bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical soliton molecular complexes in a passively mode-locked fibre laser
Authors: Wang Z. Q. , Nithyanandan K. , Coillet A. , Tchofo-Dinda P. , Grelu Ph. 
Published: February 2019

AbstractUltrashort optical pulses propagating in a dissipative nonlinear system can interact and bind stably, forming optical soliton molecules. Soliton molecules in ultrafast lasers are under intense research focus and present striking analogies with their matter molecules counterparts. The recent development of real-time spectral measurements allows probing the internal dynamics of an optical soliton molecule, mapping the dynamics of the pulses’ relative separations and phases that constitute the relevant internal degrees of freedom of the molecule. The soliton-pair molecule, which consists of two strongly bound optical solitons, has been the most studied multi-soliton structure. We here demonstrate that two soliton-pair molecules can bind subsequently to form a stable molecular complex and highlight the important differences between the intra-molecular and inter-molecular bonds. The dynamics of the experimentally observed soliton molecular complexes are discussed with the help of fitting models and numerical simulations, showing the universality of these multi-soliton optical patterns.
High-speed mechano-active multielectrode array for investigating rapid stretch effects on cardiac tissue
Authors: Imboden Matthias , de Coulon Etienne , Poulin Alexandre , Dellenbach Christian , Rosset Samuel , Shea Herbert , Rohr Stephan 
Published: February 2019

AbstractSystematic investigations of the effects of mechano-electric coupling (MEC) on cellular cardiac electrophysiology lack experimental systems suitable to subject tissues to in-vivo like strain patterns while simultaneously reporting changes in electrical activation. Here, we describe a self-contained motor-less device (mechano-active multielectrode-array, MaMEA) that permits the assessment of impulse conduction along bioengineered strands of cardiac tissue in response to dynamic strain cycles. The device is based on polydimethylsiloxane (PDMS) cell culture substrates patterned with dielectric actuators (DEAs) and compliant gold ion-implanted extracellular electrodes. The DEAs induce uniaxial stretch and compression in defined regions of the PDMS substrate at selectable amplitudes and with rates up to 18 s−1. Conduction along cardiomyocyte strands was found to depend linearly on static strain according to cable theory while, unexpectedly, being completely independent on strain rates. Parallel operation of multiple MaMEAs provides for systematic high-throughput investigations of MEC during spatially patterned mechanical perturbations mimicking in-vivo conditions.
FraC nanopores with adjustable diameter identify the mass of opposite-charge peptides with 44 dalton resolution
Authors: Huang Gang , Voet Arnout , Maglia Giovanni 
Published: February 2019

AbstractA high throughput single-molecule method for identifying peptides and sequencing proteins based on nanopores could reduce costs and increase speeds of sequencing, allow the fabrication of portable home-diagnostic devices, and permit the characterization of low abundance proteins and heterogeneity in post-translational modifications. Here we engineer the size of Fragaceatoxin C (FraC) biological nanopore to allow the analysis of a wide range of peptide lengths. Ionic blockades through engineered nanopores distinguish a variety of peptides, including two peptides differing only by the substitution of alanine with glutamate. We also find that at pH 3.8 the depth of the peptide current blockades scales with the mass of the peptides irrespectively of the chemical composition of the analyte. Hence, this work shows that FraC nanopores allow direct readout of the mass of single peptide in solution, which is a crucial step towards the developing of a real-time and single-molecule protein sequencing device.
Single gold-bridged nanoprobes for identification of single point DNA mutations
Authors: Ma Xingyi , Song Sojin , Kim Soohyun , Kwon Mi-sun , Lee Hyunsook , Park Wounjhang , Sim Sang Jun 
Published: February 2019

AbstractConsensus ranking of protein affinity to identify point mutations has not been established. Therefore, analytical techniques that can detect subtle variations without interfering with native biomolecular interactions are required. Here we report a rapid method to identify point mutations by a single nanoparticle sensing system. DNA-directed gold crystallization forms rod-like nanoparticles with bridges based on structural design. The nanoparticles enhance Rayleigh light scattering, achieving high refractive-index sensitivity, and enable the system to monitor even a small number of protein-DNA binding events without interference. Analysis of the binding affinity can compile an atlas to distinguish the potential of various point mutations recognized by MutS protein. We use the atlas to analyze the presence and type of single point mutations in BRCA1 from samples of human breast and ovarian cancer cell lines. The strategy of synthesis-by-design of plasmonic nanoparticles for sensors enables direct identification of subtle biomolecular binding distortions and genetic alterations.
A MST1–FOXO1 cascade establishes endothelial tip cell polarity and facilitates sprouting angiogenesis
Authors: Kim Yoo Hyung , Choi Jeongwoon , Yang Myung Jin , Hong Seon Pyo , Lee Choong-kun , Kubota Yoshiaki , Lim Dae-Sik , Koh Gou Young 
Published: February 2019

AbstractHypoxia is a main driver of sprouting angiogenesis, but how tip endothelial cells are directed to hypoxic regions remains poorly understood. Here, we show that an endothelial MST1–FOXO1 cascade is essential for directional migration of tip cells towards hypoxic regions. In mice, endothelial‐specific deletion of either MST1 or FOXO1 leads to the loss of tip cell polarity and subsequent impairment of sprouting angiogenesis. Mechanistically, MST1 is activated by reactive oxygen species (ROS) produced in mitochondria in response to hypoxia, and activated MST1 promotes the nuclear import of FOXO1, thus augmenting its transcriptional regulation of polarity and migration‐associated genes. Furthermore, endothelial MST1‐FOXO1 cascade is required for revascularization and neovascularization in the oxygen-induced retinopathy model. Together, the results of our study delineate a crucial coupling between extracellular hypoxia and an intracellular ROS‐MST1‐FOXO1 cascade in establishing endothelial tip cell polarity during sprouting angiogenesis.
Dual regulation of Arabidopsis AGO2 by arginine methylation
Authors: Hu Po , Zhao Hongwei , Zhu Pei , Xiao Yongsheng , Miao Weili , Wang Yinsheng , Jin Hailing 
Published: February 2019

AbstractArgonaute (AGO) proteins are core components of RNA interference (RNAi) but the mechanisms of their regulation, especially at the post-translational level, remain unclear. Among the ten AGOs in Arabidopsis, only AGO2 is induced by bacterial infection and is known to positively regulate immunity. Here we show that the N-terminal domain of AGO2 is enriched with arginine-glycine RG/GR repeats, which are methylated by protein arginine methyltransferase5 (PRMT5). Arginine methylation has dual functions in AGO2 regulation. Methylated arginine residues can promote AGO2 protein degradation and are also bound by Tudor-domain proteins (TSNs), which can degrade AGO2-associated small RNAs (sRNAs). PRMT5 is down-regulated during infection and the prmt5 mutant is more resistant to bacteria. We speculate that reduced PRMT5 expression during infection may lead to reduced arginine methylation of AGO2, resulting in accumulation of both AGO2 and, via reduced interaction with TSNs, accumulation of AGO2-associated sRNAs, to promote plant immunity. These results reveal that both the arginine methylation writer (PRMT5) and readers (TSNs) can regulate AGO2-mediated RNAi.
Arbitrary order exceptional point induced by photonic spin–orbit interaction in coupled resonators
Authors: Wang Shubo , Hou Bo , Lu Weixin , Chen Yuntian , Zhang Z. Q. , Chan C. T. 
Published: February 2019

AbstractMany novel properties of non-Hermitian systems are found at or near the exceptional points—branch points of complex energy surfaces at which eigenvalues and eigenvectors coalesce. In particular, higher-order exceptional points can result in optical structures that are ultrasensitive to external perturbations. Here we show that an arbitrary order exceptional point can be achieved in a simple system consisting of identical resonators placed near a waveguide. Unidirectional coupling between any two chiral dipolar states of the resonators mediated by the waveguide mode leads to the exceptional point, which is protected by the transverse spin–momentum locking of the guided wave and is independent of the positions of the resonators. Various analytic response functions of the resonators at the exceptional points are experimentally manifested in the microwave regime. The enhancement of sensitivity to external perturbations near the exceptional point is also numerically and analytically demonstrated.
A potential peptide derived from cytokine receptors can bind proinflammatory cytokines as a therapeutic strategy for anti-inflammation
Authors: Jiang Shinn-Jong , Tsai Pei-I , Peng Shih-Yi , Chang Chun-Chun , Chung Yi , Tsao Hao-Hsiang , Huang Hsin-Ting , Chen San-Yuan , Hsu Hao-Jen 
Published: February 2019

AbstractChronic inflammation is a pivotal event in the pathogenesis of cardiovascular diseases, including atherosclerosis, restenosis, and coronary artery disease. The efficacy of current treatment or preventive strategies for such inflammation is still inadequate. Thus, new anti-inflammatory strategies are needed. In this study, based on molecular docking and structural analysis, a potential peptide KCF18 with amphiphilic properties (positively charged and hydrophobic residues) derived from the receptors of proinflammatory cytokines was designed to inhibit cytokine-induced inflammatory response. Simulations suggested that KCF18 could bind to cytokines simultaneously, and electrostatic interactions were dominant. Surface plasmon resonance detection showed that KCF18 bound to both tumor necrosis factor-α (TNF-α) and interleukin-6, which is consistent with MM/PBSA binding free energy calculations. The cell experiments showed that KCF18 significantly reduced the binding of proinflammatory cytokines to their cognate receptors, suppressed TNF-α mRNA expression and monocyte binding and transmigration, and alleviated the infiltration of white blood cells in a peritonitis mouse model. The designed peptide KCF18 could remarkably diminish the risk of vascular inflammation by decreasing plasma cytokines release and by directly acting on the vascular endothelium. This study demonstrated that a combination of structure-based in silico design calculations, together with experimental measurements can be used to develop potential anti-inflammatory agents.
Efficient system for upstream mRNA trans-splicing to generate covalent, head-to-tail, protein multimers
Authors: Mitsuhashi Hiroaki , Homma Sachiko , Beermann Mary Lou , Ishimaru Satoshi , Takeda Hayato , Yu Bryant K. , Liu Kevin , Duraiswamy Swetha , Boyce Frederick M. , Miller Jeffrey Boone 
Published: February 2019

AbstractWe present a plasmid-based system in which upstream trans-splicing efficiently generates mRNAs that encode head-to-tail protein multimers. In this system, trans-splicing occurs between one of two downstream splice donors in the sequence encoding a C-terminal V5 epitope tag and an upstream splice acceptor in the 5′ region of the pCS2(+) host plasmid. Using deletion and fusion constructs of the DUX4 protein as an example, we found that this system produced trans-spliced mRNAs in which coding regions from independent transcripts were fused in phase such that covalent head-to-tail protein multimers were translated. For a cDNA of ~450 bp, about half of the expressed proteins were multimeric, with the efficiency of trans-splicing and extent of multimer expression decreasing as cDNA length increased. This system generated covalent heterodimeric proteins upon co-transfections of plasmids encoding separate proteins and did not require a long complementary binding domain to position mRNAs for trans-splicing. This plasmid-based trans-splicing system is adaptable to multiple gene delivery systems, and it presents new opportunities for investigating molecular mechanisms of trans-splicing, generating covalent protein multimers with novel functions within cells, and producing mRNAs encoding large proteins from split precursors.
Network Analysis of the Multidimensional Symptom Experience of Oncology
Authors: Papachristou Nikolaos , Barnaghi Payam , Cooper Bruce , Kober Kord M. , Maguire Roma , Paul Steven M. , Hammer Marilyn , Wright Fay , Armes Jo , Furlong Eileen P. , McCann Lisa , Conley Yvette P. , Patiraki Elisabeth , Katsaragakis Stylianos , Levine Jon D. , Miaskowski Christine 
Published: February 2019

AbstractOncology patients undergoing cancer treatment experience an average of fifteen unrelieved symptoms that are highly variable in both their severity and distress. Recent advances in Network Analysis (NA) provide a novel approach to gain insights into the complex nature of co-occurring symptoms and symptom clusters and identify core symptoms. We present findings from the first study that used NA to examine the relationships among 38 common symptoms in a large sample of oncology patients undergoing chemotherapy. Using two different models of Pairwise Markov Random Fields (PMRF), we examined the nature and structure of interactions for three different dimensions of patients’ symptom experience (i.e., occurrence, severity, distress). Findings from this study provide the first direct evidence that the connections between and among symptoms differ depending on the symptom dimension used to create the network. Based on an evaluation of the centrality indices, nausea appears to be a structurally important node in all three networks. Our findings can be used to guide the development of symptom management interventions based on the identification of core symptoms and symptom clusters within a network.
AEO7 Surfactant as an Eco-Friendly Corrosion Inhibitor for Carbon Steel in HCl solution
Authors: Sliem Mostafa H. , Afifi Mohammed , Bahgat Radwan A. , Fayyad Eman M. , Shibl Mohamed F. , Heakal Fakiha El-Taib , Abdullah Aboubakr M. 
Published: February 2019

AbstractThe impact of AEO7 surfactant on the corrosion inhibition of carbon steel (C-steel) in 0.5 M HCl solution at temperatures between 20 °C and 50 °C was elucidated using weight loss and different electrochemical techniques. The kinetics and thermodynamic parameters of the corrosion and inhibition processes were reported. The corrosion inhibition efficiency (IE%) improved as the concentration of AEO7 increased. In addition, a synergistic effect was observed when a concentration of 1 × 10−3 mol L−1or higher of potassium iodide (KI) was added to 40 µmol L−1of the AEO7 inhibitor where the corrosionIE% increased from 87.4% to 99.2%. Also, it was found that the adsorption of AEO7 surfactant on C-steel surface followed the Freundlich isotherm. Furthermore, electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization measurements indicated that AEO7 was physically adsorbed on the steel surface. The surface topography was examined using an optical profilometer, an atomic force microscope (AFM), and a scanning electron-microscope (SEM) coupled with an energy dispersion X-ray (EDX) unit. Quantum chemical calculations based on the density functional theory were performed to understand the relationship between the corrosionIE% and the molecular structure of the AEO7 molecule.
Anoctamin-4 is a bona fide Ca2+-dependent non-selective cation channel
Authors: Reichhart Nadine , Schöberl Simon , Keckeis Susanne , Alfaar Ahmad S. , Roubeix Christophe , Cordes Magdalena , Crespo-Garcia Sergio , Haeckel Akvile , Kociok Norbert , Föckler Renate , Fels Gabriele , Mataruga Anja , Rauh Robert , Milenkovic Vladimir M. , Zühlke Kerstin , Klussmann Enno , Schellenberger Eyk , Strauß Olaf 
Published: February 2019

AbstractChanges in cell function occur by specific patterns of intracellular Ca2+, activating Ca2+-sensitive proteins. The anoctamin (TMEM16) protein family has Ca2+-dependent ion channel activity, which provides transmembrane ion transport, and/or Ca2+-dependent phosphatidyl-scramblase activity. Using amino acid sequence analysis combined with measurements of ion channel function, we clarified the so far unknown Ano4 function as Ca2+-dependent, non-selective monovalent cation channel; heterologous Ano4 expression in HEK293 cells elicits Ca2+ activated conductance with weak selectivity of K+ > Na+ > Li+. Endogenously expressed Ca2+-dependent cation channels in the retinal pigment epithelium were identified as Ano4 by KO mouse-derived primary RPE cells and siRNA against Ano4. Exchanging a negatively charged amino acid in the putative pore region (AA702–855) into a positive one (E775K) turns Ano4-elicited currents into Cl− currents evidencing its importance for ion selectivity. The molecular identification of Ano4 as a Ca2+-activated cation channel advances the understanding of its role in Ca2+ signaling.
Dynamic Networks that Drive the Process of Irreversible Step-Growth Polymerization
Authors: Schamboeck Verena , Iedema Piet D. , Kryven Ivan 
Published: February 2019

AbstractMany research fields, reaching from social networks and epidemiology to biology and physics, have experienced great advance from recent developments in random graphs and network theory. In this paper we propose a generic model of step-growth polymerisation as a promising application of the percolation on a directed random graph. This polymerisation process is used to manufacture a broad range of polymeric materials, including: polyesters, polyurethanes, polyamides, and many others. We link features of step-growth polymerisation to the properties of the directed configuration model. In this way, we obtain new analytical expressions describing the polymeric microstructure and compare them to data from experiments and computer simulations. The molecular weight distribution is related to the sizes of connected components, gelation to the emergence of the giant component, and the molecular gyration radii to the Wiener index of these components. A model on this level of generality is instrumental in accelerating the design of new materials and optimizing their properties, as well as it provides a vital link between network science and experimentally observable physics of polymers.
Mitochondrial Haplogroup and the Risk of Acute Kidney Injury Following Cardiac Bypass Surgery
Authors: Kanagasundaram Nigel S. , Baudouin Simon V. , Rowling Sarah , Prabhu Mahesh , Dark John H. , Goodship Timothy H. J. , Chinnery Patrick F. , Hudson Gavin 
Published: February 2019

AbstractAlthough mitochondrial dysfunction plays a key role in the pathophysiology of acute kidney injury (AKI), the influence of mitochondrial genetic variability in this process remains unclear. We explored the association between the risk of post-cardiac bypass AKI and mitochondrial haplotype – inherited mitochondrial genomic variations of potentially functional significance. Our single-centre study recruited consecutive patients prior to surgery. Exclusions included stage 5 CKD, non-Caucasian race and subsequent off-pump surgery. Haplogroup analysis allowed characterisation of the study population using the common mutations and by phylogenetic supergroup (WXI and HV). Chi-square tests for association allowed the identification of potential predictors of AKI for use in logistic regression analysis. AKI occurred in 12.8% of the study population (n = 881; male 69.6%, non-diabetic 78.5%, median (interquartile range) age 68.0 (61.0–75.0) years). The haplogroup profile comprised H (42.7%), J (12.1%), T (10.9%), U (14.4%) and K (7.6%). Although the regression model was statistically significant (χ2 = 95.483, p < 0.0005), neither the phylogenetic supergroups nor any individual haplogroup was a significant contributor. We found no significant association between common European haplogroups and the risk of post-cardiac bypass AKI. However, given the major role of mitochondrial dysfunction in AKI, there is a need to replicate our findings in other cohorts and with other aetiologies of AKI.
Hydroxyoleoside-type seco-iridoids from Symplocos cochinchinensis and their insulin mimetic activity
Authors: Lee Ba-Wool , Ha Thi Kim Quy , Pham Ha Thanh Tung , Hoang Quynh Hoa , Tran Van On , Oh Won Keun 
Published: February 2019

AbstractAs part of an ongoing study of new insulin mimetic agents from medicinal plants, the 70% EtOH extract of Symplocos cochinchinensis was found to have a stimulatory effect on glucose uptake in 3T3-L1 adipocyte cells. The intensive targeted isolation of this active extract resulted in ten new hydroxyoleoside-type compounds conjugated with a phenolic acid and monoterpene (1–6 and 8–11), as well as four known compounds (7 and 12–14). The chemical structures of the new compounds were determined based on spectroscopic data analysis (1H and 13C NMR, HSQC, HMBC, NOESY and MS). The absolute configurations of the isolated compounds were determined by electronic circular dichroism (ECD) analysis of derivatives obtained after a series of reactions, such as those with dirhodium (ІІ) tetrakis (trifluoroacetate) and dimolybdenum (ІІ) tetraacetate. In vitro, compounds 3, 7 and 8 moderately increased the 2-deoxy-2-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]-D-glucose (2-NBDG) uptake level in differentiated 3T3-L1 adipocytes. For further studies, we evaluated their effects on the expression of glucose transporter-4 (GLUT4), its translocation, protein tyrosine phosphatase 1B (PTP1B) inhibition and expression of phosphorylated Akt. Our results strongly suggest that the traditional uses of this plant can be described as active constituents by hydroxyoleoside-type compounds.
A New Stress Test for Knee Joint Cartilage
Authors: Paranjape Chinmay S. , Cutcliffe Hattie C. , Grambow Steven C. , Utturkar Gangadhar M. , Collins Amber T. , Garrett William E. , Spritzer Charles E. , DeFrate Louis E. 
Published: February 2019

AbstractCartilage metabolism—both the synthesis and breakdown of cartilage constituents and architecture—is influenced by its mechanical loading. Therefore, physical activity is often recommended to maintain cartilage health and to treat or slow the progression of osteoarthritis, a debilitating joint disease causing cartilage degeneration. However, the appropriate exercise frequency, intensity, and duration cannot be prescribed because directin vivoevaluation of cartilage following exercise has not yet been performed. To address this gap in knowledge, we developed a cartilage stress test to measure thein vivostrain response of healthy human subjects’ tibial cartilage to walking exercise. We varied both walk duration and speed in a dose-dependent manner to quantify how these variables affect cartilage strain. We found a nonlinear relationship between walk duration andin vivocompressive strain, with compressive strain initially increasing with increasing duration, then leveling off with longer durations. This work provides innovative measurements of cartilage creep behavior (which has been well-documentedin vitrobut notin vivo) during walking. This study showed that compressive strain increased with increasing walking speed for the speeds tested in this study (0.9–2.0 m/s). Furthermore, our data provide novel measurements of thein vivostrain response of tibial cartilage to various doses of walking as a mechanical stimulus, with maximal strains of 5.0% observed after 60 minutes of walking. These data describe physiological benchmarks for healthy articular cartilage behavior during walking and provide a much-needed baseline for studies investigating the effect of exercise on cartilage health.