bluuebunny/crossref_metadata_2025 huggingface dataset:
Are we failing clinical trials? A case for strong aggregate outcomes
Authors: Joyce D. W. , Tracy D. K. , Shergill S. S.
Published: June 2017

Clinical trials in psychiatry inherit methods for design and statistical analysis from evidence-based medicine. However, trials in other clinical disciplines benefit from a more specific relationship between instruments that measure disease state (e.g. biomarkers, clinical signs), the underlying pathology and diagnosis such that primary outcomes can be readily defined. Trials in psychiatry use diagnosis (i.e. a categorical label for a syndrome) as a proxy for the underlying disorder, and outcomes are defined, for example, as a percentage change in a univariatetotal scoreon some clinical instrument. We label this approach to defining outcomesweak aggregationof disease state. Univariate measures are necessary, because statistical methodology is both tractable and well-developed for scalar outcomes, but we show that weak aggregate approaches do not capture disease state sufficiently, potentially leading to loss of information about response to intervention. We demonstrate how multivariate disease state can be captured using geometric concepts of spaces defined over routine clinical instruments, and show how clinically meaningful disease states (e.g. representing different profiles of symptoms, recovery or remission) can be defined as prototypes (geometric locations) in these spaces. Then, we show how to derive univariate (scalar) measures, which capture patient's relationships to these prototypes and argue these representstrong aggregatesof disease state that may be a better basis for outcome measures. We demonstrate our proposal using a large publically available dataset. We conclude by discussing the impact of strong aggregates for analyses in traditional and novel trial designs.
Firms’ Integration into Value Chains and Compliance with Adverse WTO Panel Rulings
Authors: YILDIRIM AYDIN B.
Published: June 2017

This article aims to account for the variation in the time it takes for WTO Members to bring compliance following adverse panel rulings. It seeks to answer the question: under what conditions do defendants swiftly implement adverse rulings of WTO panels? I demonstrate that defendants are more likely to comply without delay when the targeted measures involve firms that are integrated into regional and global value chains. When a dispute touches upon the interests of these firms and targets import-restricting measures, they are triggered to mobilize and press for compliance because they rely on foreign imports. In effect, the mobilization of these firms changes the domestic political conditions in favor of timely implementation. I show the plausibility of my argument in a comparative design with four case studies in which the US and Canada acted as defendants in WTO disputes. I control for a number of political factors and also consider legal sources of variation – i.e. the complexity of the form of implementation – that may impact WTO Members’ record of compliance.
The care experiences of patients who die in residential hospice: A qualitative analysis of the last three months of life from the views of bereaved caregivers
Authors: Bainbridge Daryl , Giruparajah Mohanna , Zou Hanyan , Seow Hsien
Published: June 2017

Objective:

Despite the increasing prominence of residential hospices as a place of death and that, in many regards, this specialized care represents a gold standard, little is known about the care experience in this setting. Using qualitative survey data, we examined the positive and negative perceptions of care in hospices and in other prior settings.

Method:

Qualitative comments were extracted from the CaregiverVoice survey completed by bereaved caregivers of decedents who had died in 16 residential hospices in Ontario, Canada. On this survey, caregivers reported what was good and bad about the services provided during the last three months of life as separate open-text questions. A constant-comparison method was employed to derive themes from the responses.

Results:

A total of 550 caregivers completed the survey, 94% (517) of whom commented on either something good (84%) and/or bad (49%) about the care experience. In addition to residential hospice, the majority of patients represented also received palliative care in the home (69%) or hospital (59%). Overall, most positive statements were about care in hospice (71%), whereas the negative statements tended to refer to other settings (81%). The hospice experience was found to exemplify care that was compassionate and holistic, in a comforting environment, offered by providers who were personable, dedicated, and informative. These humanistic qualities of care and the extent of support were generally seen to be lacking from the other settings.

Significance of results:

Our examination of the good and bad aspects of palliative care received is unique in qualitatively exploring palliative care experiences across multiple settings, and specifically that in hospices. Investigation of these perspectives affirmed the elements of care that dying patients and their family caregivers most value and that the hospices were largely effective at addressing. These findings highlight the need for reinforcing these qualities in other end-of-life settings to create comforting and supportive environments.
Protein kinase A activation by the anti-cancer drugs ABT-737 and thymoquinone is caspase-3-dependent and correlates with platelet inhibition and apoptosis
Authors: Rukoyatkina Natalia , Butt Elke , Subramanian Hariharan , Nikolaev Viacheslav O , Mindukshev Igor , Walter Ulrich , Gambaryan Stepan , Benz Peter M
Published: June 2017

Chemotherapy-induced thrombocytopenia is a common bleeding risk in cancer patients and limits chemotherapy dose and frequency. Recent data from mouse and human platelets revealed that activation of protein kinase A/G (PKA/PKG) not only inhibited thrombin/convulxin-induced platelet activation but also prevented the platelet pro-coagulant state. Here we investigated whether or not PKA/PKG activation could attenuate caspase-dependent apoptosis induced by the anti-cancer drugs ABT-737 (the precursor of navitoclax) and thymoquinone (TQ), thereby potentially limiting chemotherapy-induced thrombocytopenia. This is particularly relevant as activation of cyclic nucleotide signalling in combination chemotherapy is an emerging strategy in cancer treatment. However, PKA/PKG-activation, as monitored by phosphorylation of Vasodilator-stimulated phosphoprotein (VASP), did not block caspase-3-dependent platelet apoptosis induced by the compounds. In contrast, both substances induced PKA activation themselves and PKA activation correlated with platelet inhibition and apoptosis. Surprisingly, ABT-737- and TQ-induced VASP-phosphorylation was independent of cAMP levels and neither cyclases nor phosphatases were affected by the drugs. In contrast, however, ABT-737- and TQ-induced PKA activation was blocked by caspase-3 inhibitors. In conclusion, we show that ABT-737 and TQ activate PKA in a caspase-3-dependent manner, which correlates with platelet inhibition and apoptosis and therefore potentially contributes to the bleeding risk in chemotherapy patients.
Clustering of arc volcanoes caused by temperature perturbations in the back-arc mantle
Authors: Lee Changyeol , Wada Ikuko
Published: June 2017

Clustering of arc volcanoes in subduction zones indicates along-arc variation in the physical condition of the underlying mantle where majority of arc magmas are generated. The sub-arc mantle is brought in from the back-arc largely by slab-driven mantle wedge flow. Dynamic processes in the back-arc, such as small-scale mantle convection, are likely to cause lateral variations in the back-arc mantle temperature. Here we use a simple three-dimensional numerical model to quantify the effects of back-arc temperature perturbations on the mantle wedge flow pattern and sub-arc mantle temperature. Our model calculations show that relatively small temperature perturbations in the back-arc result in vigorous inflow of hotter mantle and subdued inflow of colder mantle beneath the arc due to the temperature dependence of the mantle viscosity. This causes a three-dimensional mantle flow pattern that amplifies the along-arc variations in the sub-arc mantle temperature, providing a simple mechanism for volcano clustering.
Bioavailability and pharmacokinetic comparison of tanshinones between two formulations of Salvia miltiorrhiza in healthy volunteers
Authors: Xing Lu , Tan Zhi-Rong , Cheng Jin-Le , Huang Wei-Hua , Zhang Wei , Deng Wen , Yuan Chun-Su , Zhou Hong-Hao
Published: June 2017

Salvia miltiorrhiza (SM) is widely used to treat microcirculatory disturbance-related diseases; its lipophilic components play important roles in this application. Cryptotanshinone (CTS), tanshinone I (TSI) and tanshinone IIA (TSA) are the most widely-studied lipophilic ingredients, but low oral bioavailability limits their clinical application. It has been proven that micronization could improve the bioavailability of some drugs, so we’ve conducted this randomized study to investigate whether micronized granular powder (GP) of SM could improve the bioavailability of tanshinones compared with traditional decoction (TD). An oral dose of TD or GP of SM was administrated to subjects and blood samples were collected at predetermined time points. The plasma concentrations of tanshinones were detected by a validated method and pharmacokinetic parameters were calculated using a non-compartmental model. GP of SM resulted in a significant increase in mean maximum plasma concentration (C
max
), elimination half-life and area under concentration-time curve (AUC) of tanshinones, with the plasma AUC of CTS, TSI and TSA in GP 5–184, 4–619 and 5–130 times higher than TD. In addition, the individual variances of C
max
and AUC were much lower after GP administration. Summarily, tanshinones in micronized GP of SM had higher oral bioavailability and lower individual variances, thus we speculate that it may indicate a better clinical efficacy and be a better choice than current treatments.
Perchlorates on Mars enhance the bacteriocidal effects of UV light
Authors: Wadsworth Jennifer , Cockell Charles S.
Published: June 2017

Perchlorates have been identified on the surface of Mars. This has prompted speculation of what their influence would be on habitability. We show that when irradiated with a simulated Martian UV flux, perchlorates become bacteriocidal. At concentrations associated with Martian surface regolith, vegetative cells of Bacillus subtilis in Martian analogue environments lost viability within minutes. Two other components of the Martian surface, iron oxides and hydrogen peroxide, act in synergy with irradiated perchlorates to cause a 10.8-fold increase in cell death when compared to cells exposed to UV radiation after 60 seconds of exposure. These data show that the combined effects of at least three components of the Martian surface, activated by surface photochemistry, render the present-day surface more uninhabitable than previously thought, and demonstrate the low probability of survival of biological contaminants released from robotic and human exploration missions.
Negative voltage modulated multi-level resistive switching by using a Cr/BaTiOx/TiN structure and quantum conductance through evidence of H2O2 sensing mechanism
Authors: Chakrabarti Somsubhra , Ginnaram Sreekanth , Jana Surajit , Wu Zong-Yi , Singh Kanishk , Roy Anisha , Kumar Pankaj , Maikap Siddheswar , Qiu Jian-Tai , Cheng Hsin-Ming , Tsai Ling-Na , Chang Ya-Ling , Mahapatra Rajat , Yang Jer-Ren
Published: June 2017

Negative voltage modulated multi-level resistive switching with quantum conductance during staircase-type RESET and its transport characteristics in Cr/BaTiOx/TiN structure have been investigated for the first time. The as-deposited amorphous BaTiOx film has been confirmed by high-resolution transmission electron microscopy. X-ray photo-electron spectroscopy shows different oxidation states of Ba in the switching material, which is responsible for tunable more than 10 resistance states by varying negative stop voltage owing to slow decay value of RESET slope (217.39 mV/decade). Quantum conductance phenomenon has been observed in staircase RESET cycle of the memory devices. By inspecting the oxidation states of Ba+ and Ba2+ through measuring H2O2 with a low concentration of 1 nM in electrolyte/BaTiOx/SiO2/p-Si structure, the switching mechanism of each HRS level as well as the multi-level phenomenon has been explained by gradual dissolution of oxygen vacancy filament. Along with negative stop voltage modulated multi-level, current compliance dependent multi-level has also been demonstrated and resistance ratio up to 2000 has been achieved even for a thin (<5 nm) switching material. By considering oxidation-reduction of the conducting filaments, the current-voltage switching curve has been simulated as well. Hence, multi-level resistive switching of Cr/BaTiOx/TiN structure implies the promising applications in high dense, multistate non-volatile memories in near future.
Improved stability of transparent PEDOT:PSS/Ag nanowire hybrid electrodes by using non-ionic surfactants
Authors: Kim Sunghee , Lee Su Jeong , Cho Sunghwan , Shin Sangbaie , Jeong Unyong , Myoung Jae-Min
Published: June 2017

A T-PEDOT:PSS/Ag NW hybrid electrode was developed to enhance the mechanical stability of Ag NWs and used for flexible ECL displays.
An esterase-activated click and release approach to metal-free CO-prodrugs
Authors: Ji Xingyue , Ji Kaili , Chittavong Vayou , Yu Bingchen , Pan Zhixiang , Wang Binghe
Published: June 2017

Metal-free CO prodrugs with a biological trigger and tunable release rate are described herein for the first time.
Low-toxicity metallosomes for biomedical applications by self-assembly of organometallic metallosurfactants and phospholipids
Authors: Marín-García M. , Benseny-Cases N. , Camacho M. , Suades J. , Barnadas-Rodríguez R.
Published: June 2017

New photo-CORM metallosomes prepared by a straightforward method from organometallic metallosurfactants and phospholipids show a drastic diminution of cell toxicity.
Accelerated molecular dynamics simulation analysis of MSI-594 in a lipid bilayer
Authors: Mukherjee Shruti , Kar Rajiv K. , Nanga Ravi Prakash Reddy , Mroue Kamal H. , Ramamoorthy Ayyalusamy , Bhunia Anirban
Published: June 2017

Multidrug resistance against the existing antibiotics is one of the most challenging threats across the globe.
Cancer bioimprinting and cell shape recognition for diagnosis and targeted treatment
Authors: Medlock Jevan , Das Anupam A. K. , Madden Leigh A. , Allsup David J. , Paunov Vesselin N.
Published: June 2017

We review the recent advances in a wide range of bioimprinting techniques which may provide an alternative modality for cell selectivity in separation, diagnosis and targeted treatment of cancer.
Inverse electron demand Diels–Alder reactions in chemical biology
Authors: Oliveira B. L. , Guo Z. , Bernardes G. J. L.
Published: June 2017

The emerging inverse electron demand Diels–Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility.
Graphene chemistry
Authors: Torres Tomás
Published: June 2017

Guest editor Tomás Torres introduces the Graphene Chemistry issue of Chemical Society Reviews.
Co-Doped Zn1−xCdxS nanocrystals from metal–organic framework precursors: porous microstructure and efficient photocatalytic hydrogen evolution
Authors: Tang Xiu , Zhao Jia-Hui , Li Yu-Han , Zhou Zi-Ji , Li Kui , Liu Fu-Tian , Lan Ya-Qian
Published: June 2017

Nanoporous Co-doped Zn1−xCdxS fabricated with ZnCo-ZIFs as templates afford a high H2-production rate, corresponding to 45.2 and 422.2 times larger than those of Zn0.5Cd0.5S and CdS without using ZIF as template.
Magnetically manipulated droplet splitting on a 3D-printed device to carry out a complexometric assay
Authors: Hutama T. J. , Oleschuk R. D.
Published: June 2017

Magnetic actuation is used to dispense, translate, merge and mix droplets on a 3D-printed platform.
Photorelease of nitric oxide (NO) on ruthenium nitrosyl complexes with phenyl substituted terpyridines
Authors: Amabilino Silvia , Tasse Marine , Lacroix Pascal G. , Mallet-Ladeira Sonia , Pimienta Véronique , Akl Joëlle , Sasaki Isabelle , Malfant Isabelle
Published: June 2017

Transandcisisomers of ruthenium nitrosyl complexes release NO upon irradiation by visible light and give a unique photoproduct.
Copper(i) catalyzed oxidative hydrolysis of Ugi 3-component and Ugi-azide reaction products towards 2° α-ketoamides and α-ketotetrazoles
Authors: Collet Jurriën W. , Foley Christopher , Shaw Arthur Y. , Orru Romano V. A. , Ruijter Eelco , Hulme Christopher
Published: June 2017

Catalytic Cu(i) mediated C–N oxidation of Ugi-3-component and Ugi-azide reaction products affords 2° α-ketoamides 1 and α-ketotetrazoles 2.
A practical approach to asymmetric synthesis of dolastatin 10
Authors: Zhou Wen , Nie Xiao-Di , Zhang Yu , Si Chang-Mei , Zhou Zhu , Sun Xun , Wei Bang-Guo
Published: June 2017

Dolastatin 10 has been effectively synthesized through SmI2-induced cross-coupling for Dap, asymmetric addition for Doe and an alternative route to Val-Dil.
Precipitating polyelectrolyte–surfactant systems by admixing a nonionic surfactant – a case of cononsurfactancy
Authors: Chiappisi Leonardo , David Leach Stephen , Gradzielski Michael
Published: June 2017

Thermodynamic and structural investigations reveal the origin of the unexpected formation of insoluble complexes upon admixing nonionic surfactants to polyelectrolyte/anionic surfactant complexes.
A chiral BINOL-based Gemini amphiphilic gelator and its specific discrimination of native arginine by gelation in water
Authors: Jia Lihua , Yin Jianxin , Guo Xiangfeng , Cao Guangzhou , Tian Xuhua , Zhu Bo , Pu Lin
Published: June 2017

A novel axially chiral cationic Gemini amphiphile gelator (S1) derived from (S)-BINOL has been synthesized and characterized by 1H NMR, 13C NMR, ESI-MS and FT-IR analyses.
CVD graphene‐based low pump threshold bidirectional mode‐locked fibre laser
Authors: Chow Kin Kee
Published: June 2017

A passively mode‐locked femtosecond erbium‐doped bidirectional fibre laser with low pump threshold using chemical vapour deposition grown graphene saturable absorbers is demonstrated. Two synchronised and counter‐propagating soliton output pulse trains with a repetition rate of ∼10.38 MHz and pulse widths of 660 and 860 fs are obtained simultaneously from the fibre laser. Simultaneous mode locking of the fibre laser has been realised with a threshold pump power of 56 mW from a single‐pump laser diode, indicating an ∼62% reduction in pump threshold compared to previous results.
Fast convergence evolutionary programming for economic dispatch problems
Authors: Basu Mousumi
Published: June 2017

This study develops and recommends fast convergence evolutionary programming (FCEP) to the complicated economic dispatch (ED) problem. Evolutionary programming (EP) is a bunch of evolutionary algorithms root of the basic human heritable chromosome operation. EP has the ability to ascertain the global or close to the global optimal solutions. In this study, FCEP has been suggested to boost convergence speed and superior solution. The efficacy of the suggested technique has been disclosed on four dissimilar complicated ED problems with valve‐point effect, disallowed workable county, ramp rate limits and multiple fuels with valve‐point effect. Test results acquired from the suggested technique have been fit to that acquired from other stated evolutionary techniques. It has been observed that the suggested FCEP carry out superior solution.
Functional Status in a Teenager with Phenylketonuria from the ICF Perspective
Authors: Bingöl Hasan , Günel Mintaze
Published: June 2017

Objective The case aims to present a teenager with phenylketonuria in terms of functional status, by using the World Health Organization's International Classification of Functioning, Disability, and Health (ICF) perspective.

Case Description A 17-year-old teenager with phenylketonuria, classified level V in accordance with the Functional Mobility Scale, was recruited in this study. To exhibit body structure, functional status, participation, activity, and environmental and individual factors, assessment tools classified according to ICF for Children and Youth major categories were implemented.

Result After the assessment tools were applied, we found various problems ranging from body structure, function, and activity, to participation. In addition to these problems, there were cognitive problems as well.

Conclusion Despite various physical problems, the teenager suffered from cognitive problems more, that is, compared with physical problems in the teenager with phenylketonuria, cognitive problems constituted a bigger barrier to participation in daily life.
Die (Flüchtlings-) Krise im psychotherapeutischen Behandlungszimmer
Authors: Thöle Anna-Maria , Penka Simone , Aichberger Marion , Heinz Andreas , Kluge Ulrike
Published: June 2017

Hintergrund In den Medien finden sich verschiedene Diskurse von Geflüchteten. Bisher ist allerdings kaum bekannt, ob und wie mediale Diskurse die Perspektive von Psychotherapeuten, die mit Geflüchteten arbeiten, beeinflussen.

Methoden In einer Untersuchung zu den Schwierigkeiten in der psychotherapeutischen Arbeit mit Geflüchteten wurden bundesweit 20 niedergelassene Psychotherapeuten befragt. Für die Datenerhebung wurde das Problemzentrierte Interview gewählt, die Daten wurden entsprechend den Prinzipien der Grounded Theory ausgewertet. Es zeigten sich in den Daten unterschiedliche Bilder von Geflüchteten seitens der befragten Psychotherapeuten.

Ergebnisse Aus den Interviews konnten 4 Bilder von Geflüchteten herausgearbeitet werden: ‚Der problematische Andere‘ (1), ‚Kein Anderer‘ (2), ‚Der gewinnbringende Andere‘ (3) und ‚Das ausgeschlossene Subjekt‘ (4). Darüber hinaus zeigten sich Zusammenhänge zwischen den gefundenen Bildern und der Erfahrung sowie dem Therapieverständnis der jeweiligen Psychotherapeuten.

Schlussfolgerung Der Einfluss (medialer) Diskurse über Geflüchtete kann dazu beitragen, die in den Interviews von niedergelassenen Psychotherapeuten gefundenen Bilder von Geflüchteten verständlich zu machen. Als weitere Erklärungen für die Bilder von Geflüchteten werden ein unterschiedlicher Zugang zu Wissen über die Lebenssituation von Geflüchteten, problematische Lebensbedingungen von Asylsuchenden in Deutschland und ein hauptsächlich an psychischen Störungen ausgerichteter psychotherapeutischer Behandlungsauftrag diskutiert.
Three New Abietane-Type Diterpenoids from Plectranthus africanus and Their Antibacterial Activities
Authors: Nzogong Raïssa , Nganou Blaise , Tedonkeu Alex , Awouafack Maurice , Tene Mathieu , Ito Takuya , Tane Pierre , Morita Hiroyuki
Published: June 2017

Three new abietane-type diterpenoids, plectranthroyleanones A – C (1 – 3), together with five known compounds (4 – 8) were isolated from the methanol extract of the whole plant of Plectranthus africanus using column chromatography techniques. The structures of the new compounds were elucidated using a combination of 1D and 2D NMR and HRESIMS analyses. Compound 1 exhibited weak activities with minimal inhibitory concentration values of 75 µg/mL against gram-positive bacteria, Bacillus subtilis and Staphylococcus aureus, and 150 µg/mL against two gram-negative bacteria, Pseudomonas aeruginosa and Klebsiella pneumoniae, respectively, while 2 and 3 had moderate antibacterial activity against K. pneumoniae with a minimal inhibitory concentration value of 37.5 µg/mL.
Cavity resonator for dielectric measurements of high-ε, low loss materials, demonstrated with barium strontium zirconium titanate ceramics
Authors: Marksteiner Quinn R. , Treiman Michael B. , Chen Ching-Fong , Haynes William B. , Reiten M. T. , Dalmas Dale , Pulliam Elias
Published: June 2017

A resonant cavity method is presented which can measure loss tangents and dielectric constants for materials with dielectric constant from 150 to 10 000 and above. This practical and accurate technique is demonstrated by measuring barium strontium zirconium titanate bulk ferroelectric ceramic blocks. Above the Curie temperature, in the paraelectric state, barium strontium zirconium titanate has a sufficiently low loss that a series of resonant modes are supported in the cavity. At each mode frequency, the dielectric constant and loss tangent are obtained. The results are consistent with low frequency measurements and computer simulations. A quick method of analyzing the raw data using the 2D static electromagnetic modeling code SuperFish and an estimate of uncertainties are presented.
SEM imaging of acoustically stimulated charge transport in solids
Authors: Emelin Evgeny , Cho H. D. , Insepov Zeke , Lee J. C. , Kang Tae Won , Panin Gennady , Roshchupkin Dmitry , Tynyshtykbayev Kurbangali
Published: June 2017

Acoustically stimulated charge transport in solids was studied using the scanning electron microscopy method (SEM). The surface acoustic wave on the surface of the YZ-cut of a LiNbO3 crystal was visualized by registration of low-energy secondary electrons in SEM, and the charge distribution on the crystal surface was visualized using the electron beam induced current method. To register the induced current, an interdigital transducer structure was formed from graphene on the crystal surface. It was shown that the charge distribution on the crystal surface corresponds to the distribution of the acoustic wave field on the crystal surface.
Effect of Carreau-Yasuda rheological parameters on subcritical Lapwood convection in horizontal porous cavity saturated by shear-thinning fluid
Authors: Khechiba Khaled , Mamou Mahmoud , Hachemi Madjid , Delenda Nassim , Rebhi Redha
Published: June 2017

The present study is focused on Lapwood convection in isotropic porous media saturated with non-Newtonian shear thinning fluid. The non-Newtonian rheological behavior of the fluid is modeled using the general viscosity model of Carreau–Yasuda. The convection configuration consists of a shallow porous cavity with a finite aspect ratio and subject to a vertical constant heat flux, whereas the vertical walls are maintained impermeable and adiabatic. An approximate analytical solution is developed on the basis of the parallel flow assumption, and numerical solutions are obtained by solving the full governing equations. The Darcy model with the Boussinesq approximation and energy transport equations are solved numerically using a finite difference method. The results are obtained in terms of the Nusselt number and the flow fields as functions of the governing parameters. A good agreement is obtained between the analytical approximation and the numerical solution of the full governing equations. The effects of the rheological parameters of the Carreau-Yasuda fluid and Rayleigh number on the onset of subcritical convection thresholds are demonstrated. Regardless of the aspect ratio of the enclosure and thermal boundary condition type, the subcritical convective flows are seen to occur below the onset of stationary convection. Correlations are proposed to estimate the subcritical Rayleigh number for the onset of finite amplitude convection as a function of the fluid rheological parameters. Linear stability of the convective motion, predicted by the parallel flow approximation, is studied, and the onset of Hopf bifurcation, from steady convective flow to oscillatory behavior, is found to depend strongly on the rheological parameters. In general, Hopf bifurcation is triggered earlier as the fluid becomes more and more shear-thinning.
Analysis of the scattering and absorption properties of ellipsoidal nanoparticle arrays for the design of full-color transparent screens
Authors: Monti Alessio , Toscano Alessandro , Bilotti Filiberto
Published: June 2017

The introduction of nanoparticles-based screens [C. W. Hsu, Nat. Commun. 5, 3152 (2014)] has paved the way to the realization of low-cost transparent displays with a wide viewing angle and scalability to large size. Despite the huge potentialities of this approach, the design of a nanoparticles array exhibiting a sharp scattering response in the optical spectrum is still a challenging task. In this manuscript, we investigate the suitability of ellipsoidal plasmonic nanoparticles for this purpose. First, we show that some trade-offs between the sharpness of the scattering response of the array and its absorption level apply. Starting from these considerations, we prove that prolate nanoparticles may be a plausible candidate for achieving the peculiar features required in transparent screen applications. An example of a full-color and almost-isotropic transparent screen is finally proposed and its robustness towards the geometrical inaccuracies that may arise during the fabrication process is assessed. All the analytical considerations, carried out through an analytical model taking into account the surface dispersion effect affecting the nanoparticles, are supported by a proper set of full-wave simulations.
Dust acoustic waves in an inhomogeneous plasma having dust size distribution
Authors: Banerjee Gadadhar , Maitra Sarit
Published: June 2017

Propagations of nonlinear dust acoustic solitary waves in an inhomogeneous unmagnetized dusty plasma having power law dust distribution are investigated. Using a reductive perturbation technique, a variable coefficient deformed Korteweg-deVries (VCdKdV) equation is derived from the basic set of hydrodynamic equations. The generalized expansion method is employed to obtain a solitary wave solution for the VCdKdV equation. The different propagation characteristics of the solitary waves are studied in the presence of both plasma inhomogeneity and dust distribution.
The elastic microstructures of inkjet printed polydimethylsiloxane as the patterned dielectric layer for pressure sensors
Authors: Peng Yongyi , Xiao Shugang , Yang Junliang , Lin Jian , Yuan Wei , Gu Weibing , Wu Xinzhou , Cui Zheng
Published: June 2017

A direct inkjet printing process was developed to fabricate patterned elastic microstructures for pressure sensors using n-butyl acetate diluted polymethylsiloxane (PDMS). The diluted PDMS precursor mixture with a cross-linker exhibited a controllable viscosity below 14 cP in 48 h at 25 °C, and the PDMS film had lower elastic modulus and hardness values than the non-diluted PDMS precursor after curing. The capacitor using the printed PDMS film as the microstructured dielectric layer showed a very high pressure sensitivity of up to 10.4 kPa−1 under the pressure below 70 Pa, and the pressure sensitivity would be dramatically decreased to 0.043–0.052 kPa−1 under the pressure between 2 and 8 kPa. Furthermore, the triboelectric sensors could be structured with an inkjet printed PDMS film and controllably generate the voltage signals up to 1.23 V without any amplification. The results suggest that mechanical properties and patterned elastic microstructures play the key roles in PDMS-based sensor devices, and the PDMS dielectric layer with controlled mechanical properties and microstructures fabricated via directly inkjet printing opens up the applications of the PDMS and its composites in functional devices.
A Bayesian nonparametric approach to reconstruction and prediction of random dynamical systems
Authors: Merkatas Christos , Kaloudis Konstantinos , Hatjispyros Spyridon J.
Published: June 2017

We propose a Bayesian nonparametric mixture model for the reconstruction and prediction from observed time series data, of discretized stochastic dynamical systems, based on Markov Chain Monte Carlo methods. Our results can be used by researchers in physical modeling interested in a fast and accurate estimation of low dimensional stochastic models when the size of the observed time series is small and the noise process (perhaps) is non-Gaussian. The inference procedure is demonstrated specifically in the case of polynomial maps of an arbitrary degree and when a Geometric Stick Breaking mixture process prior over the space of densities, is applied to the additive errors. Our method is parsimonious compared to Bayesian nonparametric techniques based on Dirichlet process mixtures, flexible and general. Simulations based on synthetic time series are presented.
Theoretical modeling to study the impact of different oxidizers (etchants) on the plasma-assisted catalytic carbon nanofiber growth
Authors: Gupta Ravi , Sharma Suresh C.
Published: June 2017

An analytical model based on the various surface deposition processes and plasma sheath kinetics of the plasma species (electrons, positively charged ions, radicals, and neutrals) has been developed to investigate the effects of different plasmas (different etchants) on the catalyzed plasma aided growth of carbon nanofibers (CNFs). In particular, the model accounts the poisoning of the catalyst nanoparticle, i.e., the formation of the amorphous carbon layer on the catalyst active surface due to the continuous dissociation of incoming hydrocarbon species from the plasma. It is observed that oxidizers (H2O and O2) in the typical hydrocarbon/hydrogen (C2H2 + H2) plasma act as the dominant etchants and remove the amorphous carbon layer from the catalyst surface and, thus, preserve and enhance the catalyst activity. However, the growth rate of CNFs is much higher when O2 is added as an etchant in the reactive plasma as compared to H2O. This is due to the dual role played by the oxygen, i.e., (i) removal of amorphous carbon from the catalyst active surface, (ii) removal of hydrogen radicals that interact with the carbon species generated on the catalyst surface and suppress their diffusion through the catalyst nanoparticles. The CNF grows much longer in the presence of O2, therefore, etching of CNF tip and deformation of catalyst nanoparticle is the maximum, and hence, the CNF tip diameter is least. Moreover, in the present investigation, we also found that the relative concentrations of H2O or O2 species in the reactive plasma have significant effects on the CNF growth. Our theoretical results are in good agreement with the experimental observations.
Electronic structure and switching behavior of the metastable silicene domain boundary
Authors: Oh Youngtek , Cho Yeonchoo , Kwon Hyeokshin , Lee Junsu , Jeon Insu , Ko Wonhee , Kim Hyo Won , Ku JiYeon , Kim Gunn , Suh Hwansoo , Hwang Sung Woo
Published: June 2017

Silicene, a silicon allotrope with a buckled honeycomb lattice, has been extensively studied in the search for materials with graphene-like properties. Here, we study the domain boundaries of a silicene 4 × 4 superstructure on an Ag(111) surface at the atomic resolution using scanning tunneling microscopy (STM) and spectroscopy (STS) along with density functional theory calculations. The silicene domain boundaries (β-phases) are formed at the interface between misaligned domains (α-phases) and show a bias dependence, forming protrusions or depressions as the sample bias changes. In particular, the STM topographs of the silicene–substrate system at a bias of ∼2.0 V show brightly protruding domain boundaries, which can be explained by an energy state originating from the Si 3s and 3pz orbitals. In addition, the topographs depicting the vicinity of the domain boundaries show that the structure does not follow the buckled geometry of the atomic ball-and-stick model. Inside the domain, STS data showed a step-up at ∼0.4 V, which originated from the Si 3p orbitals. We found this step-up to have shifted, which may be attributed to the strain effect at the interface regions between silver and silicene and between the domain and its boundary upon performing spatially resolved STS measurements. The metastable characteristic of the domain boundary (β-phase) causes changes, such as creation or annihilation, in the buckling structures (switching behavior). The observed low activation energy for the buckling change between distinct states may find applications in the electronic control of properties related to domain boundary structures in silicene.
Model predictions for atmospheric air breakdown by radio-frequency excitation in large gaps
Authors: Nguyen H. K. , Mankowski J. , Dickens J. C. , Neuber A. A. , Joshi R. P.
Published: June 2017

The behavior of the breakdown electric field versus frequency (DC to 100 MHz) for different gap lengths has been studied numerically at atmospheric pressure. Unlike previous reports, the focus here is on much larger gap lengths in the 1–5 cm range. A numerical analysis, with transport coefficients obtained from Monte Carlo calculations, is used to ascertain the electric field thresholds at which the growth and extinction of the electron population over time are balanced. Our analysis is indicative of a U-shaped frequency dependence, lower breakdown fields with increasing gap lengths, and trends qualitatively similar to the frequency-dependent field behavior for microgaps. The low frequency value of ∼34 kV/cm for a 1 cm gap approaches the reported DC Paschen limit.
Laguerre-Gaussian quasi-modal q-plates from nanostructured glasses
Authors: Rafayelyan Mushegh , Gertus Titas , Brasselet Etienne
Published: June 2017

A quasi-modal version of the recently introduced Laguerre-Gaussian modal q-plates [Rafayelyan and Brasselet, Opt. Lett. 42, 1966–1969 (2017)] is proposed and implemented using femtosecond direct laser writing of space-variant nanogratings in the bulk of silica glass. The corresponding design consists of linear azimuthal modulation of the optical axis orientation and polynomial radial modulation of the retardance profile. Experimental demonstration is made for Laguerre-Gaussian modes with azimuthal indices l =(1, 2, 3) and radial index p = 0. Such quasi-modal q-plates overcome previous limitations regarding the robustness of modality against the handedness of the incident circular polarization state.
Characterization of the non-resonant radiation damping in coupled cavity photon magnon system
Authors: Rao J. W. , Kaur S. , Fan X. L. , Xue D. S. , Yao B. M. , Gui Y. S. , Hu C.-M.
Published: June 2017

We have experimentally investigated the non-resonant radiation damping in the coupled cavity photon-magnon system in addition to the resonant radiation damping which results in the linewidth exchange between the magnon-like and photon-like hybrid modes. The contribution of this non-resonant effect becomes apparent when the cavity photon-magnon resonance frequencies are mismatched. By carefully examining the change in the linewidth and the shift in the magnon resonance as a function of the coupling strength between the cavity photons and magnons, we can quantitatively describe this non-resonant radiation damping by including an additional relaxation channel for the hybridized photon-magnon system. This experimental realization and theoretical modelling of the non-resonant radiation damping in the cavity photon-magnon system may help in the design and adaptation of these systems for practical applications.
Direct estimation of Byram's fire intensity from infrared remote sensing imagery
Authors: Johnston Joshua M. , Wooster Martin J. , Paugam Ronan , Wang Xianli , Lynham Timothy J. , Johnston Lynn M.
Published: June 2017

Byram’s fire intensity (IB,tot; kWm–1) is one the most important and widely accepted metrics for quantifying wildfire behaviour. Calculation of IB,tot requires measurement of fuel consumption, heat of combustion and rate of spread; existing methods for obtaining these measurements are either inexact or at times impossible to obtain in the field. This paper presents and evaluates a series of remote sensing methods for directly deriving radiative fire intensity (IB,rad; kWm–1) using the Fire Radiative Power (FRP) approach applied to thermal infrared imagery of spreading vegetation fires. Comparisons between the remote sensing data and ground-sampled measurements were used to evaluate the various estimates of IB,tot, and to determine the radiative fraction (radF) of a fire’s emitted energy. Results indicate that the IB,tot along an advancing flame front can be reasonably estimated (and agrees with traditional methods of estimation (R2=0.34–0.73)) from appropriately collected time-series of remote sensing imagery without the need for ground sampling or ancillary data. We further estimate that the radF of the fire’s emitted energy varies between 0.15 and 0.20 depending on the method of calculation, which is similar to previous estimates.
The labyrinth of ethics in journalistic translated discourse
Authors: Talebinejad Mohammad Reza , Shahi Mohammad
Published: June 2017

Given that both translation ethics and journalistic translation are still two under-explored areas in translation research, this study sets out to discover the ethical model of Iranian translators’ performance in a climate of conflict. To achieve the objective, the researchers monitored and collected the translated journalistic texts concerning the Iranian nuclear negotiations published by a state-run news agency from three days before the Almaty I nuclear talks to three days after the Almaty II negotiations. The monitoring phase resulted in 20 pairs of STs and TTs. The comparative textual analysis indicated patterned and motivated ideological interference in translations which could be accounted for by resorting to teleological models of ethics. Theoretical analysis revealed conceptual overlap between ethics and ideology that could explain the reduction of ethics into ideology in the news agency.
Pink1 and Parkin regulateDrosophilaintestinal stem cell proliferation during stress and aging
Authors: Koehler Christopher L. , Perkins Guy A. , Ellisman Mark H. , Jones D. Leanne
Published: June 2017

Intestinal stem cells (ISCs) maintain the midgut epithelium in Drosophila melanogaster. Proper cellular turnover and tissue function rely on tightly regulated rates of ISC division and appropriate differentiation of daughter cells. However, aging and epithelial injury cause elevated ISC proliferation and decreased capacity for terminal differentiation of daughter enteroblasts (EBs). The mechanisms causing functional decline of stem cells with age remain elusive; however, recent findings suggest that stem cell metabolism plays an important role in the regulation of stem cell activity. Here, we investigate how alterations in mitochondrial homeostasis modulate stem cell behavior in vivo via RNA interference–mediated knockdown of factors involved in mitochondrial dynamics. ISC/EB-specific knockdown of the mitophagy-related genes Pink1 or Parkin suppresses the age-related loss of tissue homeostasis, despite dramatic changes in mitochondrial ultrastructure and mitochondrial damage in ISCs/EBs. Maintenance of tissue homeostasis upon reduction of Pink1 or Parkin appears to result from reduction of age- and stress-induced ISC proliferation, in part, through induction of ISC senescence. Our results indicate an uncoupling of cellular, tissue, and organismal aging through inhibition of ISC proliferation and provide insight into strategies used by stem cells to maintain tissue homeostasis despite severe damage to organelles.
Phosphoinositide-dependent enrichment of actin monomers in dendritic spines regulates synapse development and plasticity
Authors: Lei Wenliang , Myers Kenneth R. , Rui Yanfang , Hladyshau Siarhei , Tsygankov Denis , Zheng James Q.
Published: June 2017

Dendritic spines are small postsynaptic compartments of excitatory synapses in the vertebrate brain that are modified during learning, aging, and neurological disorders. The formation and modification of dendritic spines depend on rapid assembly and dynamic remodeling of the actin cytoskeleton in this highly compartmentalized space, but the precise mechanisms remain to be fully elucidated. In this study, we report that spatiotemporal enrichment of actin monomers (G-actin) in dendritic spines regulates spine development and plasticity. We first show that dendritic spines contain a locally enriched pool of G-actin that can be regulated by synaptic activity. We further find that this G-actin pool functions in spine development and its modification during synaptic plasticity. Mechanistically, the relatively immobile G-actin pool in spines depends on the phosphoinositide PI(3,4,5)P3 and involves the actin monomer–binding protein profilin. Together, our results have revealed a novel mechanism by which dynamic enrichment of G-actin in spines regulates the actin remodeling underlying synapse development and plasticity.
Quark enables semi-reference-based compression of RNA-seq data
Authors: Sarkar Hirak , Patro Rob
Published: June 2017

Motivation

The past decade has seen an exponential increase in biological sequencing capacity, and there has been a simultaneous effort to help organize and archive some of the vast quantities of sequencing data that are being generated. Although these developments are tremendous from the perspective of maximizing the scientific utility of available data, they come with heavy costs. The storage and transmission of such vast amounts of sequencing data is expensive.

Results

We present Quark, a semi-reference-based compression tool designed for RNA-seq data. Quark makes use of a reference sequence when encoding reads, but produces a representation that can be decoded independently, without the need for a reference. This allows Quark to achieve markedly better compression rates than existing reference-free schemes, while still relieving the burden of assuming a specific, shared reference sequence between the encoder and decoder. We demonstrate that Quark achieves state-of-the-art compression rates, and that, typically, only a small fraction of the reference sequence must be encoded along with the reads to allow reference-free decompression.

Availability and implementation

Quark is implemented in C ++11, and is available under a GPLv3 license at www.github.com/COMBINE-lab/quark.

Supplementary information

Supplementary data are available at Bioinformatics online.
A genome-by-environment interaction classifier for precision medicine: personal transcriptome response to rhinovirus identifies children prone to asthma exacerbations
Authors: Gardeux Vincent , Berghout Joanne , Achour Ikbel , Schissler A Grant , Li Qike , Kenost Colleen , Li Jianrong , Shang Yuan , Bosco Anthony , Saner Donald , Halonen Marilyn J , Jackson Daniel J , Li Haiquan , Martinez Fernando D , Lussier Yves A
Published: June 2017

Objective

To introduce a disease prognosis framework enabled by a robust classification scheme derived from patient-specific transcriptomic response to stimulation.

Materials and Methods

Within an illustrative case study to predict asthma exacerbation, we designed a stimulation assay that reveals individualized transcriptomic response to human rhinovirus. Gene expression from peripheral blood mononuclear cells was quantified from 23 pediatric asthmatic patients and stimulated in vitro with human rhinovirus. Responses were obtained via the single-subject gene set testing methodology “N-of-1-pathways.” The classifier was trained on a related independent training dataset (n = 19). Novel visualizations of personal transcriptomic responses are provided.

Results

Of the 23 pediatric asthmatic patients, 12 experienced recurrent exacerbations. Our classifier, using individualized responses and trained on an independent dataset, obtained 74% accuracy (area under the receiver operating curve of 71%; 2-sided P = .039). Conventional classifiers using messenger RNA (mRNA) expression within the viral-exposed samples were unsuccessful (all patients predicted to have recurrent exacerbations; accuracy of 52%).

Discussion

Prognosis based on single time point, static mRNA expression alone neglects the importance of dynamic genome-by-environment interplay in phenotypic presentation. Individualized transcriptomic response quantified at the pathway (gene sets) level reveals interpretable signals related to clinical outcomes.

Conclusion

The proposed framework provides an innovative approach to precision medicine. We show that quantifying personal pathway–level transcriptomic response to a disease-relevant environmental challenge predicts disease progression. This genome-by-environment interaction assay offers a noninvasive opportunity to translate omics data to clinical practice by improving the ability to predict disease exacerbation and increasing the potential to produce more effective treatment decisions.