, T24) during first 24 h after their admission into ICU, including heart rate (HR), mean arterial pressure (MAP), central venous pressure (CVP), p(cv-a)CO2, cardiac index(CI, L/(min•m2)) and ScvO2. Patients were divided into low p(cv-a)CO2 group (n = 35) and high p(cv-a)CO2 group (n = 31) according to a threshold of 6 mmHg for p(cv-a)CO2 at T0. As a result, at T0, T6, T12, T18 and T24, there were respectively significant differences between low and high p(cv-a)CO2 groups for CI (4.1 ± 1.4 vs 2.4 ± 0.6, 4.4 ± 0.9 vs 2.8 ± 0.7, 4.1 ± 1.3 vs 2.9 ± 0.6, 4.0 ± 1.3 vs 2.7 ± 0.8, 4.2 ± 1.4 vs 2.9 ± 0.8, p < 0.001 at each time point), 28-day mortality rate was 38.7%(12/31) for high p(cv-a)CO2 group and 22.8% (8/35) for low p(cv-a)CO2 group (p > 0.05), there were significant differences for p(cv-a)CO2 (p < 0.05) between low and high p(cv-a)CO2 groups, no differences for HR, MAP, CVP, ScvO2 (p > 0.05). CI was inversely correlated with p(cv-a)CO2 value (r = −0.804, p < 0.001), but not for ScvO2(r = 0.08, p > 0.05). Receiver operating characteristic curve analysis confirmed the correlation of p(cv-a)CO2 with CI (AUC: 0.782;p < 0.001; 95% confidence interval: 0.710–0.853). The cut-off value for the best predictive value of CI ≥ 2.2 L/(min·m2) was p(cv-a)CO2 of 5.55 mmHg or lower with a sensitivity of 85.7% and specificity of 66.8%. Hence CI measured with USCOM is inversely correlated with p(cv-a)CO2 values in guiding the resuscitation of patients with septic shock.