bluuebunny/crossref_metadata_2025 huggingface dataset:
Post‐diagnosis social networks, and lifestyle and treatment factors in the After Breast Cancer Pooling Project
Authors: Kroenke Candyce H , Michael Yvonne L. , Shu Xiao‐Ou , Poole Elizabeth M. , Kwan Marilyn L. , Nechuta Sarah , Caan Bette J. , Pierce John P. , Chen Wendy Y.
Published: January 2016

Objective

Larger social networks have been associated with better breast cancer survival. To investigate potential mediators, we evaluated associations of social network size and diversity with lifestyle and treatment factors associated with prognosis.

Methods

We included 9331 women from the After Breast Cancer Pooling Project who provided data on social networks within approximately two years following diagnosis. A social network index was derived from information about the presence of a spouse or intimate partner, religious ties, community participation, friendship ties, and numbers of living relatives. Diversity was assessed as variety of ties, independent of size. We used logistic regression to evaluate associations with outcomes and evaluated whether effect estimates differed using meta‐analytic techniques.

Results

Associations were similar across cohorts though analyses of smoking and alcohol included US cohorts only because of low prevalence of these behaviors in the Shanghai cohort. Socially isolated women were more likely to be obese (OR = 1.21, 95% CI:1.03–1.42), have low physical activity (<10 MET‐hours/week, OR = 1.55, 95% CI:1.36–1.78), be current smokers (OR = 2.77, 95% CI:2.09‐3.68), and have high alcohol intake (≥15 g/d, OR = 1.23, 95% CI:1.00–1.51), compared with socially integrated women. Among node positive cases from three cohorts, socially isolated women were more likely not to receive chemotherapy (OR = 2.10, 95% CI:1.30–3.39); associations differed in a fourth cohort. Other associations (nonsignificant) were consistent with less intensive treatment in socially isolated women. Low social network diversity was independently associated with more adverse lifestyle, but not clinical, factors.

Conclusions

Small, less diverse social networks measured post‐diagnosis were associated with more adverse lifestyle factors and less intensive cancer treatment. Copyright © 2016 John Wiley & Sons, Ltd.
A de novo protein confers copper resistance in Escherichia coli
Authors: Hoegler Kenric J. , Hecht Michael H.
Published: January 2016

To survive environmental challenges, biological systems rely on proteins that were selected by evolution to function in particular cellular and conditional settings. With the advent of protein design and synthetic biology, it is now possible to construct novel proteins that are not biased by eons of selection in natural hosts. The availability of these sequences prompts us to ask whether natural biological organisms can use naïve—non‐biological—proteins to enhance fitness in stressful environments. To address this question, we transformed a library of DNA sequences encoding ∼1.5 × 106 binary patterned de novo proteins into E. coli, and selected for sequences that enable growth in concentrations of copper that would otherwise be toxic. Several novel sequences were discovered, and one of them, called Construct K (ConK), was studied in detail. Cells expressing ConK accumulate approximately 50% less copper than control cells. The function of ConK does not involve an oxidase, nor does it require two of the best characterized copper efflux systems. However, the ability of ConK to rescue cells from toxic concentrations of copper does require an active proton motive force. Further selections for growth in higher concentrations of copper led to the laboratory evolution of variants of ConK with enhanced levels of activity in vivo. These studies demonstrate that novel proteins, unbiased by evolutionary history in the natural world, can enhance the fitness of biological systems.

Synopsis: Living systems evolve to adapt to potentially lethal environmental changes. This normally involves repurposing existing genetic information (i.e. sequences that were selected by billions of years of evolution). Here we show that a completely de novo protein, not derived from nature, can enable E. coli cells to grow in otherwise toxic concentrations of copper, demonstrating that living systems also have the capacity to incorporate and protopurpose entirely novel genetic information.
NMR reveals structural rearrangements associated to substrate insertion in nucleotide‐adding enzymes
Authors: Mohanty Biswaranjan , Geralt Michael , Wüthrich Kurt , Serrano Pedro
Published: January 2016

The protein NP_344798.1 from Streptococcus pneumoniae TIGR4 exhibits a head and base‐interacting neck domain architecture, as observed in class II nucleotide‐adding enzymes. Although it has less than 20% overall sequence identity with any member of this enzyme family, the residues involved in substrate‐recognition and catalysis are highly conserved in NP_344798.1. NMR studies showed binding affinity of NP_344798.1 for nucleotides and revealed μs to ms time scale rate processes involving residues constituting the active site. The results thus obtained indicate that large‐amplitude rearrangements of regular secondary structures facilitate the penetration of the substrate into the occluded nucleotide‐binding site of NP_344798.1 and, by inference based on sequence and structural homology, probably a wide range of other nucleotide‐adding enzymes.
Analysis of amino acid substitutions in AraC variants that respond to triacetic acid lactone
Authors: Frei Christopher S. , Wang Zhiqing , Qian Shuai , Deutsch Samuel , Sutter Markus , Cirino Patrick C.
Published: January 2016

The Escherichia coli regulatory protein AraC regulates expression of ara genes in response to l‐arabinose. In efforts to develop genetically encoded molecular reporters, we previously engineered an AraC variant that responds to the compound triacetic acid lactone (TAL). This variant (named “AraC‐TAL1”) was isolated by screening a library of AraC variants, in which five amino acid positions in the ligand‐binding pocket were simultaneously randomized. Screening was carried out through multiple rounds of alternating positive and negative fluorescence‐activated cell sorting. Here we show that changing the screening protocol results in the identification of different TAL‐responsive variants (nine new variants). Individual substituted residues within these variants were found to primarily act cooperatively toward the gene expression response. Finally, X‐ray diffraction was used to solve the crystal structure of the apo AraC‐TAL1 ligand‐binding domain. The resolved crystal structure confirms that this variant takes on a structure nearly identical to the apo wild‐type AraC ligand‐binding domain (root‐mean‐square deviation 0.93 Å), suggesting that AraC‐TAL1 behaves similar to wild‐type with regard to ligand recognition and gene regulation. Our results provide amino acid sequence–function data sets for training and validating AraC modeling studies, and contribute to our understanding of how to design new biosensors based on AraC.
The diversity of H3 loops determines the antigen‐binding tendencies of antibody CDR loops
Authors: Tsuchiya Yuko , Mizuguchi Kenji
Published: January 2016

Of the complementarity‐determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen‐binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen‐binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen‐binding tendencies of all the CDR loops.
Crystal structure of the FK506 binding domain of human FKBP25 in complex with FK506
Authors: Prakash Ajit , Rajan Sreekanth , Yoon Ho Sup
Published: January 2016

Human FKBP25 (hFKBP25) is a nuclear immunophilin and interacts with several nuclear proteins, hence involving in many nuclear events. Similar to other FKBPs, FK506 binding domain (FKBD) of hFKBP25 also binds to immunosuppressive drugs such as rapamycin and FK506, albeit with a lower affinity for the latter. The molecular basis underlying this difference in affinity could not be addressed due to the lack of the crystal structure of hFKBD25 in complex with FK506. Here, we report the crystal structure of hFKBD25 in complex with FK506 determined at 1.8 Å resolution and its comparison with the hFKBD25–rapamycin complex, bringing out the microheterogeneity in the mode of interaction of these drugs, which could possibly explain the lower affinity for FK506.
Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases
Authors: Taberman Helena , Parkkinen Tarja , Rouvinen Juha
Published: January 2016

The Gfo/Idh/MocA protein family contains a number of different proteins, which almost exclusively consist of NAD(P)‐dependent oxidoreductases that have a diverse set of substrates, typically pyranoses. In this study, to clarify common structural features that would contribute to their function, the available crystal structures of the members of this family have been analyzed. Despite a very low sequence identity, the central features of the three‐dimensional structures of the proteins are surprisingly similar. The members of the protein family have a two‐domain structure consisting of a N‐terminal nucleotide‐binding domain and a C‐terminal α/β‐domain. The C‐terminal domain contributes to the substrate binding and catalysis, and contains a βα‐motif with a central α‐helix carrying common essential amino acid residues. The β‐sheet of the α/β‐domain contributes to the oligomerization in most of the proteins in the family.
Electron energy distribution in Si/TiN and Si/Ru hybrid floating gates with hafnium oxide based insulators for charge trapping memory devices
Authors: Cerbu F. , Andreev D. V. , Lisoni J. , Breuil L. , Afanas'ev V. V. , Stesmans A. , Houssa M.
Published: January 2016

Scaling the planar NAND flash cells to the 20 nm node and beyond mandates introduction of inter‐gate insulators with high dielectric constant (κ). However, because these insulators provide a smaller electron barrier at the interface with the poly‐Si floating gate, the program window and the retention properties of these scaled cells are jeopardized. To reduce the charge loss from the floating to the control gate, one may consider the introduction of a hybrid floating gate (HFG) structure comprised of poly‐Si and a high work function (WF) metal, e.g., TiNx (x ∼ 1; WF ∼ 4.7 eV) or Ru (WF ∼ 5.3 eV). However, the very HFG concept is based on the assumption that electron trapping occurs inside the HFG stack rather than on traps present in the high‐κ insulator. To examine this critical hypothesis, we analyzed the energy distribution of electrons trapped in flash cells with poly‐Si(2 nm)/TiN (6 nm)/Hf0.8Al0.2Ox(19 nm, κ ∼ 15–19)/TiNx (10 nm) and Si(2 nm)/Ru (1 nm)/Hf0.8Al0.2Ox(5 nm)/Al2O3 (5 nm)/Hf0.8Al0.2Ox (5 nm)/TiNx (10 nm) trapping gate stacks using the exhaustive photo‐depopulation spectroscopy. We found that trapped electron energy levels show a broad distribution (± 0.3 eV) centred at ∼3.2 eV below the oxide conduction band. The energy onset of electron de‐trapping at ∼2.8 eV matches the TiNx/HfO2 barrier height found from internal photoemission experiments, indicating that electrons are predominantly trapped inside the HFG.
Nanostructure, thermoelectric properties, and transport theory of V2VI3 and V2VI3/IV–VI based superlattices and nanomaterials
Authors: Dankwort Torben , Hansen Anna‐Lena , Winkler Markus , Schürmann Ulrich , Koenig Jan D. , Johnson David C. , Hinsche Nicki F. , Zahn Peter , Mertig Ingrid , Bensch Wolfgang , Kienle Lorenz
Published: January 2016

The scope of this work is to review the thermoelectric properties, the microstructures, and their correlation with theoretical calculations and predictions for recent chalcogenide based materials. The main focus is put on thin multilayered Bi2Te3, Sb2Te3 films, and bulk V2VI3/IV–VI mixed systems. For all films a systematic characterization of the thermoelectric properties as well as the micro‐ and nanostructure was performed. The degree of crystallinity of the multilayered films varied from epitaxial systems to polycrystalline films. Other multilayered thin films revealed promising thermoelectric properties. (SnSe)1.2TiSe2 thin films with rotational disorder yielded the highest Seebeck coefficient published to date for analogous materials. For bulk V2VI3/IV–VI mixed systems insides are given into a complete “material to module” process resulting in a high performance thermoelectric generator using (1–x)(GeTe) x(Bi2Se0.2Te2.8) (x = 0.038). Cyclic heating of this system with x = 0.063 resulted in a drastic change of the micro‐ and nanostructure observed by ex situ and in situ X‐ray diffraction (XRD) and transmission electron microscopy (TEM). Consequently a degradation of ZT at 450 °C from ∼2.0 to ∼1.0 was observed, while samples with x = 0.038 showed a stable ZT of 1.5.
Growth of cobalt nanoparticles in Co–Al2O3 thin films deposited by RF sputtering
Authors: Goyal Rajan , Lamba S. , Annapoorni S.
Published: January 2016

Cobalt nanoparticles in Co–Al2O3 films have been deposited by rf‐magnetron co‐sputtering of cobalt and alumina on Si <100> substrate. X‐ray diffraction (XRD) patterns were collected at room temperature for the as‐deposited as well as annealed thin films. The appearance of (002) reflection in XRD pattern indicates the presence of hcp‐Co nanoparticles with oriented growth along c‐axis. The scanning electron microscopy (SEM) result shows the formation of truncated hexagonal nanoparticles at elevated temperatures. Rutherford backscattering (RBS) has also been performed to estimate the film thickness. The effect of grain growth, after annealing at higher temperature, on surface roughness has also been studied using atomic force microscopy (AFM). Magnetic measurements carried out at room temperature both in parallel and perpendicular configuration reveal easy axis orientation along in‐plane direction. However, a large value of coercivity along c‐axis was attributed to the pinning due to the presence of oxide at grain boundaries. The pinning effect was also confirmed by the way of generating hysteresis using Monte Carlo simulation in a system of randomly distributed clusters of single domain interacting particles.
Characterization of local Al‐contacts by light beam induced current measurements and their verification by 2D simulation using flexPDE
Authors: Horbelt Renate , Micard Gabriel , Keller Philipp , Hahn Giso , Job Reinhart , Terheiden Barbara
Published: January 2016

In recent years the relevance of passivated emitter and rear contact solar cells for industrial application increased due to significantly higher cell efficiencies compared to full area back surface field solar cells. However, the formation of local Al contacts is particularly sensitive to the manufacturing process parameters. Under non‐optimized conditions, the eutectic in local Al contacts is missing and so‐called voids are formed. So far, their impact onto the electrical parameters of the solar cells is not fully understood, mainly because of their difficult spatially resolved detection. Within this work the application of scanning acoustic microscopy circumvents this difficulty and allows a classification of local contacts in terms of “voids” or “filled contacts” on large cell area. The passivation quality of the BSF in the local contacts is investigated in detail through the local internal quantum efficiency (IQE) measured by light beam induced current (LBIC). It is found that there is a large spreading for the IQE values, attributed to a variation in BSF layer thickness. In addition, LBIC measurements of voids are fitted by 2D simulations, according to a detailed modelling of the surface recombination velocities (SRV) in local contacts. The final model is based on a non‐uniform SRV in the void's vicinity, attributed to laser damage close to the interface. It is demonstrated that the electrical parameters of the solar cell are affected by voids only when their surface is not sufficiently passivated by a local BSF.
Effect of Al doping on the structural and optical properties of electrodeposited SnS thin films
Authors: Kafashan Hosein , Ebrahimi‐Kahrizsangi Reza , Jamali‐Sheini Farid , Yousefi Ramin
Published: January 2016

Al‐doped SnS thin films with different Al concentrations were deposited on fluorine doped tin oxide (FTO) substrate from aqueous solution containing 2 mM SnCl2 and 20 mM Na2S2O3 and various amounts of 5 mM AlCl3 solution. The pH, temperature, time, and deposition potential (E) of the solution were kept at 2.1, 60 °C, 30 min and −1 V, respectively. The deposited films were characterized by X‐ray diffraction (XRD), field emission scanning electron microscopy (FESEM), photoluminescence (PL), and UV‐Vis. XRD patterns obviously indicated that the synthesized Al‐doped SnS were polycrystalline with orthorhombic structure and by increasing the amount of Al concentration, the crystallinity was increased. The FESEM images showed that the morphology of the nanostructures was changed with increasing Al content. PL and UV‐Vis analysis were used to investigate the optical properties of materials. The PL spectra showed a red shift with increasing of Al concentration.
Temperature dependent studies of capped magnetic nanowires using XMCD
Authors: Duignan M. J. , Cunniffe J. P. , Glans P.‐A. , Arenholz E. , McGuinness C. , McGilp J. F.
Published: January 2016

Aligned cobalt nanowires, 1, 2, and 3 atoms wide, were grown on platinum (997) surfaces under UHV conditions and capped with five monolayers of gold. X‐ray magnetic circular dichroism (XMCD) measurements were performed at the L2,3 edges of Co. Element specific magnetic hysteresis loops were measured as a function of temperature and coercivities were extracted. The easy axis of magnetization was confirmed to be perpendicular to the (111) terrace for all samples. The temperature dependence of the coercivity, which varies by an order‐of‐magnitude over a 150 K temperature range for the 1‐atom‐wide wire, was found to be well described by the Gaunt “strong” domain wall pinning model for all three wires. The observation that capping increases the Curie temperature of the 1‐atom‐wide nanowire by at least 270 K, together with the strong temperature dependence of the coercivity and the perpendicular magnetic anisotropy, may have important implications for the technological application of low dimensional, nanoscale magnetic materials.
Raman and photoluminescence properties of ZnO nanowires grown by a catalyst‐free vapor‐transport process using ZnO nanoparticle seeds
Authors: Güell Frank , Martínez‐Alanis Paulina Raquel , Khachadorian Sevak , Rubio‐García Javier , Franke Alexander , Hoffmann Axel , Santana Guillermo
Published: January 2016

We report the synthesis of ZnO nanowires by a catalyst‐free vapor‐transport process on SiO2/Si substrates. A modification of the method was performed using small ZnO nanoparticles (∼5 nm) in low concentration suspensions. The use of dichloromethane or toluene in the suspensions influences the nanoparticle distribution over the surface. The obtained nanowires have diameters ranging from 20 to 100 nm and lengths from 0.5 to 1 µm. Raman scattering results show a narrow (∼7 cm−1) full width at half maximum of the E2high optical phonon mode, which demonstrate a good‐crystal quality of the ZnO nanowires obtained. Room temperature photoluminescence measurements show a broad emission band in the visible range at 430–830 nm, which is attributed to intrinsic defects. A notable decrease of this visible band was achieved making this method suitable for almost defect‐free ZnO nanowires. The photoluminescence results at 5 K demonstrate the role of surface defects as responsible for the visible band.
Numerical study of self‐ and heterodiffusion on clean unreconstructed and missing‐row reconstructed Pt(110) surfaces
Authors: Matrane I. , Elkoraychy E. , Sbiaai K. , Mazroui M. , Boughaleb Y.
Published: January 2016

This article sheds light on the investigation of the diffusion and the adsorption of Pt and Au adatoms on the ideal (1 × 1) and the missing‐row structures ((1 × 2), (1 × 3), and (1 × 4)) of Pt(110) surfaces. This study is performed by using quenched molecular dynamics simulations combined with an interatomic potential derived from the embedded‐atom method (EAM). For each geometry, we have considered the homo‐ and heterogeneous systems: Pt/Pt and Au/Pt. The multilayer and adatom relaxation trends and adatom bond lengths with the first nearest neighbors were examined. We have found that the atomic relaxation is quantitatively different for all configurations. The static energy barriers for hopping and adsorption energy were calculated for all configurations and both systems. Thus, the analysis of our results provides interesting insights and a tentative idea about the geometry influence on the adsorption and the diffusion on the missing‐row reconstructed surfaces. Our numerical results were compared with some experimental and theoretical data available in the literature and a good agreement was achieved.
Half‐Heusler compounds with a 1 eV (1.7 eV) direct band gap, lattice‐matched to GaAs (Si), for solar cell application: A first‐principles study
Authors: Belmiloud N. , Boutaiba F. , Belabbes A. , Ferhat M. , Bechstedt F.
Published: January 2016

A systematic theoretical study of the structural and electronic properties of new half‐Heusler compounds is performed to find the appropriate target key physical parameters for photovoltaic application. As a result, five ternary half‐Heusler compounds ScAgC, YCuC, CaZnC, NaAgO, and LiCuS are studied by density functional theory for potential applications in multi‐junction solar cells. The calculated formation enthalpies indicate that these materials are thermodynamically stable. Using state‐of‐the‐art modified Becke–Johnson exchange potential approximation, we find a direct band gap close to 1 eV (1.88 eV) for ScAgC, YCuC, CaZnC, NaAgO (LiCuS) being quasi‐lattice matched to GaAs (Si). In addition, the band offsets between half‐Heusler compounds and GaAs (Si) and their consequences for heterostructures are derived using the modified Tersoff method for the branch‐point energy. Furthermore, the elastic constants and phonon dispersion curves are calculated. They indicate the respective mechanical and dynamical stability of these half‐Heusler compounds.
Diamond‐SAW devices: a reverse fabrication method
Authors: Mukherjee Debarati , Oliveira Filipe J. , Silva Rui F. , Carreira José F. , Rino Luis , Correia Maria R. , Rotter Shlomo Z. , Alves Luis N. , Mendes Joana C.
Published: January 2016

Surface acoustic wave (SAW) devices are key components in modern wireless communication systems. Besides being used as reflective delay lines, filters or resonators, SAW devices can be used as sensors and fixed‐code identification tags. Due to their high‐acoustic velo‐city, diamond films can be combined with piezoelectric materials to fabricate diamond‐based SAW devices with potential for high frequency applications. This paper presents results of coating commercial SAW delay lines with diamond films. The films were deposited on lithium niobate under different conditions in a hot filament chemical vapour deposition system. Seeding was performed using 6‐12 μm diamond grit and 20‐30 nm nano‐diamond particles based suspensions. After tuning the deposition conditions, dies of 74 MHz delay lines were coated with diamond. The quality, morphology and conformability of the coatings were evaluated by scanning electron microscopy (SEM) and Raman spectroscopy. The integrity of the interdigitated transducers (IDTs) after deposition was evaluated by SEM. S‐parameters of as‐bought and diamond‐coated dies were measured using a network analyser. Although the frequency response is attenuated after diamond deposition, integrity of the IDTs and the operating principle of the devices are kept intact. These preliminary results open the door to a simplified fabrication procedure of diamond‐based SAW devices. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The Significance of Tinospora crispa in Treatment of Diabetes Mellitus
Authors: Thomas Alex , Rajesh E. K. , Kumar D. Suresh
Published: January 2016

Tinospora crispa is a medicinal plant belonging to the botanical family Menispermiaceae. The plant is widely distributed in Southeast Asia and the northeastern region of India. A related species Tinospora cordifolia is used in Ayurveda for treating a large spectrum of diseases. Traditional healers of Thailand, Malaysia, Guyana, Bangladesh and the southern Indian province of Kerala use this plant in the treatment of diabetes. Many diterpenes, triterpenes, phytosteroids, alkaloids and their glycosides have been isolated from T. crispa. Cell culture and animal studies suggest that the herb stimulates secretion of insulin from β‐cells. It also causes dose‐dependent and time‐dependent enhancement of glucose uptake in muscles. However, in view of the reported hepatotoxicity, this herb may be used with caution. This article reviews the animal studies and human clinical trials carried out using this herb. Areas of future research are also identified. Copyright © 2016 John Wiley & Sons, Ltd.
6‐Gingerol Mediates its Anti Tumor Activities in Human Oral and Cervical Cancer Cell Lines through Apoptosis and Cell Cycle Arrest
Authors: Kapoor Vaishali , Aggarwal Sadhna , Das Satya N.
Published: January 2016

6‐Gingerol, a potent nutraceutical, has been shown to have antitumor activity in different tumors, although its mechanism of action is not well understood. In this study, we evaluated antitumor activities of 6‐gingerol on human oral (SCC4, KB) and cervical cancer (HeLa) cell lines with or without wortmannin, rapamycin, and cisplatin. Tumor cell proliferation was observed using 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H tetrazolium, inner salt assay, cell cycle analysis by propidium iodide labeling and flow cytometry, apoptosis by Annexin‐V binding assay, and caspase activity by chemiluminescence assay. 6‐Gingerol showed dose‐dependent cytotoxicity in all three cell lines. Combinations of 6‐gingerol with wortmannin and cisplatin showed additive effects, while with rapamycin, it showed 50% cytotoxicity that was equivalent to IC50 of 6‐gingerol alone. Treatment with 6‐gingerol resulted in G2‐phase arrest in KB and HeLa cells and S‐phase arrest in SCC4 cells. 6‐Gingerol, wortmannin, and rapamycin treatment showed almost two‐fold higher expression of caspase 3 in all cell lines. The results imply that 6‐gingerol either alone or in combination with PI‐3 K inhibitor and cisplatin may provide better therapeutic effects in oral and cervical carcinoma. Thus, 6‐gingerol appears to be a safe and potent chemotherapeutic/chemopreventive compound acting through cell cycle arrest and induction of apoptosis in human oral and cervical tumor cells. Copyright © 2016 John Wiley & Sons, Ltd.
Precipitation representation over a two‐year period in regional reanalysis
Authors: Jermey P. M. , Renshaw R. J.
Published: January 2016

Precipitation is a critical aspect of climate. In Europe, extreme precipitation events are costly and represent a threat to life. Evidence suggests the frequency and intensity of these events is increasing in Europe and therefore long‐period datasets that can represent such events accurately are required. Precipitation is challenging to represent in gridded models and therefore is not well trusted in relatively low‐resolution global reanalyses. For the first time, the European Reanalyses and Observations For Monitoring (EURO4M) project has produced high‐resolution atmospheric regional reanalyses of Europe that improve representation of precipitation. These are based on operational forecast systems at the Met Office and the Swedish Meteorological and Hydrological Institute (HIRLAM). The improvement of quality of precipitation in the regional reanalysis datasets over their parent global reanalysis is demonstrated here, together with a discussion on the difficulties of validation of gridded precipitation. It is shown that regional reanalyses show particular improvement in representing high‐threshold events. It is also shown that higher resolution, time‐varying data assimilation and direct assimilation of precipitation all contribute to improving representation of precipitation. Resolution is of particular importance when representing extreme events.
Kelvin–Helmholtz waves in extratropical cyclones passing over mountain ranges
Authors: Medina Socorro , Houze Robert A.
Published: January 2016

Kelvin–Helmholtz billows with horizontal scales of 3–4 km have been observed in midlatitude cyclones moving over the Italian Alps and the Oregon Cascades when the atmosphere was mostly statically stable with high amounts of shear and Ri < 0.25. In one case, data from a mobile radar located within a windward facing valley documented a layer in which the shear between down‐valley flow below 1.2 km and strong upslope cross‐barrier flow above was large. Several episodes of Kelvin–Helmholtz waves were observed within the shear layer. The occurrence of the waves appears to be related to the strength of the shear: when the shear attained large values, an episode of billows occurred, followed by a sharp decrease in the shear. The occurrence of large values of shear and Kelvin–Helmholtz billows over two different mountain ranges suggests that they may be important features occurring when extratropical cyclones with statically stable flow pass over mountain ranges.
On homogeneous ice formation in liquid clouds
Authors: Kärcher B. , Seifert A.
Published: January 2016

Primary ice formation by homogeneous freezing of supercooled cloud droplets in moist adiabatic air parcels is investigated theoretically and by means of numerical simulations. Dependencies of nucleated ice crystal number and size and associated freezing temperatures are systematically studied as functions of updraught speed and cloud droplet number and size. Droplet freezing temperatures range between 235 and 239 K, depending on dynamical forcing and liquid water content. Vertical resolutions on the order of 10 m are required in numerical cloud models to resolve the thin layers in which homogeneous ice formation processes unfold. Only a fraction of droplets freeze in weakly forced clouds. Small‐scale variability in updraught speeds encountered by air parcels containing supercooled cloud droplets results in broad ice crystal number distributions when sampled across a parcel ensemble. The strong dynamical control of ice initiation in tropospheric clouds initiates homogeneous freezing in the presence of heterogeneous ice nuclei even at moderate mean updraught speeds, suggesting that such particles play a limited role in affecting droplet freezing in cold convective cloud outflow regions. These findings have important implications for microphysical and optical properties of condensed‐phase convective detrainment, setting the stage for the evolution of anvil cirrus.
Three‐dimensional cut‐cell modelling for high‐resolution atmospheric simulations
Authors: Yamazaki Hiroe , Satomura Takehiko , Nikiforakis Nikolaos
Published: January 2016

Owing to the recent rapid development of computer technology, the resolution of atmospheric numerical models has increased substantially. With the use of next‐generation supercomputers, atmospheric simulations using horizontal grid intervals of (100) m or less will gain popularity. At such high resolution, more of the steep gradients in mountainous terrain will be resolved, which may result in large truncation errors in those models using terrain‐following coordinates. In this study, a new three‐dimensional (3D) Cartesian coordinate non‐hydrostatic atmospheric model is developed. A cut‐cell representation of topography based on finite‐volume discretization is combined with a cell‐merging approach, in which small cut cells are merged with neighbouring cells either vertically or horizontally. In addition, a block‐structured mesh‐refinement technique is introduced to achieve a variable resolution on the model grid, with the finest resolution occurring close to the terrain surface. The model successfully reproduces a flow over a 3D bell‐shaped hill that shows a good agreement with the flow predicted by the linear theory. The ability of the model to simulate flows over steep terrain is demonstrated using a hemisphere‐shaped hill. The advantage of a locally refined grid around the hill, with cut cells at the terrain surface, is also demonstrated. The model reproduces smooth mountain waves propagating over varying grid resolution without introducing large errors associated with the change of mesh resolution. At the same time, the model shows a good scalability on the locally refined grid.
Quantum chemical modeling of the addition reactions of 1‐n‐phenylpropyl radicals to C60 fullerene
Authors: Diniakhmetova Diana Radikovna , Friesen Anna Konstantinovna , Kolesov Sergey Viktorovich
Published: January 2016

Modeling of the addition of various radicals to C60 fullerene is currently an active research area. However, the radicals considered are not able to adequately model polymeric radicals. In this work, we have performed a theoretical study of the possible reactions of C60 fullerene with 1‐n‐phenylpropyl radicals, which are used to model polystyrene radicals. Several possible ways of subsequent addition of up to four 1‐phenylpropyl radicals to C60 have been analyzed, the structures of the intermediates have been defined and thermal properties, such as the activation enthalpies of the corresponding reactions, have been calculated using density functional theory with the approximation of PBE/3z. It is shown that the topology of the spin density distribution on the fullerenyl radical causes regioselectivity for further radical addition. According to the energetic characteristics of the reactions, we assume the possibility of formation of products of one‐, two‐, three‐, and four‐ addition of the growth radical to the fullerene core in radical polymerization of styrene in the presence of C60 fullerene. © 2016 Wiley Periodicals, Inc.
Theoretical study of global and local reactivities of coumarin and its hydroxylated derivatives
Authors: Melendez Francisco J. , Durand‐Niconoff J. Sergio , Domínguez‐Ortiz Miguel A. , García‐Barradas Oscar , Caballero Norma A. , González Enrique
Published: January 2016

Coumarins are bioactive substances of the benzo‐α‐pyrone family, which have shown antioxidant, antiviral, anti‐inflammatory and antitumor activities, among others. 7‐Hydroxycoumarin and 6,7‐dihydroxycoumarin (esculetin) are two coumarin derivatives that have been reported to exhibit antitumor activity, but the action mechanism underlying this activity remains unknown. In this work, to elucidate this mechanism, a theoretical study of the local and global electronic reactivity properties of a series of hydroxylated and dihydroxylated coumarin derivatives with possible antitumor action is performed using Density Functional Theory in aqueous solution. The substitution by one or two hydroxyl groups in the benzene ring of coumarin produces better charge‐donor than charge‐acceptor compounds. All the studied compounds are generally stable in water and exhibit permanent polarization in the solvent. With one hydroxyl substitution, 7‐hydroxycoumarin is the most polar and polarizable derivative, whereas 5,7‐dihydroxycoumarin is the most polar and polarizable compound with two hydroxyl substitutions. 5,7‐Dihydroxycoumarin is suggested to possess antitumor activity. © 2016 Wiley Periodicals, Inc.
Theoretical study of atoms by the electronic kinetic energy density and stress tensor density
Authors: Nozaki Hiroo , Ichikawa Kazuhide , Tachibana Akitomo
Published: January 2016

The electronic structure of atoms in the first, second, and third periods were analyzed using the electronic kinetic energy density and stress tensor density, which are local quantities motivated by quantum field theoretic consideration, specifically the rigged quantum electrodynamics. The zero surfaces of the electronic kinetic energy density, which are called as the electronic interfaces, of the atoms were computed. It was found that their sizes exhibited clear periodicity and were comparable to the conventional atomic and ionic radii. The electronic stress tensor density and its divergence, tension density, of the atoms, were also computed and how their electronic structures were characterized by them was discussed. © 2016 Wiley Periodicals, Inc.
Structures and basicity of LiNOH (N = 1 − 5) species
Authors: Srivastava Ambrish Kumar , Misra Neeraj
Published: January 2016

LiOH is one of the strong bases among neutral molecules. What about hydroxides of small Lin (n = 2 − 5) clusters? The addition of a single atom to a cluster sometimes has dramatic effects on its reactivity. This fact motivated us to perform an ab initio MP2/6‐311++G(d, p) investigation on LinOH species (n = 1 − 5). These LinOH species are stabilized by both ionic as well as covalent interactions, and are found to be stable against elimination of LiOH and OH. We have determined their gas and aqueous phase basicity by considering hypothetical protonation reactions. The calculated proton affinities of LinOH (n ≥ 2) suggest their reduced basicity as compared to LiOH by 50–100 kJ/mol. The NBO charges and the highest occupied molecular orbitals also reveal the electride and alkalide characteristics of Li2OH and Li3OH, respectively. © 2016 Wiley Periodicals, Inc.
Homonuclear chalcogen–chalcogen bond interactions in complexes pairing YO3 and YHX molecules (Y = S, Se; X = H, Cl, Br, CCH, NC, OH, OCH3): Influence of substitution and cooperativity
Authors: Esrafili Mehdi D. , Mohammadian‐Sabet Fariba
Published: January 2016

MP2/aug‐cc‐pVTZ calculations are performed on complexes of YO3 (Y = S, Se) with a series of electron‐donating chalcogen bases YHX (X = H, Cl, Br, CCH, NC, OH, OCH3). These complexes are formed through the interaction of a positive electrostatic potential region (π‐hole) on the YO3 molecule with the negative region in YHX. Interaction energies of the binary O3Y⋅⋅⋅YHX complexes are in the range of −4.37 to −12.09 kcal/mol. The quantum theory of atoms in molecules and the natural bond orbital analysis were applied to characterize the nature of interactions. It was found that the formation and stability of these binary complexes are ruled mainly by electrostatic effects, although the electron charge transfer from YHX to YO3 unit also seems to play an important role. In addition, mutual influence between the Y⋅⋅⋅N and Y⋅⋅⋅Y interactions is studied in the ternary HCN⋅⋅⋅O3Y⋅⋅⋅YHX complexes. The results indicate that the formation of a Y⋅⋅⋅N interaction tends to weaken Y⋅⋅⋅Y bond in the ternary systems. Although the Y⋅⋅⋅Y interaction is weaker than the Y⋅⋅⋅N one, however, both types of interactions seem to compete with each other in the HCN⋅⋅⋅O3Y⋅⋅⋅YHX complexes. © 2016 Wiley Periodicals, Inc.
Use of robot‐specific resources and operating room times: the case of Telelap Alf‐X robotic hysterectomy
Authors: Rossitto Cristiano , Gueli Alletti Salvatore , Romano Federica , Fiore Alessandra , Coretti Silvia , Oradei Marco , Ruggeri Matteo , Cicchetti Americo , Marchetti Marco , Fanfani Francesco , Scambia Giovanni
Published: January 2016

Introduction

The aim of this study was to identify, quantify and evaluate the use of robotic materials and operating theatre times in Telelap ALF‐X robotic hysterectomy.

Materials and methods

Cost analysis was performed on 81 patients who underwent a Telelap ALF‐X robotic hysterectomy. Data were collected during a phase II study trial conducted at the University Hospital A. Gemelli, Catholic University, Rome. According to micro‐costing technique, surgical team costs, materials and operating theatre usage were recorded during each surgical intervention. Cost data were provided by the hospital's accounting office. Probabilistic sensitivity analysis was carried out in order to test the robustness of the results by assuming an Inv‐norm random variable.

Results

The base case analysis showed a cost/patient of €3391.82. The new robotic device requires a low consumption of robotic materials. Sensitivity analysis showed that the most sensitive cost driver was use of the operating theatre.

Conclusion

This study shows that Telelap ALF‐X robotic hysterectomy is feasible and safe and could offer specific advantages in terms of cost. Copyright © 2016 John Wiley & Sons, Ltd.
Patient‐specific assessment of dysmorphism of the femoral head–neck junction: a statistical shape model approach
Authors: Khanduja Vikas , Baelde Nick , Dobbelaere Andreas , Van Houcke Jan , Li Hao , Pattyn Christophe , Audenaert Emmanuel A.
Published: January 2016

Background

Objective quantification of anatomical variations about the femur head–neck junction in pre‐operative planning for surgical intervention in femoro‐acetabular impingement is problematic, as no clear definition of average normal anatomy for a specific subject exists.

Methods

We have defined the normal‐equivalent of a subject's anatomy by using a statistical shape model and geometric shape optimization for finding correspondences, while excluding the femoral head–neck junction during the fitting procedure. The presented technique was evaluated on a cohort of 20 patients.

Results

Difference in α‐angle measurement between the actual morphology and the predicted normal‐equivalent, averaged 1.3° (SD 1.7°) in the control group versus 8° (SD 7.3°) in the patient group (p < 0.05).

Conclusions

Defining normal equivalent anatomy is effective in quantifying anatomical dysmorphism of the femoral head–neck junction and as such can improve presurgical analysis of patients diagnosed with femoro‐acetabular impingement. Copyright © 2016 John Wiley & Sons, Ltd.
On distributed reactive power and storage control on microgrids
Authors: Cortés Andres , Martínez Sonia
Published: January 2016

This manuscript develops a dual decomposition algorithm for the distributed control of reactive power and charging/discharging rates in microgrids with distributed solar generation and \storage capacities. Our setting considers physical constraints inherent to storage systems and voltage regulation constraints with the objective of minimizing a cost function that encompasses two aspects: the total cost of the active power consumed by the microgrid and its associated transmission losses over a finite time horizon. We provide a complete analysis of the convergence of the proposed algorithm and introduce a novel approach for the distributed approximation of the voltage prediction over the power grid. Simulations demonstrate the performance of the dual decomposition algorithm on a particular microgrid case. Copyright © 2016 John Wiley & Sons, Ltd.
Adaptive perimeter traffic control of urban road networks based on MFD model with time delays
Authors: Haddad Jack , Mirkin Boris
Published: January 2016

In this work, we focus on two main themes: (i) developing a more realistic macroscopic fundamental diagram‐based nonlinear control‐oriented model of urban traffic networks with time delays incorporated into model structure; and (ii) based on its linearized form subject to input delay, designing two new perimeter control architectures for one aggregated urban traffic region under unknown bounded external disturbances and parameter uncertainties. The feedback control laws design is performed in the context of model reference adaptive control approach. Simulation results based on a linearized model are also presented, which demonstrate in this case desired closed‐loop adaptive control system performance. Copyright © 2015 John Wiley & Sons, Ltd.
Potentiodynamic anodizing of aluminum alloys in Cr(VI)‐free electrolytes
Authors: van Put M. A. , Abrahami S. T. , Elisseeva O. , de Kok J. M. M. , Mol J. M. C. , Terryn H.
Published: January 2016

The aerospace industry progressively develops alternatives for chromic acid anodizing, because Cr(VI) is known to be toxic and carcinogenic. In this work, potentiodynamic anodizing of AA1050 and AA2024‐T3 clad was performed in phosphoric‐sulfuric acid (PSA) and sulfuric acid (SAA). All anodizing cycles started with a linear voltage sweep, followed by a constant voltage, or a dynamic voltage. Current density responses were recorded during each anodizing cycle and comprised different stages, which could be related to growth phases of the anodic oxide film. Interesting differences were found between cycles with an intermediate increase in anodizing voltage versus cycles with an intermediate decrease in voltage. Cycles including an increase in voltage resulted in higher anodic oxide formation efficiencies because of a temporary exceedance of the steady state current (recovery period) directly after the voltage step. Also, a sudden decrease in voltage led to distinct border between a fine and coarse region in the film morphology, while a sudden increase in voltage did not. For prolonged anodizing in PSA, coarsening of the upper film part was observed because of the high solubility of Al2O3 in phosphoric acid. Pore walls close to the outer surface did not only get thinner, but completely dissolved in the electrolyte. Consequently, anodic oxide formation efficiencies were higher for SAA than for PSA. Copyright © 2016 John Wiley & Sons, Ltd.
Quantitative ToF‐SIMS depth profiling of a multi‐phased III–V semiconductor matrix via the analysis of secondary cluster ions
Authors: Gong Bin , Marjo Christopher E.
Published: January 2016

An approach for quantification of time‐of‐flight (ToF)‐SIMS depth profiling data is demonstrated using an independently characterised multilayer, an AlGaAs/GaAs stack from certified reference material BAM‐L200. The sample was studied with a Bi cluster ion source as the analysis projectile and a Cs+ sputter beam. Under these conditions, the negative secondary ion yield is significantly enhanced, especially for cluster ions comprising all possible elemental combinations. Each cluster ion carries a number of sputtered neutrals so if all cluster ions containing an element could be collected and identified, a large population of secondary neutrals will be included in the analysis, improving the analytical signal and approaching a ‘matrix‐effect‐free’ measurement. By measuring the intensities of a range of secondary cluster ions of AliGajAsk− where i, j, k are integers such 0, 1, 2, and so on, the atomic counts for each major element were accumulated based on the elemental contents of those cluster ions. The summed atomic counts were then normalised without using the more common approach of applying relative sensitivity factors. The resulting elemental depth profiles show an excellent match to the structure and stoichiometry of the sample. The quantitative relationship of various elements and the interface appearance derived by this cluster ion approach are strongly competitive to the results available from XPS. Copyright © 2016 John Wiley & Sons, Ltd.