bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implicit Virtual Boundary Method for Moving Boundary Problems on Non-Staggered Cartesian Patch Grids
Authors: Lee S. L. , Cyue G. S. , Chen K. W. 
Published: May 2017

AbstractA simple numerical method is proposed in the paper for fluid flow around a moving boundary of irregular shape. The unsteady term is discretized with the implicit scheme such that large time step is allowed. All of the computations are performed on non-staggered Cartesian grid system. Fine Cartesian patch grid system covering the moving object is employed to resolve the solution around the solid body. A closed curve defined by connecting the solid grid points adjacent to the solid-liquid interface is referred to as virtual boundary. The narrow irregular strip of solid between the virtual boundary and the actual solid-fluid interface is called pseudo-fluid. The general fluid region consisting of both fluid and pseudo-fluid is a regular domain that can be efficiently solved with conventional numerical method. In this connection, external force is imposed at each fluid grid point adjacent to the solid-fluid interface to compensate for the numerical error arising from the assumption of pseudo-fluid. The solution procedure is iterated until the required external force converges. Accuracy of the new numerical method is validated through three test problems. The numerical method then is used to investigate the flow induced by the flapping wings of a tethered dragonfly in literature. The corresponding CFL numbers of the four examples are infinity, 20, 100, and 3.29.
Impulsive Control of a Cam-Follower Oblique-Impact System
Authors: Lu N. , Ren X. M. , Jiang T. D. , Yang Y. F. 
Published: May 2017

AbstractThe transient impact hypothesis was extended, and the oblique collision model was established by considering the tangential slip. In order to solve this problem, the oblique-impact equations for cam-follower were transformed into a linear complementarity problem. Impulsive control method was employed to control or anti-control the nonlinear responses. The simulation results show that the cam-follower system performs very complex nonlinear characteristics, such as period, quasi-period and chaos responses. Using the impulsive control method, the nonlinear responses of the cam-follower system can be controlled to P(n, n) and P(∞, n) or anti-controlled to chaos.
The effect of increased fruit and vegetable consumption on selected macronutrient and micronutrient intakes in four randomised-controlled trials
Authors: Fulton Sharon L. , McKinley Michelle C. , Neville Charlotte E. , Baldrick Francina R. , Mulligan Ciara , McCall Damian O. , McCance David R. , Edgar J. D. , Elborn J. S. , Young Ian S. , Patterson Chris C. , Woodside Jayne V. 
Published: May 2017

AbstractFruit and vegetable (FV) intake is associated with reduced risk of a number of non-communicable diseases. Research tends to focus on antioxidants, flavonoids and polyphenols contained in FV as the main beneficial components to health; however, increasing FV may also alter overall diet profile. Extra FV may be substituted for foods thought to be less healthy, therefore altering the overall macronutrient and/or micronutrient content in the diet. This analysis merged dietary data from four intervention studies in participants with varying health conditions and examined the effect of increased FV consumption on diet profile. Dietary intake was assessed by either diet diaries or diet histories used in four FV randomised intervention studies. All food and drink intake recorded was analysed using WISP version 3.0, and FV portions were manually counted using household measures. Regression analysis revealed significant increases in intakes of energy (172 kJ (+41 kcal)), carbohydrate (+3·9 g/4184 kJ (1000 kcal)), total sugars (+6·0 g/4184 kJ (1000 kcal)) and fibre (+0·8 g/4184 kJ (1000 kcal)) and significant decreases in intakes of total fat (−1·4 g/4184 kJ (1000 kcal)), SFA (−0·6 g/4184 kJ (1000 kcal)), MUFA (−0·6 g/4184 kJ (1000 kcal)), PUFA (−0·1 g/4184 kJ (1000 kcal)) and starch (−2·1 g/4184 kJ (1000 kcal)) per one portion increase in FV. Significant percentage increases were also observed in vitamin C (+24 %) and -carotene (+20 %) intake, per one portion increase in FV. In conclusion, pooled analysis of four FV intervention studies, that used similar approaches to achieving dietary change, in participants with varying health conditions, demonstrated an increase in energy, total carbohydrate, sugars and fibre intake, and a decrease in fat intake alongside an expected increase in micronutrient intake.
An enhanced bioluminescence-based Annexin V probe for apoptosis detection in vitro and in vivo
Authors: Head Trajen , Dau Peter , Duffort Stephanie , Daftarian Pirouz , Joshi Pratibha M , Vazquez-Padron Roberto , Deo Sapna K , Daunert Sylvia 
Published: May 2017

AbstractThe process of controlled cellular death known as apoptosis has an important central role not only in normal homeostatic maintenance of tissues, but also in numerous diseases such as cancer, neurodegenerative, autoimmune, and cardiovascular diseases. As a result, new technologies with the capability to selectively detect apoptotic cells represent a central focus of research for the study of these conditions. We have developed a new biosensor for the detection of apoptotic cells, incorporating the targeted selectivity for apoptotic cells from Annexin V with the sensitivity of bioluminescence signal generation from a serum-stable mutant of Renilla luciferase (RLuc8). Our data presents a complete characterization of the structural and biochemical properties of this new Annexin-Renilla fusion protein (ArFP) construct, as well as a validation of its ability to detect apoptosis in vitro. Moreover, this work represents the first report of a bioluminescent Annexin V apoptosis sensor utilized in vivo. With this new construct, we examine apoptosis within disease-relevant animal models of surgery-induced ischemia/reperfusion, corneal injury, and retinal cell death as a model of age-related macular degeneration. In each of these experiments, we demonstrate successful application of the ArFP construct for detection and bioluminescence imaging of apoptosis within each disease or treatment model. ArFP represents an important new tool in the continuously growing kit of technologies for apoptosis detection, and our results from both in vitro and in vivo experiments suggest a diverse range of potential clinically relevant applications including cancer therapeutic screening and efficacy analysis, atherosclerosis and cardiovascular disease detection, and the monitoring of any number of other conditions in which apoptosis has a central role.
Phosphorylated CAV1 activates autophagy through an interaction with BECN1 under oxidative stress
Authors: Nah Jihoon , Yoo Seung-Min , Jung Sunmin , Jeong Eun Il , Park Moonju , Kaang Bong-Kiun , Jung Yong-Keun 
Published: May 2017

AbstractCAV1/Caveolin1, an integral membrane protein, is involved in caveolae function and cellular signaling pathways. Here, we report that CAV1 is a positive regulator of autophagy under oxidative stress and cerebral ischemic injury. Treatment with hydrogen peroxide enhanced autophagy flux and caused the localization of BECN1 to the mitochondria, whereas these changes were impaired in the absence of CAV1. Among many autophagy signals, only LC3 foci formation in response to hydrogen peroxide was abolished by CAV1 deficiency. Under oxidative stress, CAV1 interacted with a complex of BECN1/VPS34 through its scaffolding domain, and this interaction facilitated autophagosome formation. Interestingly, the phosphorylation of CAV1 at tyrosine-14 was essential for the interaction with BECN1 and their localization to the mitochondria, and the activation of autophagy in response to hydrogen peroxide. In addition, the expression of a phosphatase PTPN1 reduced the phosphorylation of CAV1 and inhibited autophagy. Further, compared to that in wild-type mice, autophagy was impaired and cerebral infarct damage was aggravated in the brain of Cav1 knockout mice. These results suggest that the phosphorylated CAV1 functions to activate autophagy through binding to the BECN1/VPS34 complex under oxidative stress and to protect against ischemic damage.
Endogenous opioids regulate social threat learning in humans
Authors: Haaker Jan , Yi Jonathan , Petrovic Predrag , Olsson Andreas 
Published: May 2017

AbstractMany fearful expectations are shaped by observation of aversive outcomes to others. Yet, the neurochemistry regulating social learning is unknown. Previous research has shown that during direct (Pavlovian) threat learning, information about personally experienced outcomes is regulated by the release of endogenous opioids, and activity within the amygdala and periaqueductal gray (PAG). Here we report that blockade of this opioidergic circuit enhances social threat learning through observation in humans involving activity within the amygdala, midline thalamus and the PAG. In particular, anticipatory responses to learned threat cues (CS) were associated with temporal dynamics in the PAG, coding the observed aversive outcomes to other (observational US). In addition, pharmacological challenge of the opioid receptor function is classified by distinct brain activity patterns during the expression of conditioned threats. Our results reveal an opioidergic circuit that codes the observed aversive outcomes to others into threat responses and long-term memory in the observer.
Gigantic negative magnetoresistance in the bulk of a disordered topological insulator
Authors: Breunig Oliver , Wang Zhiwei , Taskin A A , Lux Jonathan , Rosch Achim , Ando Yoichi 
Published: May 2017

AbstractWith the recent discovery of Weyl semimetals, the phenomenon of negative magnetoresistance (MR) is attracting renewed interest. Large negative MR is usually related to magnetism, but the chiral anomaly in Weyl semimetals is a rare exception. Here we report a mechanism for large negative MR which is also unrelated to magnetism but is related to disorder. In the nearly bulk-insulating topological insulator TlBi0.15Sb0.85Te2, we observed gigantic negative MR reaching 98% in 14 T at 10 K, which is unprecedented in a nonmagnetic system. Supported by numerical simulations, we argue that this phenomenon is likely due to the Zeeman effect on a barely percolating current path formed in the disordered bulk. Since disorder can also lead to non-saturating linear MR in Ag2+δSe, the present finding suggests that disorder engineering in narrow-gap systems is useful for realizing gigantic MR in both positive and negative directions.
A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions
Authors: Schlecht Ulrich , Liu Zhimin , Blundell Jamie R. , St.Onge Robert P. , Levy Sasha F. 
Published: May 2017

AbstractSeveral large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae. PPiSeq detects PPIs at a rate that is on par with current assays and, in contrast with current methods, quantitatively scores PPIs with enough accuracy and sensitivity to detect changes across environments. Both PPI scoring and the bulk of strain construction can be performed with cell pools, making the assay scalable and easily reproduced across environments. PPiSeq is therefore a powerful new tool for large-scale investigations of dynamic PPIs.
Production of three phenylethanoids, tyrosol, hydroxytyrosol, and salidroside, using plant genes expressing in Escherichia coli
Authors: Chung Daeun , Kim So Yeon , Ahn Joong-Hoon 
Published: May 2017

AbstractPolyphenols, which include phenolic acids, flavonoids, stilbenes, and phenylethanoids, are generally known as useful antioxidants. Tyrosol, hydroxytyrosol, and salidroside are typical phenylethanoids. Phenylethanoids are found in plants such as olive, green tea, andRhodiolaand have various biological activities, including the prevention of cardiovascular diseases, cancer, and brain damage. We usedEscherichia colito synthesize three phenylethanoids, tyrosol, hydroxytyrosol, and salidroside. To synthesize tyrosol, the aromatic aldehyde synthase (AAS) was expressed inE. coli. Hydroxytyrosol was synthesized usingE. coliharboringAASandHpaBC, which encodes hydroxylase. In order to synthesize salidroside, 12 uridine diphosphate-dependent glycosyltransferases (UGTs) were screened and UGT85A1 was found to convert tyrosol to salidroside. UsingE. coliharboringAASand UGT85A1, salidroside was synthesized. Through the optimization of these threeE. colistrains, we were able to synthesize 531 mg/L tyrosol, 208 mg/L hydroxytyrosol, and 288 mg/L salidroside, respectively.
Fatty Acid Binding Protein 3 And Transzonal Projections Are Involved In Lipid Accumulation During In Vitro Maturation Of Bovine Oocytes
Authors: del Collado Maite , da Silveira Juliano Coelho , Sangalli Juliano Rodrigues , Andrade Gabriella Mamede , Sousa Letícia Rabello da Silva , Silva Luciano Andrade , Meirelles Flavio Vieira , Perecin Felipe 
Published: May 2017

AbstractOocytes that undergo in vitro maturation (IVM) are metabolically abnormal and accumulate excess lipid content. However, the mechanism of lipid accumulation and the role of cumulus cells in this process are unclear. Recently, it was shown that fatty acid binding proteins (FABPs) performed intra- and extracellular fatty acid transport. We postulated that FABP3 might be responsible for fatty acid transport from cumulus cells to the oocytes via transzonal projections (TZPs) during IVM. Transcript and protein levels of FABP3 were analyzed in both in vivo- and in vitro-matured cumulus-oocyte-complexes and were increased in IVM samples. Further analysis showed increased lipid content in oocytes and cumulus cells in IVM samples compared to in vivo-derived. We therefore speculated that altered traffic of fatty acids via FABP3 during IVM was the mechanism leading to the excess of lipids accumulated within IVM oocytes. Furthermore, we demonstrated an increase in FABP3 levels and lipid content during the first 9 h of IVM, further strengthening the possibility of fatty acid transport via FABP3 and TZPs. Additionally, disruptions of TZPs during IVM decreased lipid accumulation in oocytes. Our results shed light on a possible mechanism involving FABP3 and TZPs that causes excess lipid accumulation in oocytes during IVM.
Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora
Authors: Wright Rachel M. , Kenkel Carly D. , Dunn Carly E. , Shilling Erin N. , Bay Line K. , Matz Mikhail V. 
Published: May 2017

AbstractDisease causes significant coral mortality worldwide; however, factors responsible for intraspecific variation in disease resistance remain unclear. We exposed fragments of eightAcropora milleporacolonies (genotypes) to putatively pathogenic bacteria (Vibrio spp.). Genotypes varied from zero to >90% mortality, with bacterial challenge increasing average mortality rates 4–6 fold and shifting the microbiome in favor of stress-associated taxa. Constitutive immunity and subsequent immune and transcriptomic responses to the challenge were more prominent in high-mortality individuals, whereas low-mortality corals remained largely unaffected and maintained expression signatures of a healthier condition (i.e., did not launch a large stress response). Our results suggest that lesions appeared due to changes in the coral pathobiome (multiple bacterial species associated with disease) and general health deterioration after the biotic disturbance, rather than the direct activity of any specific pathogen. If diseases in nature arise because of weaknesses in holobiont physiology, instead of the virulence of any single etiological agent, environmental stressors compromising coral condition might play a larger role in disease outbreaks than is currently thought. To facilitate the diagnosis of compromised individuals, we developed and independently cross-validated a biomarker assay to predict mortality based on genes whose expression in asymptomatic individuals coincides with mortality rates.
Interaction studies of carbon nanomaterials and plasma activated carbon nanomaterials solution with telomere binding protein
Authors: Attri Pankaj , Gaur Jitender , Choi Sooho , Kim Minsup , Bhatia Rohit , Kumar Naresh , Park Ji Hoon , Cho Art. E. , Choi Eun Ha , Lee Weontae 
Published: May 2017

AbstractMost cancer cells have telomerase activity because they can express the human telomerase reverse transcriptase (hTERT) gene. Therefore, the inhibition of the hTERT expression can play an important role in controlling cancer cell proliferation. Our current study aims to inhibit hTERT expression. For this, we synthesized graphene oxide (GO) and a functionalized multiwall carbon nanotube (f-MWCNT), latter treated them with cold atmospheric pressure plasma for further analysis of the hTERT expression. The inhibition of hTERT expression by GO, f-MWCNT, plasma activated GO solution (PGOS), and plasma activated f-MWCNT solution (PCNTS), was studied using two lung cancer cell lines, A549 and H460. The hTERT experimental results revealed that GO and PGOS sufficiently decreased the hTERT concentration, while f-MWCNT and PCNTS were unable to inhibit the hTERT concentration. Therefore, to understand the inhibition mechanism of hTERT, we studied the binding properties of GO and PGOS with telomere binding protein (AtTRB2). The interaction studies were carried out using circular dichroism, fluorescence, 1H-15N NMR spectroscopy, and size-exclusion chromatography (SEC) binding assay. We also used docking simulation to have an better understanding of the interactions between GO nanosheets and AtTRB2 protein. Our results may provide new insights that can benefit in biomedical treatments.
Role of interfaces on the stability and electrical properties of Ge2Sb2Te5 crystalline structures
Authors: Mio A. M. , Privitera S. M. S. , Bragaglia V. , Arciprete F. , Cecchi S. , Litrico G. , Persch C. , Calarco R. , Rimini E. 
Published: May 2017

AbstractGeSbTe-based materials exhibit multiple crystalline phases, from disordered rocksalt, to rocksalt with ordered vacancy layers, and to the stable trigonal phase. In this paper we investigate the role of the interfaces on the structural and electrical properties of Ge2Sb2Te5. We find that the site of nucleation of the metastable rocksalt phase is crucial in determining the evolution towards vacancy ordering and the stable phase. By properly choosing the substrate and the capping layers, nucleation sites engineering can be obtained, thus promoting or preventing the vacancy ordering in the rocksalt structure or the conversion into the trigonal phase. The vacancy ordering occurs at lower annealing temperatures (170 °C) for films deposited in the amorphous phase on silicon (111), compared to the case of SiO2 substrate (200 °C), or in presence of a capping layer (330 °C). The mechanisms governing the nucleation have been explained in terms of interfacial energies. Resistance variations of about one order of magnitude have been measured upon transition from the disordered to the ordered rocksalt structure and then to the trigonal phase. The possibility to control the formation of the crystalline phases characterized by marked resistivity contrast is of fundamental relevance for the development of multilevel phase change data storage.
Morphologic and biometric evaluation of chick embryo eyes in ovo using 7 Tesla MRI
Authors: Lindner Tobias , Klose Ronja , Streckenbach Felix , Stahnke Thomas , Hadlich Stefan , Kühn Jens-Peter , Guthoff Rudolf F. , Wree Andreas , Neumann Anne-Marie , Frank Marcus , Glass Änne , Langner Sönke , Stachs Oliver 
Published: May 2017

AbstractThe purposes of this study were (1) to characterize embryonic eye development during incubation in ovo and (2) to analyze the putative influence of repetitive ultrahigh-field MRI (UHF-MRI) measurements on this development. A population of 38 fertilized chicken eggs was divided into two sub-groups: two eggs (Group A) were examined repeatedly during the developmental period from embryonic day 1 (E1) to embryonic day 20 (E20) to evaluate the influence of daily MRI scanning. A second larger group of 36 eggs was examined pairwise on one day only, from E3 to E20, and the embryos were sacrificed immediately after MR imaging (Group B). Fast T2-weighted MR sequences provided biometric data on the eye with an in-plane resolution of 74 μm. The data show rapid growth of the eye with a steep increase in intraocular dimensions in all axis directions and in eyeball volume during initial development up to E10, followed by a phase of reduced growth rate in later developmental stages. Comparison of the two groups revealed no differences in ocular development.
Stopping power beyond the adiabatic approximation
Authors: Caro M. , Correa A. A. , Artacho E. , Caro A. 
Published: May 2017

AbstractEnergetic ions traveling in solids deposit energy in a variety of ways, being nuclear and electronic stopping the two avenues in which dissipation is usually treated. This separation between electrons and ions relies on the adiabatic approximation in which ions interact via forces derived from the instantaneous electronic ground state. In a more detailed view, in which non-adiabatic effects are explicitly considered, electronic excitations alter the atomic bonding, which translates into changes in the interatomic forces. In this work, we use time dependent density functional theory and forces derived from the equations of Ehrenfest dynamics that depend instantaneously on the time-dependent electronic density. With them we analyze how the inter-ionic forces are affected by electronic excitations in a model of a Ni projectile interacting with a Ni target, a metallic system with strong electronic stopping and shallow core level states. We find that the electronic excitations induce substantial modifications to the inter-ionic forces, which translate into nuclear stopping power well above the adiabatic prediction. In particular, we observe that most of the alteration of the adiabatic potential in early times comes from the ionization of the core levels of the target ions, not readily screened by the valence electrons.
Nitrogen isotopes provide clues to amino acid metabolism in human colorectal cancer cells
Authors: Krishnamurthy R. V. , Suryawanshi Yogesh R. , Essani Karim 
Published: May 2017

AbstractGlutamic acid and alanine make up more than 60 per cent of the total amino acids in the human body. Glutamine is a significant source of energy for cells and also a prime donor of nitrogen in the biosynthesis of many amino acids. Several studies have advocated the role of glutamic acid in cancer therapy. Identification of metabolic signatures in cancer cells will be crucial for advancement of cancer therapies based on the cell’s metabolic state. Stable nitrogen isotope ratios (15N/14N, δ15N) are of particular advantage to understand the metabolic state of cancer cells, since most biochemical reactions involve transfer of nitrogen. In our study, we used the natural abundances of nitrogen isotopes (δ15N values) of individual amino acids from human colorectal cancer cell lines to investigate isotope discrimination among amino acids. Significant effects were noticed in the case of glutamic acid, alanine, aspartic acid and proline between cancer and healthy cells. The data suggest that glutamic acid is a nitrogen acceptor while alanine, aspartic acid and proline are nitrogen donors in cancerous cells. One plausible explanation is the transamination of the three acids to produce glutamic acid in cancerous cells.