bluuebunny/crossref_metadata_2025 huggingface dataset:
Transient localized surface plasmon induced by femtosecond interband excitation in gold nanoparticles
Authors: Zhang Xinping , Huang Cuiying , Wang Meng , Huang Pei , He Xinkui , Wei Zhiyi
Published: July 2018

Localized surface plasmon resonance (LSPR) is essentially a collective oscillation of free electrons in nanostructured metals. Interband excitation may also produce conduction-band electrons above the Fermi level. However, a question here is whether these excited electrons can take part in plasmonic oscillation. To answer this question, femtosecond pump-probe measurements on gold nanoparticles were performed using interband excitation, where the pump pulse produced a large amount of electrons in the sp-conduction band and left holes in the d-band. Probing by transient absorption spectroscopy, we resolved an induced LSPR feature located at a red-shifted spectrum. This feature cannot be observed for a pumping photon energy lower than the threshold for interband transition. The commonly observed red-shift or broadening of LSPR spectrum due to electron-electron and electron-phonon scattering under strong optical excitation can be ruled out for understanding this feature by a comparison between the plasmonic dynamics at a pump above and below the interband-transition threshold. In particular, a “holding” time of about 1 ps was resolved for the interband-excitation-induced electrons to relax to the LSPR oscillation.
TiO(OH)2 can exceed the critical limit of conventional CO2 sorbents: modification needed for high capacity and selectivity
Authors: Wu Fan , Dellenback Paul A. , Toan Sam , Russell Christopher K. , Fan Maohong
Published: July 2018

TiO(OH)2 is much better than activated carbon and zeolite for CO2 separation in both capacity and selectivity.
Enhancement in RNase H activity of a DNA/RNA hybrid duplex using artificial cationic oligopeptides
Authors: Hara Rintaro Iwata , Maeda Yusuke , Fujimaki Haruna , Wada Takeshi
Published: July 2018

This study assessed the effects of artificial cationic oligopeptides on a DNA/RNA hybrid duplex.
A smart photosensitizer based on a red emitting solution processable porous polymer: generation of reactive oxygen species
Authors: Bandyopadhyay Sujoy , Kundu Subhankar , Giri Arkaprabha , Patra Abhijit
Published: July 2018

An efficient photosensitizer was developed employing a red emitting soluble conjugated porous organic polymer and the structure–activity relationship was established.
Biased continuous-time random walks for ordinary and equilibrium cases: facilitation of diffusion, ergodicity breaking and ageing
Authors: Hou Ru , Cherstvy Andrey G. , Metzler Ralf , Akimoto Takuma
Published: July 2018

We examine renewal processes with power-law waiting time distributions and non-zero driftviacomputing analytically and by computer simulations their ensemble and time averaged spreading characteristics.
Structural, vibrational and thermal expansion properties of Sc2W4O15
Authors: Chen Dongxia , Zhang Ying , Ge Xianghong , Cheng Yongguang , Liu Yayun , Yuan Huanli , Guo Juan , Chao Mingju , Liang Erjun
Published: July 2018

A novel oxide material with the formula of Sc2W4O15and orthorhombic symmetry is synthesized by solid state reactions and its structure, composition, vibrational properties and thermal expansion are investigated and identified by several means.
Electrochemistry at a single nanoparticle: from bipolar regime to tunnelling
Authors: Sun Tong , Wang Dengchao , Mirkin Michael V.
Published: July 2018

This paper is concerned with long-distance interactions between an unbiased metal nanoparticle (NP) and a nanoelectrode employed as a tip in the scanning electrochemical microscope (SECM).
One pot synthesis and systematic study of the photophysical and magnetic properties and thermal sensing of α and β-phase NaLnF4 and β-phase core@shell nanoparticles
Authors: Rodrigues E. M. , Gálico D. A. , Lemes M. A. , Bettini J. , T. Neto E. , Mazali I. O. , Murugesu M. , Sigoli F. A.
Published: July 2018

Hierarchical nanostructured nanoparticles showing high values of relative thermal sensitivity and magnetization at low temperatures.
Correction: Crystal-defect-induced facet-dependent electrocatalytic activity of 3D gold nanoflowers for the selective nanomolar detection of ascorbic acid
Authors: De Sandip Kumar , Mondal Subrata , Sen Pintu , Pal Uttam , Pathak Biswarup , Rawat Kuber Singh , Bardhan Munmun , Bhattacharya Maireyee , Satpati Biswarup , De Amitabha , Senapati Dulal
Published: July 2018

Correction for ‘Crystal-defect-induced facet-dependent electrocatalytic activity of 3D gold nanoflowers for the selective nanomolar detection of ascorbic acid’ by Sandip Kumar De, et al., Nanoscale, 2018, 10, 11091–11102.
Working Memory and Auditory Processing in School-Age Children
Authors: Magimairaj Beula M. , Nagaraj Naveen K.
Published: July 2018

Purpose

Our goal is to present the relationships between working memory (WM) and auditory processing abilities in school-age children.

Review and Discussion

We begin with an overview of auditory processing, the conceptualization of auditory processing disorder, and the assessment of auditory processing abilities in children. Next, we describe a model of WM and a model of auditory processing followed by their comparison. Evidence for the relationships between WM and auditory processing abilities in school-age children follows. Specifically, we present evidence for the association (or lack thereof) between WM/attention and auditory processing test performance.

Clinical Implications

In conclusion, we describe a new framework for understanding auditory processing abilities in children based on integrated evidence from cognitive science, hearing science, and language science. We also discuss clinical implications in children that could inform future research.
Alles nicht so einfach – Verletzungsprävention im Sport
Authors: Kopkow Christian
Published: July 2018

Verletzungen können Sportler lange außer Gefecht setzen. Inzwischen gibt es in einigen Bereichen Präventionsprogramme, etwa die FIFA 11+, welche die
Verletzungshäufigkeit nachweislich verringern können. Doch diese Programme haben zwei Probleme: Sie bewahren nicht jeden. Und sie werden nicht von denjenigen
ausgeführt, die sie eigentlich vor allem benötigen – den Breitensportlern. Probleme, die schwer zu lösen sind, erklärt Prof. Dr. Christian Kopkow im
Interview.
Ergotherapie in den USA – Ein Trendberuf in Übersee
Authors: Zamath Frank
Published: July 2018

In den USA hat sich die Ergotherapie anders entwickelt als in Deutschland. Zwar gibt es ähnlich wie bei uns Ergotherapeuten, die in Pädiatrie, Neurologie, Psychiatrie oder Orthopädie tätig sind. Allerdings ist es in den USA auch üblich, sie an Schulen und Universitäten in Forschung oder Lehre zu beschäftigen. Ein akademischer Abschluss ist Voraussetzung für alle.
Plasma Levels of Lipoprotein(a) Are Elevated in Patients with the Antiphospholipid Antibody Syndrome
Authors: Yamazaki Masahide , Asakura Hidesaku , Jokaji Hiroshi , Saito Masanori , Uotani Chika , Kumabashiri Ichiro , Morishita Eriko , Aoshima Keiji , Ikeda Takayuki , Matsuda Tamotsu
Published: July 2018

The mechanisms underlying clinical abnormalities associated with the antiphospholipid antibody syndrome (APAS) have not been elucidated. We measured plasma levels of lipoprotein(a) [Lp(a)], the active form of plasminogen activator inhibitor (active PAI), thrombin-antithrombin III complex (TAT) and soluble thrombomodulin (TM), to investigate the relationship of these factors to thrombotic events in APAS. Mean plasma levels of Lp(a), TAT, active PAI and TM were all significantly higher in patients with aPL than in a control group of subjects. Plasma levels of Lp(a) and active PAI were significantly higher in patients with aPL and arterial thromboses than in patients with aPL but only venous thromboses. There was a significant correlation between plasma levels of Lp(a) and active PAI in patients with aPL. These findings suggest that patients with aPL are in hypercoagulable state. High levels of Lp(a) in plasma may impair the fibrinolytic system resulting in thromboses, especially in the arterial system.
Partial Inhibition of Platelet Aggregation and Fibrinogen Binding by a Murine Monoclonal Antibody to GPIIIa: Requirement for Antibody Bivalency
Authors: Kutok Jeffery L , Coller Barry S
Published: July 2018

We produced a murine monoclonal antibody, 7H2, and localized its epitope to one or more small regions on platelet glycoprotein (GP) Ilia. 7H2-IgG and 7H2-F(ab’)2 completely inhibit platelet aggregation and fibrinogen binding at low agonist concentrations, but only partially inhibit aggregation and fibrinogen binding at high agonist concentrations; 7H2-Fab has no effect on aggregation or fibrinogen binding at any agonist concentration. 7H2-IgG binds to the entire platelet population as judged by flow cytometry. At near saturating concentrations, ∼40,000 7H2-IgG antibody molecules bind per platelet. In contrast, ∼80,000 7H2 Fab molecules bind per platelet, suggesting that 7H2-IgG binding is bivalent. 7H2 was unable to inhibit fibrinogen binding to purified, immobilized GPIIb/IIIa. These data indicate that the bivalent binding of 7H2 to GPIIIa is required for its partial inhibition of fibrinogen binding to platelets, perhaps through dimerization of GPIIb/IIIa surface receptors (or more complex GPIIb/IIIa redistribution triggered by 7H2 binding) resulting in limited accessibility of fibrinogen to its binding site(s).
The Textarin/Ecarin Ratio: A Confirmatory Test for Lupus Anticoagulants
Authors: Triplett Douglas A , Stocker Kurt F , Unger Gail A , Barna Linda K
Published: July 2018

Lupus anticoagulants (LA) are immunoglobulins (IgG, IgM, IgA or a mixture) which interfere with in vitro phospholipid (PL) dependent tests of coagulation (e.g. APTT, KCT, dilute Russell Viper Venom Time). LA are heterogeneous; consequently, the laboratory diagnosis is difficult and relies on multiple tests. We have developed a sensitive and relatively specific confirmatory test system based on fractions of two snake venoms. Textarin®, a protein fraction of Pseudonaja textilis venom (Australian Eastern brown snake), activates prothrombin in the presence of PL, factor V and calcium ions. Ecarin, a protein fraction of Echis carinatus venom, will activate prothrombin in the absence of any cofactors. The activation of prothrombin by Textarin yields thrombin while Ecarin yields meizothrombin. In the presence of LA, the Textarin time is prolonged and the Ecarin time is unaffected. The test results are reported as a ratio of Textarin/Ecarin times (abnormal greater than 1.3). We have evaluated this test system in the following patient populations: LA positive, therapeutically heparinized, stable oral anticoagulated, liver disease, routine preoperative, anticardiolipin antibody positive LA negative, hemophilia A, various other hereditary factor deficiencies or dysfunctional proteins, and specific inhibitors of factor V and factor VTII. The LA positive patients represented a mixed population of autoimmune disease, drug-induced and post-infectious states. Our findings indicate the sensitivity of the Textarin/Ecarin system in the confirmation of LA. In order to use the test system most effectively, it is recommended to incorporate poly-brene with Textarin when evaluating heparinized samples. Factor V deficiency and specific inhibitors of factor V yielded, in some instances, false positive results.
Adenosine Diphosphate Stimulates the Endothelial Release of Tissue-Type Plasminogen Activator but not von Willebrand Factor from Isolated-Perfused Rat Hind Limbs
Authors: Smalley David M , Fitzgerald John E , O'Rourke James
Published: July 2018

The acute release of tissue-type plasminogen activator (t-PA) activity and of von Willebrand Factor (vWF) antigen from vascular endothelium was studied ex vivo using the rat hindquarter isolated perfusion model. The release of these proteins has been reported to occur simultaneously in response to a variety of endothelial cell agonists including bradykinin, thrombin and platelet activating factor. It has therefore been suggested that similar endothelial cell pathways and mechanisms are involved in the release of t-PA and vWF in vivo.

This paper shows that the releases of t-PA and of vWF are not always closely linked and may depend on the agonist utilized to effect release. In our hands, the bradykinin-induced release of these proteins appears to be essentially identical, but this is not true for adenosine diphosphate (ADP). Rather, ADP is capable of causing the acute release of t-PA without the simultaneous release of vWF in the ex vivo rat hindquarter model. This indicates that the bradykinin- and ADP-induced pathways for t-PA release are probably distinct and that the releases of t-PA and vWF are not as closely linked as previously believed.
Cigarette Smoking Sensitizes and Desensitizes Impedance-measured ADP-induced Platelet Aggregation in Whole Blood
Authors: Sharp Dan S , Benowitz Neal L , Bath P M W , Martin John F , Beswick Andrew D , Elwood Peter C
Published: July 2018

The effect of smoking on platelet aggregation appears to produce conflicting results, with some studies indicating an enhancement and others a decrease of aggregation. This epidemiological study of 120 male smokers, a subset of the Caerphilly Heart Disease Study, examined the relationship of two dimensions of smoking (time proximity of last cigarette before venepuncture and serum nicotine concentration) with threshold dose of adenosine diphosphate (ADP) necessary to induce platelet aggregation in whole blood. Means (range) of ADP threshold dose and nicotine concentration were 1.66 (0.5-2.5, censored) μM and 12.2 (0-35.2) ng/ml. Men smoking within 30 min of venepuncture demonstrated lower ADP threshold doses (-0.48 μM lower [95% C. I.: -0.95, -0.02]) – reflecting increased sensitivity. Men with higher nicotine concentration had higher ADP threshold doses (Regression Coefficient: +0.032 μM per ng/ml [95% C. I.: 0.003, 0.062]) – reflecting decreased sensitivity. Men smoking 30 min or more before venepuncture who also had high nicotine concentration (25-30 ng/ml) demonstrated the highest ADP threshold doses compared to never smokers and to men smoking the previous day (≈2.20 vs 1.86 and 1.81 μM). Relations involving nicotine concentration do not necessarily reflect a pharmacological effect although the potential for a short term nicotine mediated tolerance effect cannot be dismissed. These observations support an hypothesis suggesting a temporal sequence of platelet sensitization and desensitization during smoking.
Superoxide, Xanthine Oxidase and Platelet Reactions: Further Studies on Mechanisms by which Oxidants Influence Platelets
Authors: Levine Peter H , Sladdin Danielle G , Krinsky Norman I
Published: July 2018

In the course of studying the effects on platelets of the oxidant species superoxide (O-
2), Of was generated by the interaction of xanthine oxidase plus xanthine. Surprisingly, gel-filtered platelets, when exposed to xanthine oxidase in the absence of xanthine substrate, were found to generate superoxide (O-
2), as determined by the reduction of added cytochrome c and by the inhibition of this reduction in the presence of superoxide dismutase.

In addition to generating Of, the xanthine oxidase-treated platelets display both aggregation and evidence of the release reaction. This xanthine oxidase induced aggreagtion is not inhibited by the addition of either superoxide dismutase or cytochrome c, suggesting that it is due to either a further metabolite of O-
2, or that O-
2 itself exerts no important direct effect on platelet function under these experimental conditions. The ability of Of to modulate platelet reactions in vivo or in vitro remains in doubt, and xanthine oxidase is an unsuitable source of O-
2 in platelet studies because of its own effects on platelets.
The Antithrombogenic In Vivo Effects of Calcium Channel Blockers in Experimental Thrombosis in Mice
Authors: Ortega M P , Sunkel C , Priego J G , Statkow P R
Published: July 2018

A new model of thrombotic challenge, well suited for screening agents and which acts primarily against platelet thromboembolism, has been used to test the in vivo anti-platelet effects of four calcium channel blockers (CCB). An i. v. injection of a mixture of collagen plus epinephrine (15 μg and 1.8 μg/mouse, respectively) was given to male mice. 94% control mice died or remained paralyzed for more than 15 minutes. The dihydropyridine agents, CRE-223 and Nifedipine, were highly protective against experimental thrombosis, whereas Verapamil had a weaker and much shorter effect and, on the other hand, Diltiazem had no protective effect over a range of doses. The activity on both dihydropyridines lasted for seven hours or even longer.
Calcium and the Fc Receptor on Human Platelets
Authors: Clark William F , Tevaarwerk Gerald J M , Reid Bruce D , Hall Suzanne , Caveney Anita , Parbtani Anwar , Kreeft John
Published: July 2018

We have described the calcium dependence of the IgG Fc receptor (Fc-R) on human platelets by analyzing the direct binding of radiolabelled Fc fragments, monomers and dimers of IgG. Specific binding to platelets was undetectable at 37° C in a calcium-free preparation but readily detected when calcium was restored. Scatchard analysis of the binding data for the calcium-restored platelets permitted calculation of the available Fc-R and the Ka of binding for the different IgG ligands. The mean Ka of binding for 12 normal subjects varied from 107 to 108 L/M, with an equal receptor number measured by Fc fragments and dimers of IgG, but a lesser amount for monomeric IgG. There was no apparent difference in Fc-R number for platelets from 6 normal male versus 6 normal female subjects.

At 4° C binding was detectable for dimers and polymers of IgG in a calcium-free preparation and this was markedly increased with recalcification. Thus, our data are consistent with an Fc receptor population on human platelets whose avidity for binding is significantly enhanced in a calcium-restored medium.
Excessive Deposition of Fibrin, Platelets and Platelet Thrombi on Vascular Subendothelium During Contraceptive Drug Treatment
Authors: Inauen W , Baumgartner H R , Haeberli A , Straub P W
Published: July 2018

We investigated the effect of oral contraceptives on thrombogenesis induced by subendothelium of rabbit aorta (SE), exposed to flowing non-anticoagulated blood in an annular flow chamber. Six healthy women on sequential contraceptive drugs (0.05 mg aethinylestradiol/day, 0.125 mg desogestrel/day) were compared with 6 women without hormonal contraception and 6 men. On contraceptive drug treatment, blood values were significantly increased for fibrinogen (2.6±0.2vsl.9±0.1 g/1) and fibrinopeptide A (3.9 ± 0.9 vs 0.9 ± 0.1 ng/ml), whereas antithrombin III was decreased (81 ± 4 vs 97 ± 6%). Fibrin deposition on vascular subendothelium was more than four-fold increased when measured morphologically (63.4 ± 2.5 vs 14.6 ± 6.8% coverage of SE surface with fibrin) as well as immunologically (29.3 ± 2.2 vs 4.5 ± 1.9 pg fibrin/cm2 of SE). Thrombus volumes were more than two-fold increased in women with contraceptives (9.0 ± 1.4 vs 3.7 ± 1.0 μm3/μm2).

Our study shows that during contraceptive drug treatment the exposure of flowing blood to vascular subendothelium leads to excessive deposition of fibrin and platelet thrombi. Measurement of blood interactions with subendothelium might be of predictive value in hypercoagulable states such as contraceptive treatment.
Hormonal Control of Haemostasis During Hypoglycaemia in Diabetes Mellitus
Authors: Grant P J , Stickland M H , Wiles P G , Davies J A , Wales J K , Prentice C R M
Published: July 2018

Factor VIII (FVIII) and plasminogen activator activity (PAA) rise during hypoglycaemia, and this might contribute to the vascular complications of diabetes. Similar changes in haemostasis accompany raised plasma levels of vasopressin (aVP) and adrenaline. To investigate the effects of these hormones on haemostasis during hypoglycaemia and the role of plasma insulin concentrations, eight insulin-dependent diabetic patients underwent controlled hypoglycaemia for 20 min and 13 diabetic patients were investigated during hyperinsulinaemia with blood glucose maintained at 8.0 mmol/1. During hypoglycaemia, insulin levels increased to median values of 114 mU/1, aVP rose from 0.5 to 4.4 (p <0.005) pg/ml and adrenaline from 0.4 to 4.4 nmol/l (p <0.005). FVIII coagulant activity (FVIII :C) rose from 0.75 to 1.09 iU/ml (p <0.01) and the ristocetin co-factor (FVIIIR:Co) and von Willebrand factor antigen (vWF:Ag) showed similar responses. PAA increased from 156 to 745 units (p <0.005). During hyperinsulinaemia, insulin rose following infusion from 24 to 52 and 118 mU/l, maintained for an hour at each level. Despite this, plasma aVP, FVIII :C, FVIIIR:Co, vWF:Ag and PAA remained unchanged. This study indicates that the marked changes in FVIII, vWF and PAA concentrations which accompany hypoglycaemia depend on low blood glucose and not raised plasma insulin. The response in probably mediated by increases in adrenaline and aVP, which are part of the physiological response to hypoglycaemia.
Laryngeal and Tracheobronchial Infections of the Pediatric Airway
Authors: Ida Jonathan
Published: July 2018

Infections of the pediatric airway result in partial obstruction of the airway and often require intervention to maintain the airway. Most airway infections are treated medically, but respiratory support or invasive airway protection may be required if the patient does not respond adequately to initial interventions. We review three major types of central airway infections, focusing on illustrative diagnostic and treatment dilemmas.
Judicious Use of Antibiotics and Radiologic Imaging in Diagnosis and Management of Pediatric Upper Respiratory Tract Infections
Authors: Jaggi Preeti
Published: July 2018

A considerable amount of effort has been put into the reduction of the overuse of antibiotics and reduction in radiographic studies in the pediatric population. Infections within the ear, nose, and throat and in cervical regions are a frequent source of antibiotic use in children. Quality improvement projects creating clear care pathways have been important to delineate which imaging may be most helpful.
Detecting directional couplings from multivariate flows by the joint distance distribution
Authors: Amigó José M. , Hirata Yoshito
Published: July 2018

The identification of directional couplings (or drive-response relationships) in the analysis of interacting nonlinear systems is an important piece of information to understand their dynamics. This task is especially challenging when the analyst’s knowledge of the systems reduces virtually to time series of observations. Spurred by the success of Granger causality in econometrics, the study of cause-effect relationships (not to be confounded with statistical correlations) was extended to other fields, thus favoring the introduction of further tools such as transfer entropy. Currently, the research on old and new causality tools along with their pitfalls and applications in ever more general situations is going through a time of much activity. In this paper, we re-examine the method of the joint distance distribution to detect directional couplings between two multivariate flows. This method is based on the forced Takens theorem, and, more specifically, it exploits the existence of a continuous mapping from the reconstructed attractor of the response system to the reconstructed attractor of the driving system, an approach that is increasingly drawing the attention of the data analysts. The numerical results with Lorenz and Rössler oscillators in three different interaction networks (including hidden common drivers) are quite satisfactory, except when phase synchronization sets in. They also show that the method of the joint distance distribution outperforms the lowest dimensional transfer entropy in the cases considered. The robustness of the results to the sampling interval, time series length, observational noise, and metric is analyzed too.
Unraveling thickness-dependent spin relaxation in colossal magnetoresistance manganite films
Authors: Sheu Y. M. , Trugman S. A. , Chen A. P. , Jia Q. X. , Taylor A. J. , Prasankumar R. P.
Published: July 2018

We used ultrafast optical spectroscopy to study photoinduced spin relaxation in 10–100 nm thick La0.7Ca0.3MnO3 films. The spin-lattice relaxation time displays a strong dependence on thickness below the Curie temperature. Our simulations show that the observed thickness-dependent relaxation results from much faster thermal decay through the substrate in thinner films that leads to artificially faster demagnetization. Furthermore, we provide an analytical approach to gain insight into the spin-lattice relaxation time for highly thermal dissipative films. Our study strongly suggests that careful consideration of the influence of transient thermal variations on photoinduced demagnetization is mandatory when incorporating absorbing thin magnetic films into heterostructures and devices.
Voigt effect-based wide-field magneto-optical microscope integrated in a pump-probe experimental setup
Authors: Janda T. , Nádvorník L. , Kuchařík J. , Butkovičová D. , Schmoranzerová E. , Trojánek F. , Němec P.
Published: July 2018

In this work, we describe an experimental setup for a spatially resolved pump-probe experiment with an integrated wide-field magneto-optical (MO) microscope. The MO microscope can be used to study ferromagnetic materials with both perpendicular-to-plane and in-plane magnetic anisotropy via polar Kerr and Voigt effects, respectively. The functionality of the Voigt effect-based microscope was tested using an in-plane magnetized ferromagnetic semiconductor (Ga,Mn)As. It was revealed that the presence of mechanical defects in the (Ga,Mn)As epilayer alters significantly the magnetic anisotropy in their proximity. The importance of MO experiments with simultaneous temporal and spatial resolutions was demonstrated using a (Ga,Mn)As sample attached to a piezoelectric transducer, which produces a voltage-controlled strain. We observed a considerably different behavior in different parts of the sample that enabled us to identify sample parts where the epilayer magnetic anisotropy was significantly modified by the presence of the piezoelectric transducer and where it was not. Finally, we discuss the possible applicability of our experimental setup for the research of compensated antiferromagnets, where only MO effects even in magnetic moments are present.
Vibrational spectroscopy of hydroxylated α-Al2O3(0001) surfaces with and without water: An ab initio molecular dynamics study
Authors: Melani Giacomo , Nagata Yuki , Wirth Jonas , Saalfrank Peter
Published: July 2018

Using gradient- and dispersion-corrected density functional theory in connection with ab initio molecular dynamics and efficient, parametrized Velocity-Velocity Autocorrelation Function (VVAF) methodology, we study the vibrational spectra (Vibrational Sum Frequency, VSF, and infrared, IR) of hydroxylated α-Al2O3(0001) surfaces with and without additional water. Specifically, by considering a naked hydroxylated surface and the same surface with a particularly stable, “ice-like” hexagonal water later allows us to identify and disentangle main spectroscopic bands of OH bonds, their orientation and dynamics, and the role of water adsorption. In particular, we assign spectroscopic signals around 3700 cm−1 as being dominated by perpendicularly oriented non-hydrogen bonded aluminol groups, with and without additional water. Furthermore, the thin water layer gives spectroscopic signals which are already comparable to previous theoretical and experimental findings for the solid/(bulk) liquid interface, showing that water molecules closest to the surface play a decisive role in the vibrational response of these systems. From a methodological point of view, the effects of temperature, anharmonicity, hydrogen-bonding, and structural dynamics are taken into account and analyzed, allowing us to compare the calculated IR and VSF spectra with the ones based on normal mode analysis and vibrational density of states. The VVAF approach employed in this work appears to be a computationally accurate yet feasible method to address the vibrational fingerprints and dynamical properties of water/metal oxide interfaces.
Hyperbolic lens design of local oscillator optics system for electron cyclotron emission imaging on J-TEXT
Authors: Xie X. L. , Yang Z. J. , Pan X. M. , Zhu Y. L. , Zhou J. , Zhou H. , Zhuang G.
Published: July 2018

An electron cyclotron emission imaging diagnostic system that contains two 16-antenna arrays is being developed on J-TEXT tokamak. In this heterodyne system, the mixers in the front microwave antenna are used to down-convert the electron cyclotron emission to a 2-12 GHz radio frequency. All of the 24 antenna mixers in the individual enclosure box are driven by shining local oscillator (LO) power via launching optics. The previous approach for LO optics was designed with spherical and cylinder lenses, which has limitations such as the inhomogeneity of the energy deposition on different channels and the difficulty of optics alignment. A new generation of LO optics has been designed and applied on J-TEXT with a hyperbolic lens for uniform power deposition across the entire antenna array. The robustness of the optical alignment will be significantly increased with three hyperbolic lenses. Furthermore, the simulation results and robustness analysis of these LO optics are discussed in this paper.
Nd:YAG laser Thomson scattering diagnostics for a laboratory magnetosphere
Authors: Kenmochi N. , Nishiura M. , Yoshida Z. , Yamada I. , Funaba H. , Sugata T. , Nakamura K. , Katsura S.
Published: July 2018

A new Nd:YAG laser Thomson scattering (TS) system has been developed to explore the mechanism of high-beta plasma formation in the RT-1 device. The TS system is designed to measure electron temperatures (Te) from 10 eV to 50 keV and electron densities (ne) of more than 1.0 × 1017 m−3. To measure at the low-density limit, the receiving optics views the long scattering length (60 mm) using a bright optical system with both a large collection window (260-mm diameter) and large collection lenses (300-mm diameter, a solid angle of ∼68 × 10−3 str). The scattered light of the 1.2-J Nd:YAG laser (repetition frequency: 10 Hz) is detected with a scattering angle of 90° and is transferred via a set of lenses and an optical fiber bundle to a polychromator. After Raman scattering measurement for the optical alignment and an absolute calibration, we successfully measured Te = 72.2 eV and ne = 0.43 × 1016 m−3 for the coil-supported case and Te = 79.2 eV and ne = 1.28 × 1016 m−3 for the coil-levitated case near the inner edge in the magnetospheric plasmas.
Calculations of coherent two-dimensional electronic spectra using forward and backward stochastic wavefunctions
Authors: Ke Yaling , Zhao Yi
Published: July 2018

Within the well-established optical response function formalism, a new strategy with the central idea of employing the forward-backward stochastic Schrödinger equations in a segmented way to accurately obtain the two-dimensional (2D) electronic spectrum is presented in this paper. Based on the simple excitonically coupled dimer model system, the validity and efficiency of the proposed schemes are demonstrated in detail, along with the comparison against the deterministic hierarchy equations of motion and perturbative second-order time-convolutionless quantum master equations. In addition, an important insight is provided in this paper that the characteristic frequency of the overdamped environment is an extremely crucial factor to regulate the lifetimes of the oscillating signals in 2D electronic spectra and of quantum coherence features of system dynamics. It is worth noting that the proposed scheme benefiting from its stochastic nature and wavefunction framework and many other advantages of substantially reducing the numerical cost has a great potential to systematically investigate various quantum effects observed in realistic large-scale natural and artificial photosynthetic systems.
Charging of an irregularly shaped particle in the sheath of an rf plasma
Authors: Asnaz Oguz Han , Jung Hendrik , Greiner Franko , Piel Alexander
Published: July 2018

The charging process of micrometer-sized irregularly shaped particles in the sheath of a radio frequency discharge is measured using a combination of long-distance microscopy and the phase-resolved resonance method. The applicability of the method is shown for a cylindrical zinc oxide particle by measuring its mass density. A particle with more complex geometry is compared to a spherical polymethyl methacrylate particle to investigate the charging of irregularly shaped particles in detail. The results are similar to the charging of the smallest enclosing sphere suggesting that the charging process is independent of the shape of the particle. Furthermore, molecular dynamics simulations were performed, which support the experimental results.
Indeterminate us and them: The complexities of referentiality, identity and group construction in a public online discussion
Authors: Kleinke Sonja , Bös Birte
Published: July 2018

This paper reinvestigates the polarizing effects of indeterminate first- and third-person plural pronouns and determiners (i.e. the we-set and the they-set) from a Digital Discourse perspective. Combining Critical Discourse Analysis and a cognitive-linguistic approach, it tackles the double-indexical nature of the use of the we-set and the they-set by the participants of the public discussion forum UK Debate. Our analysis of a sample thread considers both the referential and the propositional level and shows how users construct and negotiate potential in- and out-group referents at different degrees of specificity and as ranging between immediate discourse participants and external referents. Our analysis shows how major cognitive domains are triggered and how the specific selections of predications as cognitive access points form oscillating clusters of salient in- and out-group attributes. In this way, the analysis also aims to reveal manifestations of more permanent cultural and mental models.
Turn design and progression
Authors: Wu Ruey-Jiuan Regina
Published: July 2018

The temporal character of talk is one fundamental feature of language
in situ. As interaction unfolds, participants
need to not only monitor the temporal progression of talk toward
completion, but also attend to how the current turn ties back to the
preceding turns. Whereas such dual-directional consideration is
often a latent aspect of turn construction, efforts to clear up
possible ambiguity are sometimes in order. This article introduces a
Mandarin practice, the aiyou-preface, which seems
to be used to just this end, and demonstrates an intimate
relationship between the prosodic design of
aiyou-preface and the displayed orientation to the
intended directionality of the talk. The analysis draws upon a
corpus of 35 hours of conversations collected in China.
Turn-initial voilà in closings in French
Authors: Mondada Lorenza
Published: July 2018

French has several ways of responding positively to a previous turn, such as oui, ouais, d’accord, tout à fait, exactement, bien sûr, voilà, etc. This chapter deals with voilà, offering a general overview of its uses in interaction before focusing on voilà in turn-initial position in closing environments. Analyses reveal that voilà is not equally used by all of the participants in social interaction, but rather by speakers whom the co-participants recognize as experts and/or responsible for the on-going activity. Stand-alone voilà achieves sequence closing in unproblematic ways and retrospectively asserts the speaker’s epistemic, organizational and moral authority over the sequence. By contrast, turn-initial voilà often occurs in a context where the co-participants disalign with the projected closing. The use of voilà addresses a possible emerging competition by further expanding the on-going action and thereby controlling possible next sequential slots. In these competitive contexts, stand-alone voilà and turn-initial voilà are used by speakers to re-affirm their authority over the sequence. Turn-initial voilà followed by a new turn constructional unit (TCU) orients to the possible progressivity of the activity, whereas turn-initial voilà with a continuation within the same TCU expands the on-going sequence and creates new opportunities for the co-participants to realign with it.
Fibronectin rescues estrogen receptor α from lysosomal degradation in breast cancer cells
Authors: Sampayo Rocío G. , Toscani Andrés M. , Rubashkin Matthew G. , Thi Kate , Masullo Luciano A. , Violi Ianina L. , Lakins Jonathon N. , Cáceres Alfredo , Hines William C. , Coluccio Leskow Federico , Stefani Fernando D. , Chialvo Dante R. , Bissell Mina J. , Weaver Valerie M. , Simian Marina
Published: July 2018

Estrogen receptor α (ERα) is expressed in tissues as diverse as brains and mammary glands. In breast cancer, ERα is a key regulator of tumor progression. Therefore, understanding what activates ERα is critical for cancer treatment in particular and cell biology in general. Using biochemical approaches and superresolution microscopy, we show that estrogen drives membrane ERα into endosomes in breast cancer cells and that its fate is determined by the presence of fibronectin (FN) in the extracellular matrix; it is trafficked to lysosomes in the absence of FN and avoids the lysosomal compartment in its presence. In this context, FN prolongs ERα half-life and strengthens its transcriptional activity. We show that ERα is associated with β1-integrin at the membrane, and this integrin follows the same endocytosis and subcellular trafficking pathway triggered by estrogen. Moreover, ERα+ vesicles are present within human breast tissues, and colocalization with β1-integrin is detected primarily in tumors. Our work unravels a key, clinically relevant mechanism of microenvironmental regulation of ERα signaling.
Genome-edited human stem cells expressing fluorescently labeled endocytic markers allow quantitative analysis of clathrin-mediated endocytosis during differentiation
Authors: Dambournet Daphné , Sochacki Kem A. , Cheng Aaron T. , Akamatsu Matthew , Taraska Justin W. , Hockemeyer Dirk , Drubin David G.
Published: July 2018

We developed a general approach for investigation of how cellular processes become adapted for specific cell types during differentiation. Previous studies reported substantial differences in the morphology and dynamics of clathrin-mediated endocytosis (CME) sites. However, associating specific CME properties with distinct differentiated cell types and determining how these properties are developmentally specified during differentiation have been elusive. Using genome-edited human embryonic stem cells, and isogenic fibroblasts and neuronal progenitor cells derived from them, we established by live-cell imaging and platinum replica transmission electron microscopy that CME site dynamics and ultrastructure on the plasma membrane are precisely reprogrammed during differentiation. Expression levels for the endocytic adaptor protein AP2μ2 were found to underlie dramatic changes in CME dynamics and structure. Additionally, CME dependency on actin assembly and phosphoinositide-3 kinase activity are distinct for each cell type. Collectively, our results demonstrate that key CME properties are reprogrammed during differentiation at least in part through AP2μ2 expression regulation.
Intermediate filaments control collective migration by restricting traction forces and sustaining cell–cell contacts
Authors: De Pascalis Chiara , Pérez-González Carlos , Seetharaman Shailaja , Boëda Batiste , Vianay Benoit , Burute Mithila , Leduc Cécile , Borghi Nicolas , Trepat Xavier , Etienne-Manneville Sandrine
Published: July 2018

Mesenchymal cell migration relies on the coordinated regulation of the actin and microtubule networks that participate in polarized cell protrusion, adhesion, and contraction. During collective migration, most of the traction forces are generated by the acto-myosin network linked to focal adhesions at the front of leader cells, which transmit these pulling forces to the followers. Here, using an in vitro wound healing assay to induce polarization and collective directed migration of primary astrocytes, we show that the intermediate filament (IF) network composed of vimentin, glial fibrillary acidic protein, and nestin contributes to directed collective movement by controlling the distribution of forces in the migrating cell monolayer. Together with the cytoskeletal linker plectin, these IFs control the organization and dynamics of the acto-myosin network, promoting the actin-driven treadmilling of adherens junctions, thereby facilitating the polarization of leader cells. Independently of their effect on adherens junctions, IFs influence the dynamics and localization of focal adhesions and limit their mechanical coupling to the acto-myosin network. We thus conclude that IFs promote collective directed migration in astrocytes by restricting the generation of traction forces to the front of leader cells, preventing aberrant tractions in the followers, and by contributing to the maintenance of lateral cell–cell interactions.
IRSOM, a reliable identifier of ncRNAs based on supervised self-organizing maps with rejection
Authors: Platon Ludovic , Zehraoui Farida , Bendahmane Abdelhafid , Tahi Fariza
Published: July 2018

Motivation

Non-coding RNAs (ncRNAs) play important roles in many biological processes and are involved in many diseases. Their identification is an important task, and many tools exist in the literature for this purpose. However, almost all of them are focused on the discrimination of coding and ncRNAs without giving more biological insight. In this paper, we propose a new reliable method called IRSOM, based on a supervised Self-Organizing Map (SOM) with a rejection option, that overcomes these limitations. The rejection option in IRSOM improves the accuracy of the method and also allows identifing the ambiguous transcripts. Furthermore, with the visualization of the SOM, we analyze the rejected predictions and highlight the ambiguity of the transcripts.

Results

IRSOM was tested on datasets of several species from different reigns, and shown better results compared to state-of-art. The accuracy of IRSOM is always greater than 0.95 for all the species with an average specificity of 0.98 and an average sensitivity of 0.99. Besides, IRSOM is fast (it takes around 254 s to analyze a dataset of 147 000 transcripts) and is able to handle very large datasets.

Availability and implementation

IRSOM is implemented in Python and C++. It is available on our software platform EvryRNA (http://EvryRNA.ibisc.univ-evry.fr).
Computational analysis of kinase inhibitor selectivity using structural knowledge
Authors: Lo Yu-Chen , Liu Tianyun , Morrissey Kari M , Kakiuchi-Kiyota Satoko , Johnson Adam R , Broccatelli Fabio , Zhong Yu , Joshi Amita , Altman Russ B
Published: July 2018

Motivation

Kinases play a significant role in diverse disease signaling pathways and understanding kinase inhibitor selectivity, the tendency of drugs to bind to off-targets, remains a top priority for kinase inhibitor design and clinical safety assessment. Traditional approaches for kinase selectivity analysis using biochemical activity and binding assays are useful but can be costly and are often limited by the kinases that are available. On the other hand, current computational kinase selectivity prediction methods are computational intensive and can rarely achieve sufficient accuracy for large-scale kinome wide inhibitor selectivity profiling.

Results

Here, we present a KinomeFEATURE database for kinase binding site similarity search by comparing protein microenvironments characterized using diverse physiochemical descriptors. Initial selectivity prediction of 15 known kinase inhibitors achieved an >90% accuracy and demonstrated improved performance in comparison to commonly used kinase inhibitor selectivity prediction methods. Additional kinase ATP binding site similarity assessment (120 binding sites) identified 55 kinases with significant promiscuity and revealed unexpected inhibitor cross-activities between PKR and FGFR2 kinases. Kinome-wide selectivity profiling of 11 kinase drug candidates predicted novel as well as experimentally validated off-targets and suggested structural mechanisms of kinase cross-activities. Our study demonstrated potential utilities of our approach for large-scale kinase inhibitor selectivity profiling that could contribute to kinase drug development and safety assessment.

Availability and implementation

The KinomeFEATURE database and the associated scripts for performing kinase pocket similarity search can be downloaded from the Stanford SimTK website (https://simtk.org/projects/kdb).

Supplementary information

Supplementary data are available at Bioinformatics online.
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia
Authors: Frioux Clémence , Fremy Enora , Trottier Camille , Siegel Anne
Published: July 2018

Motivation

The selection of species exhibiting metabolic behaviors of interest is a challenging step when switching from the investigation of a large microbiota to the study of functions effectiveness. Approaches based on a compartmentalized framework are not scalable. The output of scalable approaches based on a non-compartmentalized modeling may be so large that it has neither been explored nor handled so far.

Results

We present the Miscoto tool to facilitate the selection of a community optimizing a desired function in a microbiome by reporting several possibilities which can be then sorted according to biological criteria. Communities are exhaustively identified using logical programming and by combining the non-compartmentalized and the compartmentalized frameworks. The benchmarking of 4.9 million metabolic functions associated with the Human Microbiome Project, shows that Miscoto is suited to screen and classify metabolic producibility in terms of feasibility, functional redundancy and cooperation processes involved. As an illustration of a host-microbial system, screening the Recon 2.2 human metabolism highlights the role of different consortia within a family of 773 intestinal bacteria.

Availability and implementation

Miscoto source code, instructions for use and examples are available at: https://github.com/cfrioux/miscoto.
Protein pocket detection via convex hull surface evolution and associated Reeb graph
Authors: Zhao Rundong , Cang Zixuan , Tong Yiying , Wei Guo-Wei
Published: July 2018

Motivation

Protein pocket information is invaluable for drug target identification, agonist design, virtual screening and receptor-ligand binding analysis. A recent study indicates that about half holoproteins can simultaneously bind multiple interacting ligands in a large pocket containing structured sub-pockets. Although this hierarchical pocket and sub-pocket structure has a significant impact to multi-ligand synergistic interactions in the protein binding site, there is no method available for this analysis. This work introduces a computational tool based on differential geometry, algebraic topology and physics-based simulation to address this pressing issue.

Results

We propose to detect protein pockets by evolving the convex hull surface inwards until it touches the protein surface everywhere. The governing partial differential equations (PDEs) include the mean curvature flow combined with the eikonal equation commonly used in the fast marching algorithm in the Eulerian representation. The surface evolution induced Morse function and Reeb graph are utilized to characterize the hierarchical pocket and sub-pocket structure in controllable detail. The proposed method is validated on PDBbind refined sets of 4414 protein-ligand complexes. Extensive numerical tests indicate that the proposed method not only provides a unique description of pocket-sub-pocket relations, but also offers efficient estimations of pocket surface area, pocket volume and pocket depth.

Availability and implementation

Source code available at https://github.com/rdzhao/ProteinPocketDetection. Webserver available at http://weilab.math.msu.edu/PPD/.