bluuebunny/crossref_metadata_2025 huggingface dataset:
Force chains as the link between particle and bulk friction angles in granular material
Authors: Booth Adam M. , Hurley Ryan , Lamb Michael P. , Andrade José E.
Published: December 2014

From sediment transport in rivers to landslides, predictions of granular motion rely on a Mohr‐Coulomb failure criterion parameterized by a friction angle. Measured friction angles are generally large for single grains, smaller for large numbers of grains, and no theory exists for intermediate numbers of grains. We propose that a continuum of friction angles exists between single‐grain and bulk friction angles due to grain‐to‐grain force chains. Physical experiments, probabilistic modeling, and discrete element modeling demonstrate that friction angles decrease by up to 15° as the number of potentially mobile grains increases from 1 to ~20. Decreased stability occurs as longer force chains more effectively dislodge downslope “keystone” grains, implying that bulk friction angles are set by the statistics of single‐grain friction angles. Both angles are distinct from and generally larger than grain contact‐point friction, with implications for a variety of sediment transport processes involving small clusters of grains.
Organic iodine in Antarctic sea ice: A comparison between winter in the Weddell Sea and summer in the Amundsen Sea
Authors: Granfors Anna , Ahnoff Martin , Mills Matthew M. , Abrahamsson Katarina
Published: December 2014

Recent studies have recognized sea ice as a source of reactive iodine to the Antarctic boundary layer. Volatile iodinated compounds (iodocarbons) are released from sea ice, and they have been suggested to contribute to the formation of iodine oxide (IO), which takes part in tropospheric ozone destruction in the polar spring. We measured iodocarbons (CH3I, CH2ClI, CH2BrI, and CH2I2) in sea ice, snow, brine, and air during two expeditions to Antarctica, OSO 10/11 to the Amundsen Sea during austral summer and ANT XXIX/6 to the Weddell Sea in austral winter. These are the first reported measurements of iodocarbons from the Antarctic winter. Iodocarbons were enriched in sea ice in relation to seawater in both summer and winter. During summer, the positive relationship to chlorophyll a biomass indicated a biological origin. We suggest that CH3I is formed biotically in sea ice during both summer and winter. For CH2ClI, CH2BrI, and CH2I2, an additional abiotic source at the snow/ice interface in winter is suggested. Elevated air concentrations of CH3I and CH2ClI during winter indicate that they are enriched in lower troposphere and may take part in the formation of IO at polar sunrise.
Species‐specific transpiration responses to intermediate disturbance in a northern hardwood forest
Authors: Matheny Ashley M. , Bohrer Gil , Vogel Christoph S. , Morin Timothy H. , He Lingli , Frasson Renato Prata de Moraes , Mirfenderesgi Golnazalsadat , Schäfer Karina V. R. , Gough Christopher M. , Ivanov Valeriy Y. , Curtis Peter S.
Published: December 2014

Intermediate disturbances shape forest structure and composition, which may in turn alter carbon, nitrogen, and water cycling. We used a large‐scale experiment in a forest in northern lower Michigan where we prescribed an intermediate disturbance by stem girdling all canopy‐dominant early successional trees to simulate an accelerated age‐related senescence associated with natural succession. Using 3 years of eddy covariance and sap flux measurements in the disturbed area and an adjacent control plot, we analyzed disturbance‐induced changes to plot level and species‐specific transpiration and stomatal conductance. We found transpiration to be ~15% lower in disturbed plots than in unmanipulated control plots. However, species‐specific responses to changes in microclimate varied. While red oak and white pine showed increases in stomatal conductance during postdisturbance (62.5 and 132.2%, respectively), red maple reduced stomatal conductance by 36.8%. We used the hysteresis between sap flux and vapor pressure deficit to quantify diurnal hydraulic stress incurred by each species in both plots. Red oak, a ring porous anisohydric species, demonstrated the largest mean relative hysteresis, while red maple, bigtooth aspen, and paper birch, all diffuse porous species, had the lowest relative hysteresis. We employed the Penman‐Monteith model for LE to demonstrate that these species‐specific responses to disturbance are not well captured using current modeling strategies and that accounting for changes to leaf area index and plot microclimate are insufficient to fully describe the effects of disturbance on transpiration.
Resolution of liver fibrosis requires myeloid cell–driven sinusoidal angiogenesis
Authors: Kantari‐Mimoun Chahrazade , Castells Magali , Klose Ralph , Meinecke Anna‐Katharina , Lemberger Ursula J. , Rautou Pierre‐Emmanuel , Pinot‐Roussel Hélène , Badoual Cécile , Schrödter Katrin , Österreicher Christoph H. , Fandrey Joachim , Stockmann Christian
Published: December 2014

Angiogenesis is a key feature of liver fibrosis. Although sinusoidal remodeling is believed to contribute to fibrogenesis, the impact of sinusoidal angiogenesis on the resolution of liver fibrosis remains undefined. Myeloid cells, particularly macrophages, constantly infiltrate the fibrotic liver and can profoundly contribute to remodeling of liver sinusoids. We observe that the development of fibrosis is associated with decreased hepatic vascular endothelial growth factor (VEGF) expression as well as sinusoidal rarefication of the fibrotic scar. In contrast, the resolution of fibrosis is characterized by a rise in hepatic VEGF levels and revascularization of the fibrotic tissue. Genetic ablation of VEGF in myeloid cells or pharmacological inhibition of VEGF receptor 2 signaling prevents this angiogenic response and the resolution of liver fibrosis. We observe increased expression of matrix metalloproteases as well as decreased expression of tissue inhibitor of metalloproteases confined to sinusoidal endothelial cells in response to myeloid cell VEGF. Remarkably, reintroduction of myeloid cell–derived VEGF upon recovery restores collagenolytic acitivity and the resolution of fibrosis. Conclusion: We identify myeloid cell–derived VEGF as a critical regulator of extracellular matrix degradation by liver endothelial cells, thereby unmasking an unanticipated link between angiogenesis and the resolution of fibrosis. (Hepatology 2015;61:2042–2055)
Gut microbiota are related to Parkinson's disease and clinical phenotype
Authors: Scheperjans Filip , Aho Velma , Pereira Pedro A. B. , Koskinen Kaisa , Paulin Lars , Pekkonen Eero , Haapaniemi Elena , Kaakkola Seppo , Eerola‐Rautio Johanna , Pohja Marjatta , Kinnunen Esko , Murros Kari , Auvinen Petri
Published: December 2014

In the course of Parkinson's disease (PD), the enteric nervous system (ENS) and parasympathetic nerves are amongst the structures earliest and most frequently affected by alpha‐synuclein pathology. Accordingly, gastrointestinal dysfunction, in particular constipation, is an important non‐motor symptom in PD and often precedes the onset of motor symptoms by years. Recent research has shown that intestinal microbiota interact with the autonomic and central nervous system via diverse pathways including the ENS and vagal nerve. The gut microbiome in PD has not been previously investigated. We compared the fecal microbiomes of 72 PD patients and 72 control subjects by pyrosequencing the V1–V3 regions of the bacterial 16S ribosomal RNA gene. Associations between clinical parameters and microbiota were analyzed using generalized linear models, taking into account potential confounders. On average, the abundance of Prevotellaceae in feces of PD patients was reduced by 77.6% as compared with controls. Relative abundance of Prevotellaceae of 6.5% or less had 86.1% sensitivity and 38.9% specificity for PD. A logistic regression classifier based on the abundance of four bacterial families and the severity of constipation identified PD patients with 66.7% sensitivity and 90.3% specificity. The relative abundance of Enterobacteriaceae was positively associated with the severity of postural instability and gait difficulty. These findings suggest that the intestinal microbiome is altered in PD and is related to motor phenotype. Further studies are warranted to elucidate the temporal and causal relationships between gut microbiota and PD and the suitability of the microbiome as a biomarker. © 2014 International Parkinson and Movement Disorder Society
Multiresolution calculation of ionic liquids
Authors: Kirchner Barbara , Hollóczki Oldamur , Canongia Lopes José Nuno , Pádua Agílio A. H.
Published: December 2014

Ionic liquids—which are special solvents composed entirely of ions—are difficult albeit interesting to study for several reasons. Owing to the many possible cation and anion combinations that form ionic liquids, common properties are hard to classify for them, which makes the theoretical investigation crucial for ionic liquids. The system size, the amount of possible isomers including cation–anion orientation and coordination, as well as the rotation of the side chain(s) prevent the use of high‐level electronic structure methods, and density functional theory is the method of choice. Dispersion forces—although they are small compared to electrostatics—play a major role in ionic liquids; therefore, methods that describe such kind of interplay are preferred. Between the cation and the anion, there is a sizable charge transfer, which has important consequences for molecular dynamics simulations and force field development. Already based on the first generation of force fields important discoveries were made, namely that ionic liquids are nanostructured. Moreover, it was possible to predict that their distillation is possible. Throughout the construction of these force fields, transferability was taken into account which allowed them to describe homologous series. For studying reactions in ionic liquid (IL) media, continuum models were found to improve the results. Ab initio molecular dynamics (AIMD) and quantum mechanics (QM)/molecular mechanics (MM) approaches are well suited for spontaneous events. In case of very large systems, such as cellulose in ionic liquids, coarse‐grained methods are providing insight and are applied more frequently. This makes ionic liquids real multiscalar systems. WIREs Comput Mol Sci 2015, 5:202–214. doi: 10.1002/wcms.1212

This article is categorized under:

Structure and Mechanism > Computational Materials Science

Electronic Structure Theory > Density Functional Theory

Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Maximum Marginal Likelihood Estimation of a Monotonic Polynomial Generalized Partial Credit Model with Applications to Multiple Group Analysis
Authors: Falk Carl F. , Cai Li
Published: December 2014

We present a semi-parametric approach to estimating item response functions (IRF) useful when the true IRF does not strictly follow commonly used functions. Our approach replaces the linear predictor of the generalized partial credit model with a monotonic polynomial. The model includes the regular generalized partial credit model at the lowest order polynomial. Our approach extends Liang’s (A semi-parametric approach to estimate IRFs, Unpublished doctoral dissertation, 2007) method for dichotomous item responses to the case of polytomous data. Furthermore, item parameter estimation is implemented with maximum marginal likelihood using the Bock–Aitkin EM algorithm, thereby facilitating multiple group analyses useful in operational settings. Our approach is demonstrated on both educational and psychological data. We present simulation results comparing our approach to more standard IRF estimation approaches and other non-parametric and semi-parametric alternatives.
Analysis of Multiple Partially Ordered Responses to Belief Items with Don’t Know Option
Authors: Ip Edward H. , Chen Shyh-Huei , Quandt Sara A.
Published: December 2014

Understanding beliefs, values, and preferences of patients is a tenet of contemporary health sciences. This application was motivated by the analysis of multiple partially ordered set (poset) responses from an inventory on layman beliefs about diabetes. The partially ordered set arises because of two features in the data—first, the response options contain a Don’t Know (DK) option, and second, there were two consecutive occasions of measurement. As predicted by the common sense model of illness, beliefs about diabetes were not necessarily stable across the two measurement occasions. Instead of analyzing the two occasions separately, we studied the joint responses across the occasions as a poset response. Few analytic methods exist for data structures other than ordered or nominal categories. Poset responses are routinely collapsed and then analyzed as either rank ordered or nominal data, leading to the loss of nuanced information that might be present within poset categories. In this paper we developed a general class of item response models for analyzing the poset data collected from the Common Sense Model of Diabetes Inventory. The inferential object of interest is the latent trait that indicates congruence of belief with the biomedical model. To apply an item response model to the poset diabetes inventory, we proved that a simple coding algorithm circumvents the requirement of writing new codes such that standard IRT software could be directly used for the purpose of item estimation and individual scoring. Simulation experiments were used to examine parameter recovery for the proposed poset model.
Buoyancy-induced turbulence in a tilted pipe
Authors: Hallez Yannick , Magnaudet Jacques
Published: December 2014

Numerical simulation is used to document the statistical structure and better understand energy transfers in a low-Reynolds-number turbulent flow generated by negative axial buoyancy in a long circular tilted pipe under the Boussinesq approximation. The flow is found to exhibit specific features which strikingly contrast with the familiar characteristics of pressure-driven pipe and channel flows. The mean flow, dominated by an axial component exhibiting a uniform shear in the core, also comprises a weak secondary component made of four counter-rotating cells filling the entire cross-section. Within the cross-section, variations of the axial and transverse velocity fluctuations are markedly different, the former reaching its maximum at the edge of the core while the latter two decrease monotonically from the axis to the wall. The negative axial buoyancy component generates long plumes travelling along the pipe, yielding unusually large longitudinal integral length scales. The axial and crosswise mean density variations are shown to be respectively responsible for a quadratic variation of the crosswise shear stress and density flux which both decrease from a maximum on the pipe axis to near-zero values throughout the near-wall region. Although the crosswise buoyancy component is stabilizing everywhere, the crosswise density flux is negative in some peripheral regions, which corresponds to apparent counter-gradient diffusion. Budgets of velocity and density fluctuations variances and of crosswise shear stress and density flux are analysed to explain the above features. A novel two-time algebraic model of the turbulent fluxes is introduced to determine all components of the diffusivity tensor, revealing that they are significantly influenced by axial and crosswise buoyancy effects. The eddy viscosity and eddy diffusivity concepts and the Reynolds analogy are found to work reasonably well within the central part of the section whereas non-local effects cannot be ignored elsewhere.
Timing of positive blood samples does not differentiate pathogens causing healthcare-associated from community-acquired bloodstream infections in children in England: a linked retrospective cohort study
Authors: HENDERSON K. L. , MÜLLER-PEBODY B. , WADE A. , SHARLAND M. , MINAJI M. , JOHNSON A. P. , GILBERT R
Published: December 2014

Paediatricians recognize that using the time-dependent community-acquired vs. hospital-acquired bloodstream infection (BSI) dichotomy to guide empirical treatment no longer distinguishes between causative pathogens due to the emergence of healthcare-associated BSIs. However, paediatric epidemiological evidence of the aetiology of BSIs in relation to hospital admission in England is lacking. For 12 common BSI-causing pathogens in England, timing of laboratory reports of positive paediatric (3 months to 5 years) bacterial blood isolates were linked to in-patient hospital data and plotted in relation to hospital admission. The majority (88·6%) of linked pathogens were isolated <2 days after hospital admission, including pathogens widely regarded as hospital acquired: Enterococcus spp. (67·2%) and Klebsiella spp. (88·9%). Neisseria meningitidis, Streptococcus pneumoniae, group A streptococcus and Salmonella spp. were unlikely to cause hospital-acquired BSI. Pathogens commonly associated with hospital-acquired BSI are being isolated <2 days after hospital admission alongside pathogens commonly associated with community-acquired BSI. We confirm that timing of blood samples alone does not differentiate between bacterial pathogens. Additional factors including clinical patient characteristics and healthcare contact should be considered to help predict the causative pathogen and guide empirical antibiotic therapy.
Medication decision making and patient outcomes in GP, nurse and pharmacist prescriber consultations
Authors: Weiss Marjorie C. , Platt Jo , Riley Ruth , Chewning Betty , Taylor Gordon , Horrocks Susan , Taylor Andrea
Published: December 2014

Aim

The aims of this study were twofold: (a) to explore whether specific components of shared decision making were present in consultations involving nurse prescribers (NPs), pharmacist prescribers (PPs) and general practitioners (GPs) and (b) to relate these to self-reported patient outcomes including satisfaction, adherence and patient perceptions of practitioner empathy.

Background

There are a range of ways for defining and measuring the process of concordance, or shared decision making as it relates to decisions about medicines. As a result, demonstrating a convincing link between shared decision making and patient benefit is challenging. In the United Kingdom, nurses and pharmacists can now take on a prescribing role, engaging in shared decision making. Given the different professional backgrounds of GPs, NPs and PPs, this study sought to explore the process of shared decision making across these three prescriber groups.

Methods

Analysis of audio-recordings of consultations in primary care in South England between patients and GPs, NPs and PPs. Analysis of patient questionnaires completed post consultation.

Findings

A total of 532 consultations were audio-recorded with 20 GPs, 19 NPs and 12 PPs. Prescribing decisions occurred in 421 (79%). Patients were given treatment options in 21% (102/482) of decisions, the prescriber elicited the patient’s treatment preference in 18% (88/482) and the patient expressed a treatment preference in 24% (118/482) of decisions. PPs were more likely to ask for the patient’s preference about their treatment regimen (χ2=6.6,P=0.036, Cramer’sV=0.12) than either NPs or GPs. Of the 275 patient questionnaires, 192(70%) could be matched with a prescribing decision. NP patients had higher satisfaction levels than patients of GPs or PPs. More time describing treatment options was associated with increased satisfaction, adherence and greater perceived practitioner empathy. While defining, measuring and enabling the process of shared decision making remains challenging, it may have patient benefit.
Diversity of theW1gene encoding flavonoid 3′,5′-hydroxylase in white- and purple-flowered soybeans
Authors: Park Gyu Tae , Sundaramoorthy Jagadeesh , Park Jong-Beum , Lee Jeong Dong , Choi Kwang Shik , Kim Jeong Hoe , Seo Hak Soo , Park Soon-Ki , Song Jong Tae
Published: December 2014

Cultivated soybeans [Glycinemax(L.) Merr.] have various flower colours such as dark purple, purple, light purple, pink, magenta, near white and white. About one-third of the soybean accessions in the United States Department of Agriculture – Germplasm Resource Information Network (USDA-GRIN) Soybean Germplasm Collections have white flowers and are the second dominant accessions after the purple-flowered accessions. Earlier studies have shown that thew1recessive allele of theW1gene encoding flavonoid 3′,5′-hydroxylase produces white flowers. In the present study, we aimed to understand why the white-flowered accessions have become abundant among the cultivated soybeans and what their genetic and regional origin is. For this purpose, 99 landraces with white flowers and 39 landraces with purple flowers from eight Asian countries and Russia were analysed with regard to the nucleotide sequences of theW1locus. We not only found that thew1alleles of the 99 white-flowered landraces were identical to those of the white-flowered Williams 82, but also found that thesew1alleles displayed no polymorphism at all. By carrying out a phylogenetic analysis, we were able to identify a group withW1alleles from which thew1allele might have diverged.
Human in Vitro ADMET and Prediction of Human Pharmacokinetics and Toxicity Liabilities at the Discovery Stage
Authors: Tsaioun Katya
Published: December 2014

The drug development process has undergone a rapid evolution due to an expanding biological and chemical toolbox that allows novel target identification and rapid synthesis of a large number of diverse chemical libraries. The discovery of novel therapeutics is an inherently complex and interdisciplinary process, which requires close integration of scientists from several disciplines in an environment in which lessons are shared and taught across an organisation. However, traditionally the industry suffered from the lack of integration between chemists and biologists. Each discipline produced results that were scientifically valid, but frequently had little relevance to the likelihood of launching a commercial product. ADMET is an area that has emerged over the past 15 years and has created a unique interdisciplinary interface between medicinal chemists, biologists, formulators, toxicologists, clinicians and regulators. The implementation of ADMET profiling of drug candidates in conjunction with biological efficacy optimisation has dramatically reduced drug failures in clinical trials for pharmacokinetic reasons and has become a lingua franca between disciplines that are involved in drug development. The goal of an ADMET programme is to guide candidate selection by identifying molecules with optimal potency and drug-like properties. The purpose of this chapter is to briefly review the current state-of-the-art of ADMET and its scientific principles and describe some of the most prevalent ADMET strategies used to de-risk drug discovery programmes.
Highly sensitive fluorescent sensor for mercury based on hyperbranched rolling circle amplification
Authors: Chen Jinfeng , Tong Ping , Lin Yifen , Lu Wei , He Yu , Lu Minghua , Zhang Lan , Chen Guonan
Published: December 2014

A label-free hyperbranched rolling circle amplification (HRCA) based fluorescent sensor has been developed for Hg2+detection.
Efficient passivated phthalocyanine-quantum dot solar cells
Authors: Blas-Ferrando Vicente M. , Ortiz Javier , González-Pedro Victoria , Sánchez Rafael S. , Mora-Seró Iván , Fernández-Lázaro Fernando , Sastre-Santos Ángela
Published: December 2014

The power conversion efficiency of CdSe and CdS quantum dot sensitized solar cells is enhanced up to 45% for CdSe and 104% for CdS by passivation with an asymmetrically disulfide substituted phthalocyanine.
Thermal C–H borylation using a CO-free iron boryl complex
Authors: Mazzacano Thomas J. , Mankad Neal P.
Published: December 2014

Thermal C–H borylation was observed from a phosphine-supported iron boryl complex.
Expanding the toolbox of organic chemists: directed evolution of P450 monooxygenases as catalysts in regio- and stereoselective oxidative hydroxylation
Authors: Roiban Gheorghe-Doru , Reetz Manfred T.
Published: December 2014

Cytochrome P450 enzymes (CYPs) have been used for more than six decades as catalysts for the CH-activating oxidative hydroxylation of organic compounds with formation of added-value products.
Sulfonamide formation from sodium sulfinates and amines or ammonia under metal-free conditions at ambient temperature
Authors: Yang Kai , Ke Miaolin , Lin Yuanguang , Song Qiuling
Published: December 2014

A practical and highly efficient method for the construction of a variety of sulfonamides mediated by I2 was demonstrated. The reaction proceeds readily at room temperature using a variety of sodium sulfinates and amines or ammonia in water in a metal-, base-, ligand-, or additive-free protocol. Primary, secondary and tertiary sulfonamides were obtained in good to excellent yields with a broad range of substrate tolerability.
ESIPT based Hg2+and fluoride chemosensor for sensitive and selective ‘turn on’ red signal and cell imaging
Authors: Goswami Shyamaprosad , Maity Sibaprasad , Maity Annada C. , Das Avijit kumar , Pakhira Bholanath , Khanra Kalyani , Bhattacharyya Nandan , Sarkar Sabyasachi
Published: December 2014

An excited state intramolecular proton transfer (ESIPT) enabled fluorescent sensor phenanthroline diimino phenol (PDP) for Hg2+and F−has been designed and synthesized.
A convenient synthetic route to sulfonimidamides from sulfonamides
Authors: Chen Yantao , Gibson James
Published: December 2014

This one-pot synthesis of sulfonimidamides provides a new structural modification approach for sulfonamides, and might benefit drug discovery and development in the future.
Dynamic membrane patterning, signal localization and polarity in living cells
Authors: Zamparo M. , Chianale F. , Tebaldi C. , Cosentino-Lagomarsino M. , Nicodemi M. , Gamba A.
Published: December 2014

We review the molecular and physical aspects of the dynamic localization of signaling molecules on the plasma membranes of living cells.
Amorphous boron–indium–zinc-oxide active channel layers for thin-film transistor fabrication
Authors: Parthiban Shanmugam , Kwon Jang-Yeon
Published: December 2014

Thin-film transistor fabrication was investigated using a novel amorphous boron–indium–zinc-oxide active channel layer.
A dynamic ball compression test for understanding rock crushing
Authors: Huang S. , Liu H. , Xia K.
Published: December 2014

During crushing, rock particles are subjected to complicated loading. It is desired to establish the relation between the loading and the fragmentation parameters for better understanding rock crushing mechanism. In this work, a split Hopkinson pressure bar system in combination with high speed cameras is utilized in the dynamic ball compression test, in which the spherical rock sample is adopted to avoid the shape effect. Using elasticity theory, the loading rate and the dynamic indirect tensile strength are first calculated. With the aid of the moment-trap technique and high speed cameras, the surface energy is determined for each sample. The relations between the loading rate and the fragmentation parameters, i.e., the number of fragments and the surface energy are established. The application of this method to a granitic rock shows that it is flexible and can be applied to the crushing study of generic brittle solids.
Identification of a kinetic length scale which dictates alloy phase composition in Ni-Al interfaces on annealing at low temperatures
Authors: Swain Mitali , Singh Surendra , Basu Saibal , Bhattacharya Debarati , Gupta Mukul
Published: December 2014

Ni-aluminides are an important class of intermetallics from technological point of view. Ni-Al phase diagram has been studied in detail experimentally as well as theoretically. It is known that if annealed at low temperature, the first alloy phase is usually NiAl3 according to Bené's rule. It is also understood that heat of formation may get modified by local densities of the constituents forming the alloy. In this regard, it is important to identify a kinetic length scale for defining “local density” in a system. We have deposited ultrathin multilayers of Ni and Al of layer thickness in tens of nanometres with Ni:Al stoichiometric ratio as 3:1 and 1:3, respectively. Considering these stoichiometry, Ni3Al and NiAl3 are the thermodynamically favoured alloy phases in these samples. We used x-ray reflectivity, polarized neutron reflectivity, x-ray diffraction, and secondary ion mass spectroscopy to follow the alloy formation after annealing and identified the alloy phases at interfaces with nanometre resolution. Diffusion length of Ni and Al was obtained using Darken's law. Our results predict that ‘diffusion length’ is the unique length scale that connects kinetics to local density. In another interesting observation, using “virtual Kirkendall markers” at the interfaces, we showed asymmetry in consumption of Al for alloy formation, at Al on Ni (Al/Ni) and Ni on Al (Ni/Al) interfaces by comparing as-deposited and annealed states with respect to the markers.
Modeling light-induced charge transfer dynamics across a metal-molecule-metal junction: Bridging classical electrodynamics and quantum dynamics
Authors: Hu Zixuan , Ratner Mark A. , Seideman Tamar
Published: December 2014

We develop a numerical approach for simulating light-induced charge transport dynamics across a metal-molecule-metal conductance junction. The finite-difference time-domain method is used to simulate the plasmonic response of the metal structures. The Huygens subgridding technique, as adapted to Lorentz media, is used to bridge the vastly disparate length scales of the plasmonic metal electrodes and the molecular system, maintaining accuracy. The charge and current densities calculated with classical electrodynamics are transformed to an electronic wavefunction, which is then propagated through the molecular linker via the Heisenberg equations of motion. We focus mainly on development of the theory and exemplify our approach by a numerical illustration of a simple system consisting of two silver cylinders bridged by a three-site molecular linker. The electronic subsystem exhibits fascinating light driven dynamics, wherein the charge density oscillates at the driving optical frequency, exhibiting also the natural system timescales, and a resonance phenomenon leads to strong conductance enhancement.
Field emission properties of ZnO nanosheet arrays
Authors: Naik Kusha Kumar , Khare Ruchita , Chakravarty Disha , More Mahendra A. , Thapa Ranjit , Late Dattatray J. , Rout Chandra Sekhar
Published: December 2014

Electron emission properties of electrodeposited ZnO nanosheet arrays grown on Indium tin oxide coated glass substrates have been studied. Influence of oxygen vacancies on electronic structures and field emission properties of ZnO nanosheets are investigated using density functional theory. The oxygen vacancies produce unshared d electrons which form an impurity energy state; this causes shifting of Fermi level towards the vacuum, and so the barrier energy for electron extraction reduces. The ZnO nanosheet arrays exhibit a low turn-on field of 2.4 V/μm at 0.1 μA/cm2 and current density of 50.1 μA/cm2 at an applied field of 6.4 V/μm with field enhancement factor, β = 5812 and good field emission current stability. The nanosheet arrays grown by a facile electrodeposition process have great potential as robust high performance vertical structure electron emitters for future flat panel displays and vacuum electronic device applications.
Phase coexistence and transformations in field-cooled ternary piezoelectric single crystals near the morphotropic phase boundary
Authors: Luo Chengtao , Wang Yaojin , Wang Zhiguang , Ge Wenwei , Li Jiefang , Luo Haosu , Viehland D.
Published: December 2014

Structural phase transformations in (100)-oriented Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 single crystals have been investigated by X-ray diffraction. A cubic (C) → tetragonal (T) → monoclinic-C (MC) transformation sequence was observed in the field-cooled condition. Two phase coexistence regions of C + T and T + MC were found. In addition to an increase in the C → T phase transition temperature and a decrease of the T → MC one, a broadening of the coexistence regions was also found with increasing field. This broadening can be explained by the presence of polar nano regions within the C, T, and MC phase regions.
Accurate formula for dissipative interaction in frequency modulation atomic force microscopy
Authors: Suzuki Kazuhiro , Kobayashi Kei , Labuda Aleksander , Matsushige Kazumi , Yamada Hirofumi
Published: December 2014

Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.
Molecular crowding effect on dynamics of DNA-binding proteins search for their targets
Authors: Liu Lin , Luo Kaifu
Published: December 2014

DNA-binding proteins locate and bind their target sequences positioned on DNA in crowded environments, but the molecular crowding effect on this search process is not clear. Using analytical techniques and Langevin dynamics simulations in two dimensions (2D), we find that the essential physics for facilitated diffusion in 2D search and 3D search is the same. We observe that the average search times have minima at the same optimal nonspecific binding energy for the cases with and without the crowding particle. Moreover, the molecular crowding increases the search time by increasing the average search rounds and the one-dimensional (1D) sliding time of a round, but almost not changing the average 2D diffusion time of a round. In addition, the fraction of 1D sliding time out of the total search time increases with increasing the concentration of crowders. For 2D diffusion, the molecular crowding decreases the jumping length and narrows its distribution due to the cage effect from crowders. These results shed light on the role of facilitated diffusion in DNA targeting kinetics in living cells.
Superpoissonian shot noise in organic magnetic tunnel junctions
Authors: Cascales Juan Pedro , Hong Jhen-Yong , Martinez Isidoro , Lin Minn-Tsong , Szczepański Tomasz , Dugaev Vitalii K. , Barnaś Józef , Aliev Farkhad G.
Published: December 2014

Organic molecules have recently revolutionized ways to create new spintronic devices. Despite intense studies, the statistics of tunneling electrons through organic barriers remains unclear. Here, we investigate conductance and shot noise in magnetic tunnel junctions with 3,4,9,10-perylene-teracarboxylic dianhydride (PTCDA) barriers a few nm thick. For junctions in the electron tunneling regime, with magnetoresistance ratios between 10% and 40%, we observe superpoissonian shot noise. The Fano factor exceeds in 1.5–2 times the maximum values reported for magnetic tunnel junctions with inorganic barriers, indicating spin dependent bunching in tunneling. We explain our main findings in terms of a model which includes tunneling through a two level (or multilevel) system, originated from interfacial bonds of the PTCDA molecules. Our results suggest that interfaces play an important role in the control of shot noise when electrons tunnel through organic barriers.
Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur
Authors: Hussain Hanzala B. , Wilson Katie A. , Wetmore Stacey D.
Published: December 2014

Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.
Second language verb-argument constructions are sensitive to form, function, frequency, contingency, and prototypicality
Authors: Ellis Nick C. , O’Donnell Matthew B. , Römer Ute
Published: December 2014

We used free association tasks to investigate second language (L2) verb-argument constructions (VACs) and the ways in which their access is sensitive to statistical patterns of usage (verb type-token frequency distribution, VAC-verb contingency, verb-VAC semantic prototypicality). 131 German, 131 Spanish, and 131 Czech advanced L2 learners of English generated the first word that came to mind to fill the V slot in 40 sparse VAC frames such as ‘he __ across the …’, ‘it __ of the …’, etc. For each VAC, we compared these results with corpus analyses of verb selection preferences in 100 million words of usage and with the semantic network structure of the verbs in these VACs. For all language groups, multiple regression analyses predicting the frequencies of verb types generated for each VAC show independent contributions of (i) verb frequency in the VAC, (ii) VAC-verb contingency, and (iii) verb prototypicality in terms of centrality within the VAC semantic network. L2 VAC processing involves rich associations, tuned by verb type and token frequencies and their contingencies of usage, which interface syntax, lexis, and semantics.
Combined effects of age of onset and input on the development of different grammatical structures
Authors: Ågren Malin , Granfeldt Jonas , Thomas Anita
Published: December 2014

This study investigates the combined effects of Age of Onset of Acquisition (AOA) and quality and quantity of input on the development of three grammatical structures in French. In a longitudinal and multiple case study including successive (L2) Swedish-French bilingual children (n = 3), simultaneous (2L1) Swedish-French bilingual children (n = 3) and monolingual French children (n = 3), we examine the development of finite verb forms, object pronouns and subject-verb agreement. A distinction is made between structures that are early/ late in different modes of acquisition and less/more difficult. The operationalization of quantity and quality of input is based on individual input profiles. The results show that AOA affects the development of less difficult and early grammatical structures whereas AOA has no influence on more difficult structures that are acquired late. An effect of input is found in the 2L1 children, and in some of the L2 children. This effect is most clear with more difficult and late structures.
A holin and an endopeptidase are essential for chitinolytic protein secretion in Serratia marcescens
Authors: Hamilton Jaeger J. , Marlow Victoria L. , Owen Richard A. , Costa Marília de Assis Alcoforado , Guo Manman , Buchanan Grant , Chandra Govind , Trost Matthias , Coulthurst Sarah J. , Palmer Tracy , Stanley-Wall Nicola R. , Sargent Frank
Published: December 2014

Pathogenic bacteria adapt to their environment and manipulate the biochemistry of hosts by secretion of effector molecules. Serratia marcescens is an opportunistic pathogen associated with healthcare-acquired infections and is a prolific secretor of proteins, including three chitinases (ChiA, ChiB, and ChiC) and a chitin binding protein (Cbp21). In this work, genetic, biochemical, and proteomic approaches identified genes that were required for secretion of all three chitinases and Cbp21. A genetic screen identified a holin-like protein (ChiW) and a putative l-alanyl-d-glutamate endopeptidase (ChiX), and subsequent biochemical analyses established that both were required for nonlytic secretion of the entire chitinolytic machinery, with chitinase secretion being blocked at a late stage in the mutants. In addition, live-cell imaging experiments demonstrated bimodal and coordinated expression of chiX and chiA and revealed that cells expressing chiA remained viable. It is proposed that ChiW and ChiX operate in tandem as components of a protein secretion system used by gram-negative bacteria.
Was the Treatment of my Psychosis Fair and Just?
Authors: Chadwick Peter K.
Published: December 2014

In this article, the author reflects on his experience as a psychiatric patient, from the time he was admitted into the hospital in 1979 to his final discharge two years later. He reveals what he felt upon being told that he was diagnosed with a ‘schizophrenic episode;’ how talking about his problems and experiences with doctors, social workers, vicars, and chaplains helped in his recovery; and how the change from chlorpromazine to haloperidol as medication for his Tourette’s Syndrome after he left the hostel exerted a transformational effect on him. The author also talks about the research he conducted for a second PhD on delusions and on creativity and psychosis. Finally, he shares his thoughts about the medical model of psychiatry and its language and concludes that the psychiatric treatment he received was fair and just.
Identity and Agency
Authors: Graham George
Published: December 2014

Even the best moral principles for patient care and psychiatric ethics are likely to be misapplied or stumble in clinical practice, without sound and sensible recognition of how to understand the concepts of a patient’s personal identity and self-responsible or reflective agency. In this chapter I sketch an account of how personal identity and self-responsible agentive capacity are best described for understanding mental illness and in clinical practice. The account aims to be true to the subjective experience of reflective personhood and self-responsible agency as well as to the perspective of the mental health care clinician. Special attention is given to certain background moral principles that help to clinically frame the importance of patient identity and agency.
Roman Catholic Perspectives on Psychiatric Ethics
Authors: Mordini Emilio
Published: December 2014

The Roman Catholic Church is the oldest Western institution. Today, with more than 1.2 billion believers worldwide, it is the largest Christian community in the world. While Revelation in the other Abrahamic religions (Hebraism and Islamism) is chiefly law and social order (Torah, Shari’a), Revelation in Christianity is a creed in a person, Jesus Christ, a young Hebrew teacher, who used to live in Palestine about two thousand years ago, and was executed because of an accusation of blasphemy. That “marginal Jew,” for Christians, was God’s incarnation. Christians’ God is not then a ruler in human sense, on the contrary, he is someone unjustly put to death by his rulers. This has had deep influences on Christian moral teaching and psychiatric ethics. In this article, I will discuss specific Roman Catholic moral teaching concerning mental health. I will also illustrate a few cases in which Catholic moral perspectives may conflict with professional ethical standards.
5150
Authors: Reynolds Matthew E.
Published: December 2014

5150: On Unethical Privacy is an autobiographical piece where Matthew Reynolds recounts the situation wherein he was involuntarily committed shortly before his 21st birthday. He describes the situation that led to his psychotic break, and the problems his parents had, who he is very close to and have had a large place in his treatment. He was incapable of informed consent and, after being tranquilized, due to his manic depression, he slept for 36 hours wherein neither his parents, physician, psychiatrist, or anybody else were contacted. Finally, his main moral dilemma is discussed. He highlights just what went wrong ethically based on his own memory of events, which he learned of during and after his involuntary committal. His main argument is: “what use is a psychotic patient’s undeniable rights to privacy, if he is incapable of helping himself?” He notes how these systems backfired throughout.
Translation and Ethics in Psychiatry
Authors: Payne Roberta
Published: December 2014

In this article, the author reflects on the importance of translation and ethics in psychiatry based on his personal experience as a patient suffering from paranoid schizophrenia, alcoholism, and cancer. He talks about his sessions with psychiatrists he has met—what he terms their “human translating.” More specifically, he emphasizes the translation activities between patients and psychiatrists that matter to him, mainly because they are not only fraught with ethical dangers but also present an opportunity for both patient and psychiatrist to excel. The author recalls his exchange with a psychiatrist and how they translated each other’s words very well, and how their session illustrates many ethical qualities for which the doctor should be proud. Finally, he lists the qualities that he deems important and useful and accessible today as they were in 1990, including respect for the patient’s intellect and pace of thinking, appreciation for the patient’s pain, and absence of intellectual competition with the patient.
Contagion, Identity, Misinformation
Authors: Charland Louis C.
Published: December 2014

The evolution of the internet and associated social media pose novel challenges for psychiatric ethics. Issues surrounding emotional contagion, personal identity, and misinformation figure importantly among these new challenges, with important consequences for consumers of mental health services, as well as psychiatrists and other mental health professionals. The evolution of the internet and associated social media pose novel challenges for psychiatric ethics. Issues surrounding emotional contagion, personal identity, and misinformation figure importantly among these new challenges, with important consequences for consumers of mental health services, as well as psychiatrists and other mental health professionals.
Nonsuicidal Self-Injury and Its Relation to Suicidal Behavior
Authors: Franklin Joseph C. , Nock Matthew K.
Published: December 2014

Nonsuicidal self-injury (NSSI) is the direct and intentional destruction of one’s own body tissue in the absence of suicidal intent. Although NSSI itself is explicitly nonsuicidal, nearly half of individuals who engage in NSSI also engage in suicidal behavior, and nearly all individuals who engage in suicidal behavior also engage in NSSI. Moreover, recent studies suggest that NSSI is one of the strongest known predictors of future suicide attempts, even exceeding the predictive power of prior suicide attempts in some instances. In this chapter we review the basic features and correlates of NSSI, evaluate the evidence for traditional models of NSSI, and discuss how an emerging model of NSSI may provide insight into the strong association between NSSI and suicidal behavior. We conclude by recommending how to evaluate when NSSI is a behavioral emergency and by noting the most crucial future directions for research on this topic.