bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface
Authors: Park Ji-Won , Jeong Hyobin , Kang Byeongsoo , Kim Su Jin , Park Sang Yoon , Kang Sokbom , Kim Hark Kyun , Choi Joon Sig , Hwang Daehee , Lee Tae Geol
Published: June 2015

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.
Identifying ultrasound and clinical features of breast cancer molecular subtypes by ensemble decision
Authors: Zhang Lei , Li Jing , Xiao Yun , Cui Hao , Du Guoqing , Wang Ying , Li Ziyao , Wu Tong , Li Xia , Tian Jiawei
Published: June 2015

Breast cancer is molecularly heterogeneous and categorized into four molecular subtypes: Luminal-A, Luminal-B, HER2-amplified and Triple-negative. In this study, we aimed to apply an ensemble decision approach to identify the ultrasound and clinical features related to the molecular subtypes. We collected ultrasound and clinical features from 1,000 breast cancer patients and performed immunohistochemistry on these samples. We used the ensemble decision approach to select unique features and to construct decision models. The decision model for Luminal-A subtype was constructed based on the presence of an echogenic halo and post-acoustic shadowing or indifference. The decision model for Luminal-B subtype was constructed based on the absence of an echogenic halo and vascularity. The decision model for HER2-amplified subtype was constructed based on the presence of post-acoustic enhancement, calcification, vascularity and advanced age. The model for Triple-negative subtype followed two rules. One was based on irregular shape, lobulate margin contour, the absence of calcification and hypovascularity, whereas the other was based on oval shape, hypovascularity and micro-lobulate margin contour. The accuracies of the models were 83.8%, 77.4%, 87.9% and 92.7%, respectively. We identified specific features of each molecular subtype and expanded the scope of ultrasound for making diagnoses using these decision models.
Experimental and theoretical investigations on temperature modulated translocation of IgG molecules through nanopore arrays
Authors: Liu Lei , Zhu Lizhong
Published: June 2015

In this work, the temperature modulated translocation of IgG molecules through nanopore arrays has been investigated. Our results show that the IgG concentration corresponding to the maximum influence on the modulated ionic current by the physical place-holding effect shifts to a higher value with the system temperature rising.
The detection of multiple DNA targets with a single probe using a conformation-sensitive acoustic sensor
Authors: Tsortos Achilleas , Grammoustianou Aristea , Lymbouridou Rena , Papadakis George , Gizeli Electra
Published: June 2015

Acoustic sensing of DNA targets using a single probe that produces hybridization products of different conformations.
Rapid fabrication of silver microplates under an oxidative etching environment consisting of O2/Cl−, NH4OH/H2O2, and H2O2
Authors: Gatemala Harnchana , Pienpinijtham Prompong , Thammacharoen Chuchaat , Ekgasit Sanong
Published: June 2015

Chloride ions are essential for creating an etching environment capable of selective dissolution of singly and multiply twinned crystals, while leaving plate structures unaffected.
Interaction of iron with a wagon wheel-like ultrathin TiOx film grown on Pt(111)
Authors: Artiglia Luca , Cavaliere Emanuele , Gavioli Luca , Rizzi Gian Andrea
Published: June 2015

Fe migration through a TiOx ultrathin film grown on Pt(111).
A computational view of the change in the geometric and electronic properties of perovskites caused by the partial substitution of Pb by Sn
Authors: Ju Ming-Gang , Sun Guangxu , Zhao Yi , Liang WanZhen
Published: June 2015

It is essential to understand the structure-property relationship of mixed Sn/Pb perovskites, which helps to avoid the toxicology issue of lead in perovskite-based devices.
The puzzling first-order phase transition in water–glycerol mixtures
Authors: Popov Ivan , Greenbaum (Gutina) Anna , Sokolov Alexei P. , Feldman Yuri
Published: June 2015

Over the last decade, discussions on a possible liquid–liquid transition (LLT) have strongly intensified.
Size- and shape-dependent peroxidase-like catalytic activity of MnFe2O4 Nanoparticles and their applications in highly efficient colorimetric detection of target cancer cells
Authors: Peng Yunhua , Wang Zhiyi , Liu Weisheng , Zhang Haoli , Zuo Wei , Tang Huiang , Chen Fengjuan , Wang Baodui
Published: June 2015

FA- and FITC-labeled MnFe2O4 nanohybrid exhibits highly efficient colorimetric detection of target cancer cells.
Discrimination between alkyl and aryl substituents of chiral monoamines by m-phthalic diamide-linked zinc bisporphyrinates
Authors: Fang Xianshi , Han Zhen , Xu Chenglong , Li Xiaohong , Wang Yong , Hu Chuanjiang
Published: June 2015

m-Phthalic diamide-linked zinc bisporphyrinates can not only determine the absolute configuration of monoamines but also distinguish between alkyl and aryl substituents of chiral monoamines.
Accessing perfluoroalkyl nickel(ii), (iii), and (iv) complexes bearing a readily attached [C4F8] ligand
Authors: Yu S. , Dudkina Y. , Wang H. , Kholin K. V. , Kadirov M. K. , Budnikova Y. H. , Vicic D. A.
Published: June 2015

The [C4F8] ligand supports a family of related fluoroalkyl nickel complexes spanning the +2 to +4 oxidation states.
Muscadine grape seed oil as a novel source of tocotrienols to reduce adipogenesis and adipocyte inflammation
Authors: Zhao Lu , Yagiz Yavuz , Xu Changmou , Lu Jiang , Chung Soonkyu , Marshall Maurice R.
Published: June 2015

This is the first report showing that muscadine grape seed oil can attenuate obesity-associated metabolic diseases in a cell model.
A comparison of antioxidative and anti-inflammatory activities of sword beans and soybeans fermented with Bacillus subtilis
Authors: Han Seon Su , Hur Sun Jin , Lee Si Kyung
Published: June 2015

This study was conducted to determine the antioxidative and anti-inflammatory activities of non-fermented orBacillus subtilis-fermented soybeans and sword beans (red and white).
Copper(i)/phosphine-catalyzed tandem carboxylation/annulation of terminal alkynes under ambient pressure of CO2: one-pot access to 3a-hydroxyisoxazolo[3,2-a]isoindol-8(3aH)-ones
Authors: Xie Jia-Ning , Yu Bing , Guo Chun-Xiang , He Liang-Nian
Published: June 2015

A tandem carboxylation/annulation sequence promoted by a copper(i)/phosphine catalytic system was developed with simultaneous formation of four novel bonds i.e. two C–C bonds and two C–O bonds in a one-pot stepwise manner.
Discovery, synthesis and structure–activity analysis of symmetrical 2,7-disubstituted fluorenones as urea transporter inhibitors
Authors: Lee Sujin , Esteva-Font Cristina , Phuan Puay-Wah , Anderson Marc O. , Verkman A. S.
Published: June 2015

Kidney urea transporters are targets for development of small-molecule inhibitors with action as salt-sparing diuretics.
Synthesis of 2-deoxy-2,2-difluoro-α-maltosyl fluoride and its X-ray structure in complex with Streptomyces coelicolor GlgEI-V279S
Authors: Thanna Sandeep , Lindenberger Jared J. , Gaitonde Vishwanath V. , Ronning Donald R. , Sucheck Steven J.
Published: June 2015

Mycobacterium tuberculosis (Mtb)GlgE is a genetically validated TB drug target involved in α-glucan biosynthesis. TheStreptomyces coelicolor (Sco)GlgEI-V279S variant described here is used as a model enzyme for structure-based inhibitor design.
Asymmetric synthesis of γ-aryl-substituted GABA derivatives via a highly diastereoselective Rh-catalyzed boronic acid addition at room temperature
Authors: Ramachandran P. Veeraraghavan , Mitsuhashi Wataru , Biswas Bidyut
Published: June 2015

A highly diastereoselective Rh-catalyzed boronic acid addition to enantiopure sulfinylimines at room temperature providing γ-aryl GABA derivatives has been described.
ZnFe2O4nanoparticles and a clay encapsulated ZnFe2O4nanocomposite: synthesis strategy, structural characteristics and the adsorption of dye pollutants in water
Authors: Tadjarodi Azadeh , Imani Mina , Salehi Mohammad
Published: June 2015

Zinc ferrite nanoparticles were prepared by a one-pot microwave assisted combustion in the solid state and encapsulated in an organoclay to obtain a zinc ferrite/organoclay nanocomposite for the adsorption of organic dye pollutants from aqueous solutions.
Biodegradable and conductive chitosan–graphene quantum dot nanocomposite microneedles for delivery of both small and large molecular weight therapeutics
Authors: Justin Richard , Román Sabiniano , Chen Dexin , Tao Ke , Geng Xiangshuai , Grant Richard T. , MacNeil Sheila , Sun Kang , Chen Biqiong
Published: June 2015

Chitosan–graphene quantum dot nanocomposites are used in microneedle arrays for transdermal delivery of small and large molecular weight drugs.
Development and validation of kinetic and atomic absorption spectrophotometric methods for the determination of salbutamol sulfate
Authors: Mahmoud Nejem R'afat , Mohamed Issa Mahmoud , Hosny AL-Kholy Mozer , Amin Saleh Akila , Abu Shanab Alaa , Ioana Stefan van Staden Raluca , Y. Aboul-Enein Hassan
Published: June 2015

Two sensitive kinetic and atomic absorption spectrophotometric (AAS) methods were developed for the determination of salbutamol sulfate (SLS) in its dosage forms.
Design, synthesis and in vivo antitumor efficacy of novel eight-arm-polyethylene glycol–pterostilbene prodrugs
Authors: Liu Ke-feng , Li Chun-xiao , Dai Lin , Liu Jing , Wang Lu-ying , Lei Jian-du , Guo Li-qun
Published: June 2015

Illustration of 8arm-PEG–pterostilbene. In contrast to linear PEG, the 8arm-PEG significantly increased drug-binding capacity.
A facile low temperature method for the synthesis of CoFe2O4 nanoparticles possessing excellent microwave absorption properties
Authors: Moitra D. , Hazra S. , Ghosh B. K. , Jani R. K. , Patra M. K. , Vadera S. R. , Ghosh N. N.
Published: June 2015

CoFe2O4 nanoparticles, synthesized via a co-precipitation method at 120 °C, exhibited excellent microwave absorption properties, with minimum reflection loss of −55 dB (∼99.99%) at 9.25 GHz.
Greener synthetic route for superparamagnetic and luminescent α-Fe2O3nanoparticles in binary mixtures of ionic liquid and ethylene glycol
Authors: Shikha Preet , Randhawa B. S. , Kang Tejwant Singh
Published: June 2015

The composition of IL and EG binary solvent mixture affects the structural, morphological, luminescent and magnetic properties of α-Fe2O3nanoparticles.
Theranostic fluorescent silica encapsulated magnetic nanoassemblies for in vitro MRI imaging and hyperthermia
Authors: Kumar Sunil , Daverey Amita , Khalilzad-Sharghi Vahid , Sahu Niroj K. , Kidambi Srivatsan , Othman Shadi F. , Bahadur Dhirendra
Published: June 2015

This article reports the synthesis of manganese ferrite nano-assemblies (MNAs) encapsulated with fluorescent silica and demonstrates their applicability for magnetic hyperthermia, optical and T2 contrast MRI imaging with HeLa cancer cells.
Lightweight and solution processible thin sheets of poly(o-toluidine)-carbon fiber-novolac composite for EMI shielding
Authors: Joon Seema , Kumar Rakesh , Singh Avanish Pratap , Shukla Rajni , Dhawan S. K.
Published: June 2015

Light weight poly(o-toluidine)-carbon fiber (PoTCF) thin sheets were fabricated for control of EMI shielding. These thin films exhibit flexural strength of 36.0 MPa and a shielding effectiveness of 24 dB in X-band, which can find applications for techno-commercial uses.
A novel label free long non-coding RNA electrochemical biosensor based on green l-cysteine electrodeposition and Au–Rh hollow nanospheres as tags
Authors: Liu Fei , Xiang Guiming , Zhang Liqun , Jiang Dongneng , Liu Linlin , Li Yi , Liu Chang , Pu Xiaoyun
Published: June 2015

lncRNA biosensor based on single-wall carbon nanotubes wrapped with Au–Rh hollow nanospheres (Au/Rh-HNP@SWCNT) complex signal amplification and an l-Cys Au nano-film provided ultrasensitive detection for the nuclear paraspeckle assembly transcript 1 (NEAT1).
Exploitation of a new Schiff-base ligand for boric acid fluorescent sensing in aqueous medium with bio-imaging studies in a living plant system
Authors: Sarkar Yeasmin , Das Sanju , Datta Riddhi , Chattopadhyay Sharmila , Ray Ambarish , Parui Partha Pratim
Published: June 2015

A new Schiff-base ligand owing to 1 : 1 chelation with boric acid exhibits selective boric acid fluorosensor at physiological condition along with bio-imaging facilities.
Phosphorus-doped porous carbon derived from rice husk as anode for lithium ion batteries
Authors: Wang Jiaqing , Yang Zhenzhong , Pan Fusen , Zhong Xiongwu , Liu Xiaowu , Gu Lin , Yu Yan
Published: June 2015

We developed a simple and scalable chemical method to obtain phosphorus-doped porous carbon (P-PC–RH) by optimized acid treatment and thermal annealing of rice husk with triphenylphosphine (TPP).
Rhodium-catalyzed synthesis of quinolines and imines under mild conditions
Authors: Yadav Dilip Kumar T. , Bhanage Bhalchandra M.
Published: June 2015

An efficient protocol for the synthesis of quinolines in aqueous medium using a Rh(ii)acetate/TPPTS recyclable catalytic system has been developed. Furthermore, imines were also synthesized from benzylamines in moderate to good yields under solvent free conditions.
Controlled synthesis and luminescent properties of assembled spherical YPxV1−xO4:Ln3+ (Ln = Eu, Sm, Dy or Tm) phosphors with high quantum efficiency
Authors: An Zhibin , Xiao Xiuzhen , Yu Jun , Mao Dongsen , Lu Guanzhong
Published: June 2015

Controlled morphology and energy transfer in assembled spherical YPxV1−xO4:Ln3+ (Ln = Eu, Sm, Dy or Tm) phosphors with higher luminescent quantum efficiency by the EDTA-assisted hydrothermal method.
Deciphering the electron transfer mechanisms for biogas upgrading to biomethane within a mixed culture biocathode
Authors: Batlle-Vilanova Pau , Puig Sebastià , Gonzalez-Olmos Rafael , Vilajeliu-Pons Anna , Balaguer M. Dolors , Colprim Jesús
Published: June 2015

This study describes the electron transfer mechanism of a BES fed with the effluent from water scrubbing to improve biogas upgrading.
Controllable synthesis of 3D hierarchical bismuth compounds with good electrochemical performance for advanced energy storage devices
Authors: Sun Jinfeng , Wang Jinqing , Li Zhangpeng , Yang Zhigang , Yang Shengrong
Published: June 2015

3D hierarchical bismuth (Bi)-based compounds with controllable sizes and morphologies exhibit high specific capacitance and superior rate capability.
Preparation, characterization and magnetic behavior of a spin-labelled physical hydrogel containing a chiral cyclic nitroxide radical unit fixed inside the gelator molecule
Authors: Takemoto Yusa , Yamamoto Takayuki , Ikuma Naohiko , Uchida Yoshiaki , Suzuki Katsuaki , Shimono Satoshi , Takahashi Hiroki , Sato Nobuhiro , Oba Yojiro , Inoue Rintaro , Sugiyama Masaaki , Tsue Hirohito , Kato Tatsuhisa , Yamauchi Jun , Tamura Rui
Published: June 2015

The magnetic behavior of a physical hydrogel of (S,S,R)-5a was evaluated by VT-EPR spectroscopy.
High-quality functionalized few-layer graphene: facile fabrication and doping with nitrogen as a metal-free catalyst for the oxygen reduction reaction
Authors: Sun Zhenyu , Masa Justus , Weide Philipp , Fairclough Simon M. , Robertson Alex W. , Ebbinghaus Petra , Warner Jamie H. , Tsang S. C. Edman , Muhler Martin , Schuhmann Wolfgang
Published: June 2015

A highly efficient and mild covalent functionalization of graphene is developed, yielding oxidized few-layer graphene in both high quantity and high quality.
Co-deposition of catechol/polyethyleneimine on porous membranes for efficient decolorization of dye water
Authors: Qiu Wen-Ze , Yang Hao-Cheng , Wan Ling-Shu , Xu Zhi-Kang
Published: June 2015

Porous membranesviathe co-deposition of catechol and polyethyleneimine were fabricated with excellent hydrophilicity and distinguished surface charges for decolorizing anionic dye solutions.
Effects of a ferroelectric interface on thermionic injection-induced cooling in single-heterojunction devices based on thin-film electrode/medium/electrode design
Authors: Liu Qing , Wu Ting , Hsiao Yu-Che , Li Mingxing , Hu Dehua , Wang Hongfeng , Xu Hengxing , Tisdale Jeremy , Hu Bin
Published: June 2015

The mechanism of phonon absorption from injected carriers is used to generate a thermionic cooling effect in organic thin-film electrode/medium/electrode devices.
Secondary growth of hierarchical nanostructures composed only of Nb3O7F single-crystalline nanorods as a new photocatalyst for hydrogen production
Authors: Duan Junyuan , Mou Guangying , Zhang Shuai , Wang Sheng , Guan Jianguo
Published: June 2015

Controllable hydrolysis of H2NbF7 with the assistance of 2-propanol can produce Nb3O7F hierarchical nanostructures of single-crystalline nanorods for photocatalytic H2 production.
BiOBr visible-light photocatalytic films in a rotating disk reactor for the degradation of organics
Authors: Huo Yuning , Hou Rujing , Chen Xiaofang , Yin Haibo , Gao Yuan , Li Hexing
Published: June 2015

BiOBr visible-light photocatalytic films utilized in a rotating disk reactor have achieved improved photoactivity for the degradation of color organics.
A facile one-step method to reduce surface impurities in solution-processed CuInS2 nanocrystal solar cells
Authors: Stahl Melissa S. , Azimi Hamed , Brabec Christoph J.
Published: June 2015

This work presents a simple method for post-processing of washing away the impurities formed on the films of solution processed CuInS2 thin films.
Unravelling the chemical design of spin-crossover nanoparticles based on iron(ii)–triazole coordination polymers: towards a control of the spin transition
Authors: Giménez-Marqués Mónica , García-Sanz de Larrea M. Luisa , Coronado Eugenio
Published: June 2015

We present a systematic study of the key synthetic parameters that control the growth of Fe–triazole spin-crossover nanoparticles and the effect of this size modulation on the spin transition.
Utility of Computed Tomography following Anterior Cervical Diskectomy and Fusion
Authors: Derakhshan Adeeb , Lubelski Daniel , Steinmetz Michael P. , Benzel Edward C. , Mroz Thomas E.
Published: June 2015

Study Design

Retrospective case series.

Objective

To assess the utility of postoperative computed tomography (CT) following anterior cervical diskectomy and fusion (ACDF) and to determine the clinical circumstances most likely to lead to an abnormal CT scan.

Methods

Patients who underwent ACDF at a tertiary center over a span of 5 years were investigated. Only patients who had a minimum of 6 months’ postoperative follow-up and a CT within 2 years after the surgery were included in the study group. All the postoperative notes were reviewed to determine indications for the CT, abnormalities identified, and whether the scan led to an alteration in the treatment course.

Results

The charts of 690 patients who underwent ACDF were reviewed. Of the 690 patients, 45 (7%) had postoperative CTs. These patients accounted for 53 postoperative CT scans, 45 (85%) of which were taken for patients who expressed persistent postoperative symptoms and/or had abnormal imaging. There were no indications for 8 (15%) of the CTs. Patients who had a CT for persistent symptoms and/or abnormal preliminary imaging were significantly more likely to have an abnormal CT ( p = 0.03) and/or an alteration in treatment course ( p = 0.04) compared with those with no symptomatic or radiologic indication for CT.

Conclusions

CT is associated with minimal utility regarding the alteration of treatment course when employed in asymptomatic patients. Postoperative CT should be ordered solely for symptomatic patients or those with other abnormal preliminary imaging. Judicious use of postoperative CT will limit the radiation exposure and cost.
Open versus Minimally Invasive Fixation Techniques for Thoracolumbar Trauma: A Meta-Analysis
Authors: McAnany Steven J. , Overley Samuel C. , Kim Jun S. , Baird Evan O. , Qureshi Sheeraz A. , Anderson Paul A.
Published: June 2015

Study Design

Systematic literature review and meta-analysis of studies published in English.

Objective

This study evaluated differences in outcome variables between percutaneous and open pedicle screws for traumatic thoracolumbar fractures.

Methods

A systematic review of PubMed, Cochrane, and Embase was performed. The variables of interest included postoperative visual analog scale (VAS) pain score, kyphosis angle, and vertebral body height, as well as intraoperative blood loss and operative time. The results were pooled by calculating the effect size based on the standardized difference in means. The studies were weighted by the inverse of the variance, which included both within- and between-study error. Confidence intervals were reported at 95%. Heterogeneity was assessed using the Q statistic and I2.

Results

After two-reviewer assessment, 38 studies were eliminated. Six studies were found to meet inclusion criteria and were included in the meta-analysis. The combined effect size was found to be in favor of percutaneous fixation for blood loss and operative time ( p < 0.05); however, there were no differences in vertebral body height (VBH), kyphosis angle, or VAS scores between open and percutaneous fixation. All of the studies demonstrated relative homogeneity, with I2 < 25.

Conclusions

Patients with thoracolumbar fractures can be effectively managed with percutaneous or open pedicle screw placement. There are no differences in VBH, kyphosis angle, or VAS between the two groups. Blood loss and operative time were decreased in the percutaneous group, which may represent a potential benefit, particularly in the polytraumatized patient. All variables in this study demonstrated near-perfect homogeneity, and the effect is likely close to the true effect.
Microstructural characterization and current conduction mechanisms of front-side contact of n-type crystalline Si solar cells with Ag/Al pastes
Authors: Liang L. , Li Z. G. , Cheng L. K. , Takeda N. , Carroll A. F.
Published: June 2015

Recently, high efficiency n-type crystalline Si cells made with the screen printed Ag/Al metallization have received considerable attention. We report here our microstructural investigations of the critical interfacial region between the front-side contact and the Si wafer of n-type cells fired under progressively higher temperatures. Our study revealed that the key characteristic microstructures of the interfacial region changed from one with a large fraction of residual SiNx, to one consisting of a thin glass layer with nano-Ag colloids, and finally to one decorated with Ag and Ag/Al crystallites attached to the emitter surface for cells with under-, optimally-, and over-fired conditions, respectively. We did not find any Al-Si eutectic layer on the emitter surface that would support a silicon dissolution and re-growth mechanism, which is operative in the back surface field formation process for the Al back contact of p-type industrial solar cells. The presence of the SiNx antireflection coating has likely altered the chemistry between Si and Al significantly. The observed microstructures lead us to conclude that the main current conduction mechanism in optimally-fired n-type cells is tunneling through those areas of thin interfacial glass containing nano-Ag colloids. This mechanism is similar to the current conduction model we have proposed previously for optimally-fired p-type crystalline Si solar cells. We believe that the intrusion of Ag/Al (and/or Ag) crystallites into the p+-Si emitter in over-fired cells is one of the major sources of metallization-induced recombination losses, which degrades cell performance.
Detection of dark states in two-dimensional electronic photon-echo signals via ground-state coherence
Authors: Egorova Dassia
Published: June 2015

Several recent experiments report on possibility of dark-state detection by means of so called beating maps of two-dimensional photon-echo spectroscopy [Ostroumov et al., Science 340, 52 (2013); Bakulin et al., Ultrafast Phenomena XIX (Springer International Publishing, 2015)]. The main idea of this detection scheme is to use coherence induced upon the laser excitation as a very sensitive probe. In this study, we investigate the performance of ground-state coherence in the detection of dark electronic states. For this purpose, we simulate beating maps of several models where the excited-state coherence can be hardly detected and is assumed not to contribute to the beating maps. The models represent strongly coupled electron-nuclear dynamics involving avoided crossings and conical intersections. In all the models, the initially populated optically accessible excited state decays to a lower-lying dark state within few hundreds femtoseconds. We address the role of Raman modes and of interstate-coupling nature. Our findings suggest that the presence of low-frequency Raman active modes significantly increases the chances for detection of dark states populated via avoided crossings, whereas conical intersections represent a more challenging task.
Computation of virial coefficients from integral equations
Authors: Zhang Cheng , Lai Chun-Liang , Pettitt B. Montgomery
Published: June 2015

A polynomial-time method of computing the virial coefficients from an integral equation framework is presented. The method computes the truncated density expansions of the correlation functions by series transformations, and then extracts the virial coefficients from the density components. As an application, the method was used in a hybrid-closure integral equation with a set of self-consistent conditions, which produced reasonably accurate virial coefficients for the hard-sphere fluid and Gaussian model in high dimensions.
The effect of particle size on the morphology and thermodynamics of diblock copolymer/tethered-particle membranes
Authors: Zhang Bo , Edwards Brian J.
Published: June 2015

A combination of self-consistent field theory and density functional theory was used to examine the effect of particle size on the stable, 3-dimensional equilibrium morphologies formed by diblock copolymers with a tethered nanoparticle attached either between the two blocks or at the end of one of the blocks. Particle size was varied between one and four tenths of the radius of gyration of the diblock polymer chain for neutral particles as well as those either favoring or disfavoring segments of the copolymer blocks. Phase diagrams were constructed and analyzed in terms of thermodynamic diagrams to understand the physics associated with the molecular-level self-assembly processes. Typical morphologies were observed, such as lamellar, spheroidal, cylindrical, gyroidal, and perforated lamellar, with the primary concentration region of the tethered particles being influenced heavily by particle size and tethering location, strength of the particle-segment energetic interactions, chain length, and copolymer radius of gyration. The effect of the simulation box size on the observed morphology and system thermodynamics was also investigated, indicating possible effects of confinement upon the system self-assembly processes.
Sequential data assimilation for single-molecule FRET photon-counting data
Authors: Matsunaga Yasuhiro , Kidera Akinori , Sugita Yuji
Published: June 2015

Data assimilation is a statistical method designed to improve the quality of numerical simulations in combination with real observations. Here, we develop a sequential data assimilation method that incorporates one-dimensional time-series data of smFRET (single-molecule Förster resonance energy transfer) photon-counting into conformational ensembles of biomolecules derived from “replicated” molecular dynamics (MD) simulations. A particle filter using a large number of “replicated” MD simulations with a likelihood function for smFRET photon-counting data is employed to screen the conformational ensembles that match the experimental data. We examine the performance of the method using emulated smFRET data and coarse-grained (CG) MD simulations of a dye-labeled polyproline-20. The method estimates the dynamics of the end-to-end distance from smFRET data as well as revealing that of latent conformational variables. The particle filter is also able to correct model parameter dependence in CG MD simulations. We discuss the applicability of the method to real experimental data for conformational dynamics of biomolecules.
Pair extended coupled cluster doubles
Authors: Henderson Thomas M. , Bulik Ireneusz W. , Scuseria Gustavo E.
Published: June 2015

The accurate and efficient description of strongly correlated systems remains an important challenge for computational methods. Doubly occupied configuration interaction (DOCI), in which all electrons are paired and no correlations which break these pairs are permitted, can in many cases provide an accurate account of strong correlations, albeit at combinatorial computational cost. Recently, there has been significant interest in a method we refer to as pair coupled cluster doubles (pCCD), a variant of coupled cluster doubles in which the electrons are paired. This is simply because pCCD provides energies nearly identical to those of DOCI, but at mean-field computational cost (disregarding the cost of the two-electron integral transformation). Here, we introduce the more complete pair extended coupled cluster doubles (pECCD) approach which, like pCCD, has mean-field cost and reproduces DOCI energetically. We show that unlike pCCD, pECCD also reproduces the DOCI wave function with high accuracy. Moreover, pECCD yields sensible albeit inexact results even for attractive interactions where pCCD breaks down.
Velocity map imaging of O-atom products from UV photodissociation of the CH2OO Criegee intermediate
Authors: Li Hongwei , Fang Yi , Beames Joseph M. , Lester Marsha I.
Published: June 2015

UV excitation of jet-cooled CH2OO X1A′ to the excited B1A′ electronic states results in dissociation to two spin-allowed product channels: H2CO X1A1 + O 1D and H2CO a3A″ + O 3P. In this study, the higher energy H2CO a3A″ + O 3P channel is characterized by velocity map imaging and UV action spectroscopy, in both cases utilizing 2 + 1 resonance enhanced multiphoton ionization detection of O 3P products, which complements a prior experimental study on the lower energy H2CO X1A1 + O 1D channel [Lehman et al., J. Chem. Phys. 139, 141103 (2013)]. Anisotropic angular distributions indicative of rapid dissociation are obtained at 330 and 350 nm, along with broad and unstructured total kinetic energy distributions that provide insight into the internal excitation of the H2CO a3A″ co-fragment. A harmonic normal mode analysis points to significant vibrational excitation of the CH2 wag and C–O stretch modes of the H2CO a3A″ fragment upon dissociation. At each UV wavelength, the termination of the kinetic energy distribution reveals the energetic threshold for the H2CO a3A″ + O 3P product channel of ca. 76 kcal mol−1 (378 nm) and also establishes the dissociation energy from CH2OO X1A′ to H2CO X1A1 + O1D products of D0 ≤ 49.0 ± 0.3 kcal mol−1, which is in accord with prior theoretical studies. The threshold for the H2CO a3A″ + O 3P channel is also evident as a more rapid falloff on the long wavelength side of the O 3P action spectrum as compared to the previously reported UV absorption spectrum for jet-cooled CH2OO [Beames et al., J. Am. Chem. Soc. 134, 20045 (2012)]. Modeling suggests that the O 3P yield increases uniformly from 378 to 300 nm.
Properties of the Katugampola fractional derivative with potential application in quantum mechanics
Authors: Anderson Douglas R. , Ulness Darin J.
Published: June 2015

Katugampola [e-print arXiv:1410.6535] recently introduced a limit based fractional derivative, Dα (referred to in this work as the Katugampola fractional derivative) that maintains many of the familiar properties of standard derivatives such as the product, quotient, and chain rules. Typically, fractional derivatives are handled using an integral representation and, as such, are non-local in character. The current work starts with a key property of the Katugampola fractional derivative, Dα[y]=t1−αdydt, and the associated differential operator, Dα = t1−αD1. These operators, their inverses, commutators, anti-commutators, and several important differential equations are studied. The anti-commutator serves as a basis for the development of a self-adjoint operator which could potentially be useful in quantum mechanics. A Hamiltonian is constructed from this operator and applied to the particle in a box model.
Vertical and adiabatic excitations in anthracene from quantum Monte Carlo: Constrained energy minimization for structural and electronic excited-state properties in the JAGP ansatz
Authors: Dupuy Nicolas , Bouaouli Samira , Mauri Francesco , Sorella Sandro , Casula Michele
Published: June 2015

We study the ionization energy, electron affinity, and the π → π∗ (1La) excitation energy of the anthracene molecule, by means of variational quantum Monte Carlo (QMC) methods based on a Jastrow correlated antisymmetrized geminal power (JAGP) wave function, developed on molecular orbitals (MOs). The MO-based JAGP ansatz allows one to rigorously treat electron transitions, such as the HOMO → LUMO one, which underlies the 1La excited state. We present a QMC optimization scheme able to preserve the rank of the antisymmetrized geminal power matrix, thanks to a constrained minimization with projectors built upon symmetry selected MOs. We show that this approach leads to stable energy minimization and geometry relaxation of both ground and excited states, performed consistently within the correlated QMC framework. Geometry optimization of excited states is needed to make a reliable and direct comparison with experimental adiabatic excitation energies. This is particularly important in π-conjugated and polycyclic aromatic hydrocarbons, where there is a strong interplay between low-lying energy excitations and structural modifications, playing a functional role in many photochemical processes. Anthracene is an ideal benchmark to test these effects. Its geometry relaxation energies upon electron excitation are of up to 0.3 eV in the neutral 1La excited state, while they are of the order of 0.1 eV in electron addition and removal processes. Significant modifications of the ground state bond length alternation are revealed in the QMC excited state geometry optimizations. Our QMC study yields benchmark results for both geometries and energies, with values below chemical accuracy if compared to experiments, once zero point energy effects are taken into account.
Reduction of a collisional-radiative mechanism for argon plasma based on principal component analysis
Authors: Bellemans A. , Munafò A. , Magin T. E. , Degrez G. , Parente A.
Published: June 2015

This article considers the development of reduced chemistry models for argon plasmas using Principal Component Analysis (PCA) based methods. Starting from an electronic specific Collisional-Radiative model, a reduction of the variable set (i.e., mass fractions and temperatures) is proposed by projecting the full set on a reduced basis made up of its principal components. Thus, the flow governing equations are only solved for the principal components. The proposed approach originates from the combustion community, where Manifold Generated Principal Component Analysis (MG-PCA) has been developed as a successful reduction technique. Applications consider ionizing shock waves in argon. The results obtained show that the use of the MG-PCA technique enables for a substantial reduction of the computational time.
Response to “Comment on ‘Effective thermal conductivity of metal and non-metal particulate composites with interfacial thermal resistance at high volume fraction of nano to macro-sized spheres’” [J. Appl. Phys. 117, 216101 (2015)]
Authors: Faroughi Salah Aldin , Huber Christian
Published: June 2015

In this response, we clarify some of the misconceptions that were brought up by Pal's Comments about our manuscript [S. A. Faroughi and C. Huber, J. Appl. Phys. 117, 055104 (2015)]. The main issue that was raised is that we account for the correction on the excluded volume (the net volume of the continuous phase in a finite composite decreases with increasing filler content) twice. We show here that this statement is incorrect and that our model is consistent with other models derived from a different standpoint. We also address the other comments raised by Pal.
A scheme for a single molecule phase-shift gate in a solid matrix
Authors: Cui Xiao-Dong , Zheng Yujun
Published: June 2015

We propose a feasible scheme to implement a phase-shift gate 100eiγ based on a two-state single molecule in a solid matrix, where γ is a geometric phase controlled through a fast on-resonant laser field and a slow off-resonant radio-frequency field. In our scheme, a non-Hermitian quantum model is employed to characterize the single molecule in a solid matrix including the spontaneous decay effect. By the coupling between the radio-frequency field and the two-state permanent dipole difference resulting from the solid matrix, the spontaneous decay fatal to the preservation of geometric phase can be effectively suppressed for a considerably long waiting time.
The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations
Authors: Vener M. V. , Odinokov A. V. , Wehmeyer C. , Sebastiani D.
Published: June 2015

Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)–glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898–915 (2011)]. These structures are stabilized by the short +N–H⋯O− bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm−1. It is caused by the asymmetric stretching vibrations of the +N–H⋯O− fragment. Result of the present paper suggests that infrared spectroscopy in the 2000–2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins.
Fully localised nonlinear energy growth optimals in pipe flow
Authors: Pringle Chris C. T. , Willis Ashley P. , Kerswell Rich R.
Published: June 2015

A new, fully localised, energy growth optimal is found over large times and in long pipe domains at a given mass flow rate. This optimal emerges at a threshold disturbance energy below which a nonlinear version of the known (streamwise-independent) linear optimal [P. J. Schmid and D. S. Henningson, “Optimal energy density growth in Hagen-Poiseuille flow,” J. Fluid Mech. 277, 192–225 (1994)] is selected and appears to remain the optimal up until the critical energy at which transition is triggered. The form of this optimal is similar to that found in short pipes [Pringle et al., “Minimal seeds for shear flow turbulence: Using nonlinear transient growth to touch the edge of chaos,” J. Fluid Mech. 702, 415–443 (2012)], but now with full localisation in the streamwise direction. This fully localised optimal perturbation represents the best approximation yet of the minimal seed (the smallest perturbation which is arbitrarily close to states capable of triggering a turbulent episode) for “real” (laboratory) pipe flows. Dependence of the optimal with respect to several parameters has been computed and establishes that the structure is robust.
Photoelectric properties of the metamorphic InAs/InGaAs quantum dot structure at room temperature
Authors: Golovynskyi S. L. , Seravalli L. , Trevisi G. , Frigeri P. , Gombia E. , Dacenko O. I. , Kondratenko S. V.
Published: June 2015

We present the study of optical and photoelectric properties of InAs quantum dots (QDs) grown on a metamorphic In0.15Ga0.85As buffer layer: such nanostructures show efficient light emission in the telecom window at 1.3 μm (0.95 eV) at room temperature. We prepared a sample with vertical geometry of contacts isolated from the GaAs substrate. The structure is found to be photosensitive in the spectral range above 0.9 eV at room temperature, showing distinctive features in the photovoltage and photocurrent spectra attributed to QDs, InAs wetting layer, and In0.15Ga0.85As metamorphic buffer, while a drop in the photoelectric signal above 1.36 eV is related to the GaAs layer. No effect of defect centers on the photoelectrical properties is found, although they are observed in the absorption spectrum. We conclude that metamorphic QDs have a low amount of interface-related defects close to the optically active region and charge carriers can be effectively collected into InAs QDs.
Product sustainability within phase 1 and phase 2 life cycle: An approach to derivation measurement
Authors: Johnson Anthony
Published: June 2015

The creation, use, and eventual disposal of products can be sustainably managed so that the use of energy can be minimised during all the processes from sourcing the material to the disposal of the product. Energy applied during the creation of a product is termed phase 1 life cycle: phase 2 life cycle (usage, maintenance, end of life disposal) is at the mercy of the consumer who may not use, maintain, or dispose of the product as the designers originally intended. This paper briefly explains the elements that constitute phase 1 and phase 2 life cycles and proposes an energy measurement methodology concentrating on phase 2 life cycle elements of usage, maintenance, disposal, and the new energy accounting for element of “Give-back.” The example of a stone tumbler is used to evaluate net embodied energy using the maintenance process as the key to collating data and managing phase 2 life cycle energy.
North Kimberley Mammals – on the fringe of the high-rainfall zone
Authors: Turpin Jeff
Published: June 2015

Six areas were surveyed for terrestrial fauna during remote hiking expeditions in the Kimberley during 2009, 2010, 2013 and 2014. A total of 19 mammal species were recorded, comprising one introduced and 18 native taxa. Significant populations of the northern quoll, monjon, golden-backed tree-rat and scaly-tailed possum were recorded, including from areas where the species were previously unknown. Fractured, rocky terrain in association with rainforest appears to provide important habitat for these species. The use of motion-sensitive cameras, particularly in areas where foraging signs are evident (tracks, diggings, feeding middens, scats) is shown to be a successful and complementary survey technique in detecting critical-weight-range species in the north Kimberley. Such taxa appear to persist in the far north Kimberley in the absence of several threatening processes attributable to large-scale mammal decline across northern Australia.
Alkaloid production and capacity for methyljasmonate induction by hairy roots of two species in Tribe Anthocercideae, family Solanaceae
Authors: Ryan Suzanne M. , DeBoer Kathleen D. , Hamill John D.
Published: June 2015

In addition to producing medicinally important tropane alkaloids, some species in the mainly Australian Solanaceous tribe Anthocercideae, sister to genus Nicotiana, are known to also contain substantial levels of the pyridine alkaloids nicotine and nornicotine. Here, we demonstrate that axenic hairy root cultures of two tribe Anthocercideae species, Cyphanthera tasmanica Miers and Anthocercis ilicifolia ssp. ilicifolia Hook, contain considerable amounts of both nicotine and nornicotine (~0.5–1% DW), together with lower levels of the tropane alkaloid hyoscyamine (<0.2% DW). Treatment of growing hairy roots of both species with micromolar levels of the wound stress hormone methyl-jasmonate (MeJa) led to significant increases (P < 0.05) in pyridine alkaloid concentrations but not of hyoscyamine. Consistent with previous studies involving Nicotiana species, we also observed that transcript levels of key genes required for pyridine alkaloid synthesis increased in hairy roots of both Anthocercideae species following MeJa treatment. We hypothesise that wound-associated induction of pyridine alkaloid synthesis in extant species of tribe Anthocercideae and genus Nicotiana was a feature of common ancestral stock that existed before the separation of both lineages ~15 million years ago.
Androgen and oestrogen modulation by D-aspartate in rat epididymis
Authors: Falvo S. , Di Fiore M. M. , Burrone L. , Baccari G. Chieffi , Longobardi S. , Santillo A.
Published: June 2015

Testosterone (T) synthesised in Leydig cells enters the epididymis and may there be converted into dihydrotestosterone (DHT) by 5α-reductase (5α-red) or into 17β-oestradiol (E2) by P450 aromatase (P450-aro). D-aspartate (D-Asp) is known to induce T synthesis in the testis. In this study, we investigated the effects of in vivo D-Asp administration in two major regions of the rat epididymis (Region I: initial segment, caput, corpus; Region II: cauda). The results suggest that exogenous D-Asp was taken up by both regions of rat epididymis. D-Asp administration induced a rapid increase in T, followed by a more gradual decrease in the T : DHT ratio in Region I. In Region II, T levels rapidly decreased and the T : DHT ratio was consistently lower relative to the control. Expression of 5α-red and androgen receptor genes showed a good correlation with DHT levels in both regions. D-Asp treatment also induced an increase of both E2 levels and oestradiol receptor-α (ERα) expression in Region I, whereas neither E2 levels nor ERα expression were affected in Region II. The early increase of P450-aro expression in Region I and late increase in Region II suggests a direct involvement of D-Asp modulation in P450-aro gene expression. Our results suggest that D-Asp modulates androgen and oestrogen levels and expression of androgen and oestrogen receptors in the rat epididymis by acting on the expression of 5α-red and P450-aro genes.