bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of PEGylation on Multivalent Binding: A Surface Plasmon Resonance and Isothermal Titration Calorimetry Study with Structurally Diverse PEG‐Dendritic GATG Copolymers
Authors: Fernandez‐Villamarin Marcos , Sousa‐Herves Ana , Correa Juan , Munoz Eva Maria , Taboada Pablo , Riguera Ricardo , Fernandez‐Megia Eduardo
Published: February 2016

A general synthetic strategy to polyethylene glycol (PEG)‐dendritic block copolymers of the GATG (gallic acid–triethylene glycol) family is described from commercially available PEG of different molecular weights and architectures. Glycosylation of the resulting azide‐terminated copolymers with fucose by copper‐catalyzed azide–alkyne cycloaddition (CuAAC) afforded a toolbox to study the effect of PEG on the multivalent binding with the lectin UEA‐I by surface plasmon resonance (SPR, on surface) and isothermal titration calorimetry (ITC, in solution). Our results indicate that PEG reduces the affinity of glycodendrimers towards lectins by steric hindrance in a molecular‐weight‐dependent fashion. Great differences were observed as a function of the PEG architecture, with diblock PEG‐dendritic copolymers benefiting from a positive entropic contribution (PEG folding), not seen in the dendritic‐PEG‐dendritic systems. The self‐inflicted steric stabilization of the PEGylated copolymers onto lectin clusters reveals the necessity of additional competitive experiments to fully assess the antiadhesive properties of PEG in biological environments.
Nanostructure‐Dependent Ratiometric NIR Fluorescence Enabled by Ordered Dye Aggregation
Authors: Charron Danielle M. , Chen Juan , Zheng Gang
Published: February 2016

Nanocarriers incorporating therapeutic and imaging agents within a single nanostructure are emerging tools for drug development and treatment planning. Additional information can be provided using activatable fluorescence that dynamically reports nanocarrier disruption and drug release. Dual‐wavelength activation encodes a unique fluorescence signal for each nanocarrier state, enabling use of ratiometric imaging to measure the proportion of intact and disrupted nanocarriers within tissues. Here we investigate dual‐wavelength activation using a single dye whose optical properties are intricately linked to the nanocarrier structure. Natural bacteriochlorophyll incorporated within a compact lipoprotein nanocarrier forms ordered dye aggregates with red‐shifted fluorescence emission from 765 nm to 825 nm. We demonstrate that bacteriochlorophyll‐ordered aggregation is a feasible strategy to distinguish intact and disrupted theranostic nanocarriers by ratiometric fluorescence imaging.
The Role of Resonant Vibrations in Electronic Energy Transfer
Authors: Malý Pavel , Somsen Oscar J. G. , Novoderezhkin Vladimir I. , Mančal Tomáš , van Grondelle Rienk
Published: February 2016

Nuclear vibrations play a prominent role in the spectroscopy and dynamics of electronic systems. As recent experimental and theoretical studies suggest, this may be even more so when vibrational frequencies are resonant with transitions between the electronic states. Herein, a vibronic multilevel Redfield model is reported for excitonically coupled electronic two‐level systems with a few explicitly included vibrational modes and interacting with a phonon bath. With numerical simulations the effects of the quantized vibrations on the dynamics of energy transfer and coherence in a model dimer are illustrated. The resonance between the vibrational frequency and energy gap between the sites leads to a large delocalization of vibronic states, which then results in faster energy transfer and longer‐lived mixed coherences.
The Equally Important Role of Adenine Derivatives to That of Pyrimidine Derivatives in Near‐0 eV Electron‐Induced DNA Lesions
Authors: Wang Shoushan , Zhao Peiwen , Zhang Changzhe , Bu Yuxiang
Published: February 2016

The role of adenine (A) derivatives in DNA damage is scarcely studied due to the low electron affinity of base A. Experimental studies demonstrate that low‐energy electron (LEE) attachment to adenine derivatives complexed with amino acids induces barrier‐free proton transfer producing the neutral N7‐hydrogenated adenine radicals rather than conventional anionic species. To explore possible DNA lesions at the A sites under physiological conditions, probable bond ruptures in two models—N7‐hydrogenated 2′‐deoxyadenosine‐3′‐monophosphate (3′‐dA(N7H)MPH) and 2′‐deoxyadenosine‐5′‐monophosphate (5′‐dA(N7H)MPH), without and with LEE attachment—are studied by DFT. In the neutral cases, DNA backbone breakage and base release resulting from C3′−O3′ and N9−C1′ bond ruptures, respectively, by an intramolecular hydrogen‐transfer mechanism are impossible due to the ultrahigh activation energies. On LEE attachment, the respective C3′−O3′ and N9−C1′ bond ruptures in [3′‐dA(N7H)MPH]− and [5′‐dA(N7H)MPH]− anions via a pathway of intramolecular proton transfer (PT) from the C2′ site of 2′‐deoxyribose to the C8 atom of the base moiety become effective, and this indicates that substantial DNA backbone breaks and base release can occur at non‐3′‐end A sites and the 3′‐end A site of a single‐stranded DNA in the physiological environment, respectively. In particular, compared to the results of previous theoretical studies, not only are the electron affinities of 3′‐dA(N7H)MPH and 5′‐dA(N7H)MPH comparable to those of hydrogenated pyrimidine derivatives, but also the lowest energy requirements for the C3′−O3′ and N9‐glycosidic bond ruptures in [3′‐dA(N7H)MPH]− and [5′‐dA(N7H)MPH]− anions, respectively, are comparable to those for the C3′−O3′ and N1‐glycosidic bond cleavages in corresponding anionic hydrogenated pyrimidine derivatives. Thus, it can be concluded that the role of adenine derivatives in single‐stranded DNA damage is equally important to that of pyrimidine derivatives in an irradiated cellular environment.
Inhibition of AKT promotes FOXO3a-dependent apoptosis in prostate cancer
Authors: Das T P , Suman S , Alatassi H , Ankem M K , Damodaran C
Published: February 2016

Growth factor-induced activation of protein kinase-B (PKB), also known as AKT, induces pro-survival signaling and inhibits activation of pro-apoptotic signaling molecules including the Forkhead box O-3a (FOXO3a) transcription factor and caspase in transformed prostate cells in vitro. Earlier we reported that Withaferin-A (WA), a small herbal molecule, induces pro-apoptotic response-4 (Par-4) mediated apoptosis in castration-resistant prostate cancer (CRPC) cells. In the present study, we demonstrate that inhibition of AKT facilitates nuclear shuttling of FOXO3a where it regulates Par-4 transcription in CRPC cells. FOXO3a is upstream of Par-4 signaling, which is required for induction of apoptosis in CRPC cells. Promoter bashing studies and Ch-IP analysis confirm a direct interaction of FOXO3a and Par-4; a sequential deletion of FOXO3a-binding sites in the Par-4 promoter fails to induce Par-4 activation. To confirm these observations, we either overexpressed AKT or silenced FOXO3a activation in CRPC cells. Both methods inhibit Par-4 function and apoptosis is significantly compromised. In xenograft tumors derived from AKT-overexpressed CRPC cells, FOXO3a and Par-4 expression is downregulated, leading to aggressive tumor growth. Oral administration of WA to mice with xenograft tumors restores FOXO3a-mediated Par-4 functions and results in inhibited tumor growth. Finally, an inverse correlation of nuclear localization of AKT expression corresponds to cytoplasmic Par-4 localization in human prostate tissue array. Our studies suggest that Par-4 is one of the key transcriptional targets of FOXO3a, and Par-4 activation is required for induction of apoptosis in CRPC cells. Activation of FOXO3a appears to be an attractive target for the treatment of CRPC and molecules such as WA can be explored further for the treatment of CRPC.
Correction: Corrigendum: Dnmts and Tet target memory-associated genes after appetitive olfactory training in honey bees
Authors: Biergans Stephanie D. , Galizia C. Giovanni , Reinhard Judith , Claudianos Charles
Published: February 2016

Scientific Reports 5: Article number: 16223; published online: 04 November 2015; updated: 25 February 2016. This Article contains an error in the order of the Figures. Figures 3 and 4 were published as Figures 4 and 3 respectively. The correct Figures 3 and 4 appear below as Figs 1 and 2 respectively.
Universal structures of normal and pathological heart rate variability
Authors: Gañán-Calvo Alfonso M. , Fajardo-López Juan
Published: February 2016

The circulatory system of living organisms is an autonomous mechanical system softly tuned with the respiratory system and both developed by evolution as a response to the complex oxygen demand patterns associated with motion. Circulatory health is rooted in adaptability, which entails an inherent variability. Here, we show that a generalized N-dimensional normalized graph representing heart rate variability reveals two universal arrhythmic patterns as specific signatures of health one reflects cardiac adaptability and the other the cardiac-respiratory rate tuning. In addition, we identify at least three universal arrhythmic profiles whose presences raise in proportional detriment of the two healthy ones in pathological conditions (myocardial infarction; heart failure; and recovery from sudden death). The presence of the identified universal arrhythmic structures together with the position of the centre of mass of the heart rate variability graph provide a unique quantitative assessment of the health-pathology gradient.
In a demanding task, three-handed manipulation is preferred to two-handed manipulation
Authors: Abdi Elahe , Burdet Etienne , Bouri Mohamed , Himidan Sharifa , Bleuler Hannes
Published: February 2016

Equipped with a third hand under their direct control, surgeons may be able to perform certain surgical interventions alone; this would reduce the need for a human assistant and related coordination difficulties. However, does human performance improve with three hands compared to two hands? To evaluate this possibility, we carried out a behavioural study on the performance of naive adults catching objects with three virtual hands controlled by their two hands and right foot. The subjects could successfully control the virtual hands in a few trials. With this control strategy, the workspace of the hands was inversely correlated with the task velocity. The comparison of performance between the three and two hands control revealed no significant difference of success in catching falling objects and in average effort during the tasks. Subjects preferred the three handed control strategy, found it easier, with less physical and mental burden. Although the coordination of the foot with the natural hands increased trial after trial, about two minutes of practice was not sufficient to develop a sense of ownership towards the third arm.
Diffusion and self-assembly of C60 molecules on monolayer graphyne sheets
Authors: Ozmaian Masoumeh , Fathizadeh Arman , Jalalvand Morteza , Ejtehadi Mohammad Reza , Allaei S. Mehdi Vaez
Published: February 2016

The motion of a fullerene (C60) on 5 different types of graphyne is studied by all-atom molecular dynamics simulations and compared with former studies on the motion of C60 on graphene. The motion shows a diffusive behavior which consists of either a continuous motion or discrete movements between trapping sites depending on the type of the graphyne sheet. For graphyne-4 and graphyne-5, fullerenes could detach from the surface of the graphyne sheet at room temperature which was not reported for similar cases on graphene sheets. Collective motion of a group of fullerenes interacting with a graphyne studied and it is shown that fullerenes exhibit stable assemblies. Depending on the type of graphyne, these assemblies can have either single or double layers. The mobility of the assembled structures is also dependent on the type of the graphyne sheet. The observed properties of the motion suggests novel applications for the complexes of fullerene and monolayer graphynes.
Cyclodextrin-Based Metal-Organic Nanotube as Fluorescent Probe for Selective Turn-On Detection of Hydrogen Sulfide in Living Cells Based on H2S-Involved Coordination Mechanism
Authors: Xin Xuelian , Wang Jingxin , Gong Chuanfang , Xu Hai , Wang Rongming , Ji Shijie , Dong Hanxiao , Meng Qingguo , Zhang Liangliang , Dai Fangna , Sun Daofeng
Published: February 2016

Hydrogen sulfide (H2S) has been considered as the third biologically gaseous messenger (gasotransmitter) after nitric oxide (NO) and carbon monoxide (CO). Fluorescent detection of H2S in living cells is very important to human health because it has been found that the abnormal levels of H2S in human body can cause Alzheimer’s disease, cancers and diabetes. Herein, we develop a cyclodextrin-based metal-organic nanotube, CD-MONT-2, possessing a {Pb14} metallamacrocycle for efficient detection of H2S. CD-MONT-2′ (the guest-free form of CD-MONT-2) exhibits turn-on detection of H2S with high selectivity and moderate sensitivity when the material was dissolved in DMSO solution. Significantly, CD-MONT-2′ can act as a fluorescent turn-on probe for highly selective detection of H2S in living cells. The sensing mechanism in the present work is based on the coordination of H2S as the auxochromic group to the central Pb(II) ion to enhance the fluorescence intensity, which is studied for the first time.
Detection of substrate-dependent conformational changes in the P450 fold by nuclear magnetic resonance
Authors: Colthart Allison M. , Tietz Drew R. , Ni Yuhua , Friedman Jessica L. , Dang Marina , Pochapsky Thomas C.
Published: February 2016

Cytochrome P450 monooxygenases typically catalyze the insertion of one atom of oxygen from O2 into unactivated carbon-hydrogen and carbon-carbon bonds, with concomitant reduction of the other oxygen atom to H2O by NAD(P)H. Comparison of the average structures of the camphor hydroxylase cytochrome P450cam (CYP101) obtained from residual dipolar coupling (RDC)-restrained molecular dynamics (MD) in the presence and absence of substrate camphor shows structural displacements resulting from the essential collapse of the active site upon substrate removal. This collapse has conformational consequences that extend across the protein structure, none of which were observed in analogous crystallographic structures. Mutations were made to test the involvement of the observed conformational changes in substrate binding and recognition. All of the mutations performed based upon the NMR-detected perturbations, even those remote from the active site, resulted in modified substrate selectivity, enzyme efficiency and/or haem iron spin state. The results demonstrate that solution NMR can provide insights into enzyme structure-function relationships that are difficult to obtain by other methods.
Molecular Form Differences Between Prostate-Specific Antigen (PSA) Standards Create Quantitative Discordances in PSA ELISA Measurements
Authors: McJimpsey Erica L.
Published: February 2016

The prostate-specific antigen (PSA) assays currently employed for the detection of prostate cancer (PCa) lack the specificity needed to differentiate PCa from benign prostatic hyperplasia and have high false positive rates. The PSA calibrants used to create calibration curves in these assays are typically purified from seminal plasma and contain many molecular forms (intact PSA and cleaved subforms). The purpose of this study was to determine if the composition of the PSA molecular forms found in these PSA standards contribute to the lack of PSA test reliability. To this end, seminal plasma purified PSA standards from different commercial sources were investigated by western blot (WB) and in multiple research grade PSA ELISAs. The WB results revealed that all of the PSA standards contained different mass concentrations of intact and cleaved molecular forms. Increased mass concentrations of intact PSA yielded higher immunoassay absorbance values, even between lots from the same manufacturer. Standardization of seminal plasma derived PSA calibrant molecular form mass concentrations and purification methods will assist in closing the gaps in PCa testing measurements that require the use of PSA values, such as the % free PSA and Prostate Health Index by increasing the accuracy of the calibration curves.
Influence of Particle Size Distribution on the Performance of Ionic Liquid-based Electrochemical Double Layer Capacitors
Authors: Rennie Anthony J. R. , Martins Vitor L. , Smith Rachel M. , Hall Peter J.
Published: February 2016

Electrochemical double layer capacitors (EDLCs) employing ionic liquid electrolytes are the subject of much research as they promise increased operating potentials, and hence energy densities, when compared with currently available devices. Herein we report on the influence of the particle size distribution of activated carbon material on the performance of ionic liquid based EDLCs. Mesoporous activated carbon was ball-milled for increasing durations and the resultant powders characterized physically (using laser diffraction, nitrogen sorption and SEM) and investigated electrochemically in the form of composite EDLC electrodes. A bi-modal particle size distribution was found for all materials demonstrating an increasing fraction of smaller particles with increased milling duration. In general, cell capacitance decreased with increased milling duration over a wide range of rates using CV and galvanostatic cycling. Reduced coulombic efficiency is observed at low rates (<25 mVs−1) and the efficiency decreases as the volume fraction of the smaller particles increases. Efficiency loss was attributed to side reactions, particularly electrolyte decomposition, arising from interactions with the smaller particles. The effect of reduced efficiency is confirmed by cycling for over 15,000 cycles, which has the important implication that diminished performance and reduced cycle life is caused by the presence of submicron-sized particles.
A miniature closed-loop gas chromatography system
Authors: Hsieh Hao-Chieh , Kim Hanseup
Published: February 2016

This work introduces a circulatory chromatography column system that adaptively magnifies the effective column length and the resultant separation capacity.
Fluorescent chiral fluorinated liquid crystalline polymers containing rare earth complexes
Authors: Yao Bing , Cong Yuehua , Zhang Baoyan
Published: February 2016

Chiral liquid-crystalline polymers with lanthanide complexes distributed in helical matrices can emit soft red or green light when being excited.
Cellulase stabilization by crosslinking with ethylene glycol dimethacrylate and evaluation of its activity including in a water–ionic liquid mixture
Authors: Jamwal Shivani , Chauhan Ghanshyam S. , Ahn Jou-Hyeon , Reddy N. S.
Published: February 2016

Synthesis of immobilized enzymes via crosslinking is an easy route to develop a biocatalyst with enhanced activity and recyclability.
In situ measurement of contact angles and surface tensions of interfacial nanobubbles in ethanol aqueous solutions
Authors: Zhao Binyu , Wang Xingya , Wang Shuo , Tai Renzhong , Zhang Lijuan , Hu Jun
Published: February 2016

Nanobubbles present larger contact angles and lower surface tensions in ethanol aqueous solutions than the corresponding values at the macroscopic scale.
The continuous fabrication of mechanochromic fibers
Authors: Zhang Jing , He Sisi , Liu Lianmei , Guan Guozhen , Lu Xin , Sun Xuemei , Peng Huisheng
Published: February 2016

New mechanochromic fibers are being continuously fabricated by coating concentrated core–shell microspheres onto elastic polymer fibers with low cost and high efficiency.
Facile preparation of graphite particles fully coated with thin Ag shell layers for high performance conducting and electromagnetic shielding composite materials
Authors: Wang Yilong , Luo Shigang , Ren Ke , Zhao Suling , Chen Zhihong , Li Wei , Guan Jianguo
Published: February 2016

The facile synthesis of dense NSH on NGPs facilitates the fabrication of NG@Ag CSCPs with low silver content and high performances.
Stability and electronic properties of new inorganic perovskites from high-throughput ab initio calculations
Authors: Körbel Sabine , Marques Miguel A. L. , Botti Silvana
Published: February 2016

Ab initio high-throughput materials screening of inorganic perovskites yields candidates for applications in photovoltaics, ferroelectrics, magnetoelectrics, and as transparent contacts.
Low-cost microarray thin-film electrodes with ionic liquid gel-polymer electrolytes for miniaturised oxygen sensing
Authors: Lee Junqiao , Silvester Debbie S.
Published: February 2016

The use of a platinum microarray thin-film electrode together with a gellified ionic-liquid has shown to be highly favourable for long-term oxygen gas sensing.
Copper(i)-catalyzed olefination of N-sulfonylhydrazones with sulfones
Authors: Xu Shuai , Gao Yunpeng , Chen Ri , Wang Kang , Zhang Yan , Wang Jianbo
Published: February 2016

A new methylenation method has been developed, which is based on the Cu(i)-catalyzed reaction of N-sulfonylhydrazones with dimethyl sulfone.
Enantioselective total synthesis and structural reassignment of (+)-alsmaphorazine E via a traceless chirality transfer strategy
Authors: Yu Kuan , Gao Beiling , Liu Zhaobo , Ding Hanfeng
Published: February 2016

The first enantioselective total synthesis of (+)-alsmaphorazine E was described, which led to the structural reassignment of the title molecule.
Hierarchical carbon nanopetal/polypyrrole nanocomposite electrodes with brush-like architecture for supercapacitors
Authors: Cherusseri Jayesh , Kar Kamal K.
Published: February 2016

Hierarchical 3D nanocomposite electrodes with tube brush-like morphology are synthesized by electrochemically depositing polypyrrole on carbon nanopetal-coated carbon fibers.
Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein
Authors: Kim Tae Wu , Yang Cheolhee , Kim Youngmin , Kim Jong Goo , Kim Jeongho , Jung Yang Ouk , Jun Sunhong , Lee Sang Jin , Park Sungjun , Kosheleva Irina , Henning Robert , van Thor Jasper J. , Ihee Hyotcherl
Published: February 2016

Structural changes in global conformation and chromophore of photoactive yellow protein are probed in real time by time-resolved X-ray solution scattering and transient absorption spectroscopy.
Correction: Stability of thin film glasses of toluene and ethylbenzene formed by vapor deposition: an in situ nanocalorimetric study
Authors: Leon-Gutierrez Edgar , Sepúlveda Alfonso , Garcia Gemma , Clavaguera-Mora Maria Teresa , Rodríguez-Viejo Javier
Published: February 2016

Correction for ‘Stability of thin film glasses of toluene and ethylbenzene formed by vapor deposition: an in situ nanocalorimetric study’ by Edgar Leon-Gutierrez et al., Phys. Chem. Chem. Phys., 2010, 12, 14693–14698.
Palladacycles of unsymmetrical (N,C−,E) (E = S/Se) pincers based on indole: their synthesis, structure and application in the catalysis of Heck coupling and allylation of aldehydes
Authors: Singh Mahabir P. , Saleem Fariha , Rao Gyandshwar K. , Kumar S. , Joshi Hemant , Singh Ajai K.
Published: February 2016

Palladacycles of Schiff bases of 1-(2-phenylsulfanyl/selenylethyl)-1H-indole-3-carbaldehyde with benzyl amine catalyze Heck coupling and allylation at 0.1–0.3 and 1.0 mol% respectively.
Genome-wide targets identification of “core” pluripotency transcription factors with integrated features in human embryonic stem cells
Authors: Li Leijie , Chen Zhaobin , Zhang Liangcai , Liu Guiyou , Hua Jinlian , Jia Lianghui , Liao Mingzhi
Published: February 2016

LMA: A novel model to predict target of pluripotency transcriptional factors in human embryonic stem cell.
One-pot relay catalysis: divergent synthesis of furo[3,4-b]indoles and cyclopenta[b]indoles from 3-(2-aminophenyl)-1,4-enynols
Authors: Manisha Manisha , Dhiman Seema , Mathew Jopaul , Ramasastry S. S. V.
Published: February 2016

Described herein a divergent strategy for the synthesis of furo[3,4-b]indolesviaa sequential Ag(i)/Bi(iii)/Pd(ii) catalysis and cyclopenta[b]indolesviaa one-pot Ag(i)/Brønsted acid relay catalysis, starting from the easily accessible 3-(2 aminophenyl)-4-pentenyn-3-ols.
Chemical vapour deposition of rhenium disulfide and rhenium-doped molybdenum disulfide thin films using single-source precursors
Authors: Al-Dulaimi Naktal , Lewis David J. , Zhong Xiang Li , Azad Malik M. , O'Brien Paul
Published: February 2016

Polycrystalline thin films of rhenium disulfide (ReS2) and the alloys Mo1−xRexS2(0 ≤x≤ 0.06) have been deposited by aerosol-assisted chemical vapour deposition (AA-CVD) using [Re(μ-SiPr)3(SiPr)6] and [Mo(S2CNEt2)4] at 475 °C.
Cerebral Medulloepithelioma: A Rare Aggressive Brain Tumor in Child – A Case Report
Authors: Kindra Aman , Mansoori Nasim , Sinha Sumit , Bhaskar Suryanarayanan , Agarwal Poojan , Bansil Rohit
Published: February 2016

Medulloepithelioma of the central nervous system (CNS) is a rare primitive neuroectodermal tumor (PNET) usually occurring in early childhood. It is a highly aggressive tumor with poor outcomes despite aggressive treatment. The ideal treatment appears to be gross total surgical resection, followed by radiation therapy. We report a case of a cerebral medulloepithelioma in a child with an aggressive tumor growth despite the gross total resection, who is surviving 1 year after diagnosis.
Density-functional theory molecular dynamics simulations of a-HfO2/Ge(100)(2 × 1) and a-ZrO2/Ge(100)(2 × 1) interface passivation
Authors: Chagarov E. A. , Porter L. , Kummel A. C.
Published: February 2016

The structural properties of a-HfO2/Ge(2 × 1)-(001) and a-ZrO2/Ge(2 × 1)-(001) interfaces were investigated with and without a GeOx interface interlayer using density-functional theory (DFT) molecular dynamics (MD) simulations. Realistic a-HfO2 and a-ZrO2 samples were generated using a hybrid classical-DFT MD “melt-and-quench” approach and tested against experimental properties. The oxide/Ge stacks were annealed at 700 K, cooled to 0 K, and relaxed providing the system with enough freedom to form realistic interfaces. For each high-K/Ge stack type, two systems with single and double interfaces were investigated. All stacks were free of midgap states; however, stacks with a GeOx interlayer had band-edge states which decreased the band gaps by 0%-30%. These band-edge states were mainly produced by under-coordinated Ge atoms in GeOx layer or its vicinity due to deformation, intermixing, and bond-breaking. The DFT-MD simulations show that electronically passive interfaces can be formed either directly between high-K dielectrics and Ge or with a monolayer of GeO2 if the processing does not create or properly passivate under-coordinated Ge atoms and Ge’s with significantly distorted bonding angles. Comparison to the charge states of the interfacial atoms from DFT to experimental x-ray photoelectron spectroscopy results shows that while most studies of gate oxide on Ge(001) have a GeOx interfacial layer, it is possible to form an oxide/Ge interface without a GeOx interfacial layer. Comparison to experiments is consistent with the dangling bonds in the suboxide being responsible for midgap state formation.
High resolution spectroscopy of six SOCl2 isotopologues from the microwave to the far-infrared
Authors: Martin-Drumel M. A. , Roucou A. , Brown G. G. , Thorwirth S. , Pirali O. , Mouret G. , Hindle F. , McCarthy M. C. , Cuisset A.
Published: February 2016

Despite its potential role as an atmospheric pollutant, thionyl chloride, SOCl2, remains poorly characterized in the gas phase. In this study, the pure rotational and ro-vibrational spectra of six isotopologues of this molecule, all detected in natural abundance, have been extensively studied from the cm-wave band to the far-infrared region by means of three complementary techniques: chirped-pulse Fourier transform microwave spectroscopy, sub-millimeter-wave spectroscopy using frequency multiplier chain, and synchrotron-based far-infrared spectroscopy. Owing to the complex line pattern which results from two nuclei with non-zero spins, new, high-level quantum-chemical calculations of the hyperfine structure played a crucial role in the spectroscopic analysis. From the combined experimental and theoretical work, an accurate semi-experimental equilibrium structure (reSE) of SOCl2 has been derived. With the present data, spectroscopy-based methods can now be applied with confidence to detect and monitor this species, either by remote sensing or in situ.
Molecular energies from an incremental fragmentation method
Authors: Meitei Oinam Romesh , Heßelmann Andreas
Published: February 2016

The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.
Structure and spectroscopic properties of low-lying states of the HOC(O)O radical
Authors: Linguerri Roberto , Puzzarini Cristina , Francisco Joseph S.
Published: February 2016

The HOC(O)O radical is a product of the reaction of HOCO radicals with oxygen atoms. The present study provides theoretical prediction of critical spectroscopic features of this radical that should aid in its experimental characterization. Energies, structures, rotational constants, and harmonic frequencies are presented for the ground and two low-lying excited electronic states of HOC(O)O. The energies for the Ã2A″←X̃2A′ and B̃2A′←X̃2A′ electronic transitions are reported. The band origin of the B̃←X̃ transition of HOC(O)O is predicted to occur in the near infrared region of the spectrum at around 1.5 eV and it is suggested to be the most promising one for observing this radical spectroscopically. The structural and spectroscopic similarities between HOC(O)O and the isoelectronic radical FC(O)O are discussed. The abundance of experimental data on the FC(O)O radical should guide the spectroscopic characterization of HOC(O)O and serve as a benchmark for the structural and spectroscopic parameters obtained from theory.
Transport theory for energetic alpha particles in finite aspect ratio tokamaks with broken symmetry
Authors: Shaing K. C. , Schlutt M. , Lai A. L.
Published: February 2016

Transport theory for the energetic alpha particles in finite aspect ratio tokamaks with broken symmetry is developed for the case where the slowing down collision operator dominates. The transport fluxes in the 1/ν and superbanana plateau regimes are derived. Here, ν is the typical collision frequency. They can be used in modeling the energy loss of the alpha particles in thermonuclear fusion reactors. Numerical realizations of the superbanana orbits of alpha particles in tokamaks with broken symmetry are also presented. The existence of the superbananas corroborates the predictions of the theories presented here and elsewhere.
Si-rich W silicide films composed of W-atom-encapsulated Si clusters deposited using gas-phase reactions of WF6 with SiH4
Authors: Okada Naoya , Uchida Noriyuki , Kanayama Toshihiko
Published: February 2016

We formed Si-rich W silicide films composed of Sin clusters, each of which encapsulates a W atom (WSin clusters with 8 < n ≤ ∼ 12), by using a gas-phase reaction between WF6 and SiH4 in a hot-wall reactor. The hydrogenated WSinHx clusters with reduced F concentration were synthesized in a heated gas phase and subsequently deposited on a substrate heated to 350–420 °C, where they dehydrogenated and coalesced into the film. Under a gas pressure of SiH4 high enough for the WSinHx reactant to collide a sufficient number of times with SiH4 molecules before reaching the substrate, the resulting film was composed of WSin clusters with a uniform n, which was determined by the gas temperature. The formed films were amorphous semiconductors with an optical gap of ∼0.8–1.5 eV and an electrical mobility gap of ∼0.05–0.12 eV, both of which increased as n increased from 8 to 12. We attribute this dependence to the reduction of randomness in the Si network as n increased, which decreased the densities of band tail states and localized states.
The Dirac oscillator in the presence of a chain of delta-function potentials
Authors: Aouadi O. , Chargui Y. , Fayache M. S.
Published: February 2016

We study the spectroscopy of the one-dimensional Dirac oscillator perturbed by a chain of delta-shaped potentials. We consider two cases: scalar and vector couplings. The transfer matrix method is used for the determination of the general condition of quantization of energy, and a detailed example is presented.
Domain wall motion in ultrathin Co70Fe30/Pd multilayer nanowires with perpendicular anisotropy
Authors: Meng Zhaoliang , He Shikun , Qiu Jinjun , Zhou Tiejun , Han Guchang , Teo Kie-Leong
Published: February 2016

We report the investigation of spin polarized current induced domain wall (DW) displacement in the perpendicularly magnetized nanowires patterned on ultrathin CoFe/Pd multilayer films by anomalous Hall-effect measurement. We find that DWs can be driven to propagate in the nanowire by the threshold current density (Jth) as low as 5.2 × 1010 A/m2 under a bias field H = 115 Oe. The spin-torque efficiency ε = (1.68 ± 0.09) × 10−14 T·m2/A is derived by measuring the effective field (HJ) generated by the pulsed current as well as through the dependency of Jth on H from the DW depinning field experiment. Our result indicates that the current induced DW motion is essentially dominated by the non-adiabatic spin transfer torque effect and the non-adiabaticity factor β is estimated to be as high as 0.96 ± 0.04.
Critical thickness for stripe domain formation in FePt thin films: Dependence on residual stress
Authors: Álvarez N. R. , Gómez J. E. , Moya Riffo A. E. , Vicente Álvarez M. A. , Butera A.
Published: February 2016

Magnetically soft FePt thin films of varying thickness (20 nm ≤ d ≤ 100 nm) were sputter-deposited at different Ar pressures in order to systematically modify the residual stress and hence the magnetic anisotropy. The magnetic domain structure of FePt thin films showed a transition from planar to nearly parallel stripes above a critical thickness, dcr, which was found to depend on an anisotropy contribution perpendicular to the film plane, originated essentially in magnetoelastic effects. A careful structural characterization was made in order to obtain the strain and the stress induced magnetic anisotropy in the samples. Vibrating sample magnetometry and magnetic force microscopy were used to investigate the changes occurring in the magnetic domain structure and the critical thickness of each set of films. Joining together structural and magnetic results, we have been able to construct a phase diagram that divided regions of different domain structures, either by changing the film thickness or the perpendicular magnetic anisotropy. The experimental results could be satisfactorily explained by using a model developed by Murayama. The observed dependence of the magnetic properties of soft FePt thin films on the fabrication conditions opens the possibility to tune the magnetic domain configuration from planar to stripe-like domains by changing the argon sputtering pressure used during film deposition.
Photon noise from chaotic and coherent millimeter-wave sources measured with horn-coupled, aluminum lumped-element kinetic inductance detectors
Authors: Flanigan D. , McCarrick H. , Jones G. , Johnson B. R. , Abitbol M. H. , Ade P. , Araujo D. , Bradford K. , Cantor R. , Che G. , Day P. , Doyle S. , Kjellstrand C. B. , Leduc H. , Limon M. , Luu V. , Mauskopf P. , Miller A. , Mroczkowski T. , Tucker C. , Zmuidzinas J.
Published: February 2016

We report photon-noise limited performance of horn-coupled, aluminum lumped-element kinetic inductance detectors at millimeter wavelengths. The detectors are illuminated by a millimeter-wave source that uses an active multiplier chain to produce radiation between 140 and 160 GHz. We feed the multiplier with either amplified broadband noise or a continuous-wave tone from a microwave signal generator. We demonstrate that the detector response over a 40 dB range of source power is well-described by a simple model that considers the number of quasiparticles. The detector noise-equivalent power (NEP) is dominated by photon noise when the absorbed power is greater than approximately 1 pW, which corresponds to NEP≈2×10−17 W Hz−1/2, referenced to absorbed power. At higher source power levels, we observe the relationships between noise and power expected from the photon statistics of the source signal: NEP∝P for broadband (chaotic) illumination and NEP∝P1/2 for continuous-wave (coherent) illumination.
Inter-sublevel dynamics in single InAs/GaAs quantum dots induced by strong terahertz excitation
Authors: Stephan D. , Bhattacharyya J. , Huo Y. H. , Schmidt O. G. , Rastelli A. , Helm M. , Schneider H.
Published: February 2016

We combine micro-photoluminescence (PL) with terahertz excitation to investigate the response of single self-assembled InAs/GaAs quantum dots to intense terahertz pulses tuned to the s-to-p transition. Spectra and transients of single photoluminescence lines reveal the dynamics of electrons upon excitation and subsequent relaxation back into the initial state. Under certain circumstances, the terahertz pulse can release trapped charge carriers, which relax into the quantum dot. Furthermore, we demonstrate near-total depletion of the positive trion PL by an intense terahertz pulse.
How do rural placements affect urban-based Australian junior doctors’ perceptions of working in a rural area?
Authors: Brodribb Wendy , Zadoroznyj Maria , Martin Bill
Published: February 2016

Objectives The aim of the present study was to provide qualitative insights from urban-based junior doctors (graduation to completion of speciality training) of the effect of rural placements and rotations on career aspirations for work in non-metropolitan practices. Methods A qualitative study was performed of junior doctors based in Adelaide, Brisbane and Melbourne. Individual face-to-face or telephone semistructured interviews were held between August and October 2014. Thematic analysis focusing on participants’ experience of placements and subsequent attitudes to rural practice was undertaken. Results Most participants undertook rural placements in the first 2 years after graduation. Although experiences varied, positive perceptions of placements were consistently linked with the degree of supervision and professional support provided. These experiences were linked to attitudes about working outside metropolitan areas. Participants expressed concerns about being ‘forced’ to work in non-metropolitan hospitals in their first postgraduate year; many received little warning of the location or clinical expectations of the placement, causing anxiety and concern. Conclusions Adequate professional support and supervision in rural placements is essential to encourage junior doctors’ interests in rural medicine. Having a degree of choice about placements and a positive and supported learning experience increases the likelihood of a positive experience. Doctors open to working outside a metropolitan area should be preferentially allocated an intern position in a non-metropolitan hospital and rotated to more rural locations. What is known about the topic? The maldistribution of the Australian medical workforce has led to the introduction of several initiatives to provide regional and rural experiences for medical students and junior doctors. Although there have been studies outlining the effects of rural background and rural exposure on rural career aspirations, little research has focused on what hinders urban-trained junior doctors from pursuing a rural career. What does this paper add? Exposure to medical practice in regional or rural areas modified and changed the longer-term career aspirations of some junior doctors. Positive experiences increased the openness to and the likelihood of regional or rural practice. However, junior doctors were unlikely to aspire to non-metropolitan practice if they felt they had little control over and were unprepared for a rural placement, had a negative experience or were poorly supported by other clinicians or health services. What are the implications for practitioners? Changes to the process of allocating junior doctors to rural placements so that the doctors felt they had some choice, and ensuring these placements are well supervised and supported, would have a positive impact on junior doctors’ attitudes to non-metropolitan practice.
Life History Diversity in Klamath River Steelhead
Authors: Hodge Brian W. , Wilzbach Margaret A. , Duffy Walter G. , Quiñones Rebecca M. , Hobbs James A.
Published: February 2016

Oncorhynchus mykiss exhibits a vast array of life histories, which increases its likelihood of persistence by spreading risk of extirpation among different pathways. The Klamath River basin (California–Oregon) provides a particularly interesting backdrop for the study of life history diversity in O. mykiss, in part because the river is slated for a historic and potentially influential dam removal and habitat recolonization project. We used scale and otolith strontium isotope (87Sr/86Sr) analyses to characterize life history diversity in wild O. mykiss from the lower Klamath River basin. We also determined maternal origin (anadromous or nonanadromous) and migratory history (anadromous or nonanadromous) of O. mykiss and compared length and fecundity at age between anadromous (steelhead) and nonanadromous (Rainbow Trout) phenotypes of O. mykiss. We identified a total of 38 life history categories at maturity, which differed in duration of freshwater and ocean rearing, age at maturation, and incidence of repeat spawning. Approximately 10% of adult fish sampled were nonanadromous. Rainbow Trout generally grew faster in freshwater than juvenile steelhead; however, ocean growth afforded adult steelhead greater length and fecundity than adult Rainbow Trout. Although 75% of individuals followed the migratory path of their mother, steelhead produced nonanadromous progeny and Rainbow Trout produced anadromous progeny. Overall, we observed a highly diverse array of life histories among Klamath River O. mykiss. While this diversity should increase population resilience, recent declines in the abundance of Klamath River steelhead suggest that life history diversity alone is not sufficient to stabilize a population. Our finding that steelhead and Rainbow Trout give rise to progeny of the alternate form (1) suggests that dam removal might lead to a facultatively anadromous O. mykiss population in the upper basin and (2) raises the question of whether both forms of O. mykiss in the Klamath River should be managed under the same strategy.

Received June 20, 2015; accepted October 16, 2015
A critical analysis of weld heat input measurement through a water-cooled stationary anode calorimeter
Authors: Hurtig K. , Choquet I. , Scotti A. , Svensson L.-E.
Published: February 2016

Comprehensive models of heat transfer require specification of the total amount of heat received by the workpiece. The objective of this work was to critically examine the use of a water-cooled stationary anode calorimeter to obtain both arc efficiency and total heat input into the workpiece. For simplicity and clarity, this last quantity is called the gross heat input. The effects of current, material type and water flow rate on the calorimeter performance were determined experimentally. Some measures for reducing errors in calorimetry were evaluated. Improvements were made to reduce heat losses from the top surface of the test coupon and boost heat removal from the opposite surface. A sensitivity test was conducted to estimate the effect of measurement inaccuracies. The results demonstrate the effectiveness of calorimetry for measuring gross heat input in arc welding.
Climate change predicted to lengthen transatlantic travel times
Authors: Simpson Isla R
Published: February 2016

Among the many consequences of rising atmospheric greenhouse gas concentrations, is a change to the medium through which planes fly. An emerging area of research is the impact that these changes may have on the airline industry, with studies addressing aspects ranging from the impact of rising temperatures on aeroplane weight restrictions (Coffel and Horton 2015 Wea. Climate Soc.

7 94–102) to the impact of changing wind shears on the occurrence of clear air turbulence (Williams and Joshi 2014 Nat. Clim. Change

3 644–8). Now, a recent study by Paul Williams (2016 Environ. Res. Lett.

11 024008), assesses the impact that changing winds may have on the duration of transatlantic flights.
Developing a set of guidelines for your research field: a practical approach
Authors: Klionsky Daniel J.
Published: February 2016

Since 2008, the autophagy community has periodically published a set of guidelines, currently titled “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy.” The newest version of the guidelines was published in 2016. There are many reasons for establishing a set of guidelines in a given research field. This Perspective explores some of these reasons, including standardizing nomenclature for better communication, improving reproducibility, and making it easier for newcomers to enter the field. It also includes the approach I have used to generate and update the guidelines that are now widely used in the autophagy field. The suggestions are not meant to be formulaic, and the method is certainly not perfect. Instead, this should be viewed as a starting set of, well, guidelines.