bluuebunny/crossref_metadata_2025 huggingface dataset:
RETRACTED ARTICLE: Verteporfin-induced formation of protein cross-linked oligomers and high molecular weight complexes is mediated by light and leads to cell toxicity
Authors: Konstantinou Eleni K. , Notomi Shoji , Kosmidou Cassandra , Brodowska Katarzyna , Al-Moujahed Ahmad , Nicolaou Fotini , Tsoka Pavlina , Gragoudas Evangelos , Miller Joan W. , Young Lucy H. , Vavvas Demetrios G.
Published: April 2017

Verteporfin (VP) was first used in Photodynamic therapy, where a non-thermal laser light (689 nm) in the presence of oxygen activates the drug to produce highly reactive oxygen radicals, resulting in local cell and tissue damage. However, it has also been shown that Verteporfin can have non-photoactivated effects such as interference with the YAP-TEAD complex of the HIPPO pathway, resulting in growth inhibition of several neoplasias. More recently, it was proposed that, another non-light mediated effect of VP is the formation of cross-linked oligomers and high molecular weight protein complexes (HMWC) that are hypothesized to interfere with autophagy and cell growth. Here, in a series of experiments, using human uveal melanoma cells (MEL 270), human embryonic kidney cells (HEK) and breast cancer cells (MCF7) we showed that Verteporfin-induced HMWC require the presence of light. Furthermore, we showed that the mechanism of this cross-linking, which involves both singlet oxygen and radical generation, can occur very efficiently even after lysis of the cells, if the lysate is not protected from ambient light. This work offers a better understanding regarding VP’s mechanisms of action and suggests caution when one studies the non-light mediated actions of this drug.
A large-scale benchmark of gene prioritization methods
Authors: Guala Dimitri , Sonnhammer Erik L. L.
Published: April 2017

In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations. The Gene Ontology(GO) contains genes clustered around annotation terms. This intrinsic property of GO can be utilized in construction of robust benchmarks, objective to the problem domain. We demonstrate how this can be achieved for network-based gene prioritization tools, utilizing the FunCoup network. We use cross-validation and a set of appropriate performance measures to compare state-of-the-art gene prioritization algorithms: three based on network diffusion, NetRank and two implementations of Random Walk with Restart, and MaxLink that utilizes network neighborhood. Our benchmark suite provides a systematic and objective way to compare the multitude of available and future gene prioritization tools, enabling researchers to select the best gene prioritization tool for the task at hand, and helping to guide the development of more accurate methods.
Micelle-template synthesis of hollow silica spheres for improving water vapor permeability of waterborne polyurethane membrane
Authors: Bao Yan , Wang Tong , Kang Qiaoling , Shi Chunhua , Ma Jianzhong
Published: April 2017

Hollow silica spheres (HSS) with special interior spaces, high specific surface area and excellent adsorption and permeability performance were synthesized via micelle-template method using cetyl trimethyl ammonium bromide (CTAB) micelles as soft template and tetraethoxysilane (TEOS) as silica precursor. SEM, TEM, FT-IR, XRD, DLS and BET-BJH were carried out to characterize the morphology and structure of as-obtained samples. The results demonstrated that the samples were amorphous with a hollow structure and huge specific surface area. The growth of HSS was an inward-growth mechanism along template. Notably, we have provided a new and interesting fundamental principle for HSS materials by precisely controlling the ethanol-to-water volume ratio. In addition, the as-obtained HSS were mixed with waterborne polyurethane (WPU) to prepare WPU/HSS composite membrane. Various characterizations (SEM, TEM, FT-IR and TGA) revealed the morphology, polydispersity and adherence between HSS and WPU. Performance tests showed that the introduction of HSS can improve the water vapor permeability of composite membrane, promoting its water resistance and mechanical performance at the same time.
The small G protein Arf6 expressed in keratinocytes by HGF stimulation is a regulator for skin wound healing
Authors: Miura Yuki , Ngo Thai Bich Van , Furuya Momoko , Hasegawa Hiroshi , Takahashi Satoru , Katagiri Naohiro , Hongu Tsunaki , Funakoshi Yuji , Ohbayashi Norihiko , Kanaho Yasunori
Published: April 2017

The earlier step of cutaneous wound healing process, re-epithelialization of the wounded skin, is triggered by a variety of growth factors. However, molecular mechanisms through which growth factors trigger skin wound healing are less understood. Here, we demonstrate that hepatocyte growth factor (HGF)/c-Met signaling-induced expression of the small G protein Arf6 mRNA in keratinocytes is essential for the skin wound healing. Arf6 mRNA expression was dramatically induced in keratinocytes at the wounded skin, which was specifically suppressed by the c-Met inhibitor. Wound healing of the skin was significantly delayed in keratinocyte-specific Arf6 conditional knockout mice. Furthermore, Arf6 deletion from keratinocytes remarkably suppressed HGF-stimulated cell migration and peripheral membrane ruffle formation, but did not affect skin morphology and proliferation/differentiation of keratinocytes. These results are consistent with the notion that Arf6 expressed in skin keratinocytes through the HGF/c-Met signaling pathway in response to skin wounding plays an important role in skin wound healing by regulating membrane dynamics-based motogenic cellular function of keratinocytes.
Attogram mass sensing based on silicon microbeam resonators
Authors: Baek In-Bok , Byun Sangwon , Lee Bong Kuk , Ryu Jin-Hwa , Kim Yarkyeon , Yoon Yong Sun , Jang Won Ik , Lee Seongjae , Yu Han Young
Published: April 2017

Using doubly-clamped silicon (Si) microbeam resonators, we demonstrate sub-attogram per Hertz (ag/Hz) mass sensitivity, which is extremely high sensitivity achieved by micro-scale MEMS mass sensors. We also characterize unusual buckling phenomena of the resonators. The thin-film based resonator is composed of a Si microbeam surrounded by silicon nitride (SiN) anchors, which significantly improve performance by providing fixation on the microbeam and stabilizing oscillating motion. Here, we introduce two fabrication techniques to further improve the mass sensitivity. First, we minimize surface stress by depositing a sacrificial SiN layer, which prevents damage on the Si microbeam. Second, we modify anchor structure to find optimal design that allows the microbeam to oscillate in quasi-one dimensional mode while achieving high quality factor. Mass loading is conducted by depositing Au/Ti thin films on the local area of the microbeam surface. Using sequential mass loading, we test effects of changing beam dimensions, position of mass loading, and distribution of a metal film on the mass sensitivity. In addition, we demonstrate that microbeams suffer local micro-buckling and global buckling by excessive mass loading, which are induced by two different mechanisms. We also find that the critical buckling length is increased by additional support from the anchors.
CD200-positive cancer associated fibroblasts augment the sensitivity of Epidermal Growth Factor Receptor mutation-positive lung adenocarcinomas to EGFR Tyrosine kinase inhibitors
Authors: Ishibashi Masayuki , Neri Shinya , Hashimoto Hiroko , Miyashita Tomoyuki , Yoshida Tatsuya , Nakamura Yuka , Udagawa Hibiki , Kirita Keisuke , Matsumoto Shingo , Umemura Shigeki , Yoh Kiyotaka , Niho Seiji , Tsuboi Masahiro , Masutomi Kenkichi , Goto Koichi , Ochiai Atsushi , Ishii Genichiro
Published: April 2017

Cancer associated fibroblasts (CAFs) play important roles in the chemotherapeutic process, especially through influencing the resistance of tumor cells to molecular targeted therapy. Here we report the existence of a special subpopulation of patient-specific-CAFs that augment the sensitivity of EGFR gene mutation-positive lung cancer to the EGFR-tyrosine kinase inhibitor (EGFR-TKI), gefitinib. When cocultured with EGFR mutation positive lung cancer cells, these CAFs increased the apoptic effect of gefitinib on cancer cells, whereas, in the absence of gefitinib, they did not affect cancer cell viability. The assay using different single cell-derived clones demonstrated that the aforementioned sensitizing ability is clone-specific. Microarray analysis revealed that CD200 was expressed at much higher levels in this CAFs. Knocking down of CD200 expression deprived CAFs of their sensitizing potential, suggesting that CD200 is the functional molecule responsible for the effect. Immunohistochemical analysis of samples from patients receiving postoperative gefitinib treatment revealed that the individuals whose resected lung adenocarcinomas contained CD200-positive CAFs tended to have longer progression free survival of gefitinib when they recurred after surgery. These results suggest that CD200-positive CAFs can augment the sensitivity to EGFR-TKIs and may possess far reaching applications in the therapeutic use of EGFR-TKIs.
Soft Electronics Enabled Ergonomic Human-Computer Interaction for Swallowing Training
Authors: Lee Yongkuk , Nicholls Benjamin , Sup Lee Dong , Chen Yanfei , Chun Youngjae , Siang Ang Chee , Yeo Woon-Hong
Published: April 2017

We introduce a skin-friendly electronic system that enables human-computer interaction (HCI) for swallowing training in dysphagia rehabilitation. For an ergonomic HCI, we utilize a soft, highly compliant (“skin-like”) electrode, which addresses critical issues of an existing rigid and planar electrode combined with a problematic conductive electrolyte and adhesive pad. The skin-like electrode offers a highly conformal, user-comfortable interaction with the skin for long-term wearable, high-fidelity recording of swallowing electromyograms on the chin. Mechanics modeling and experimental quantification captures the ultra-elastic mechanical characteristics of an open mesh microstructured sensor, conjugated with an elastomeric membrane. Systematic in vivo studies investigate the functionality of the soft electronics for HCI-enabled swallowing training, which includes the application of a biofeedback system to detect swallowing behavior. The collection of results demonstrates clinical feasibility of the ergonomic electronics in HCI-driven rehabilitation for patients with swallowing disorders.
Correction: Corrigendum: A Doping Lattice of Aluminum and Copper with Accelerated Electron Transfer Process and Enhanced Reductive Degradation Performance
Authors: Zhang Lin , Gao Xue , Zhang Zhixuan , Zhang Mingbo , Cheng Yiqian , Su Jixin
Published: April 2017

Scientific Reports 6: Article number: 31797; published online: 18 August 2016; updated: 21 April 2017. In this Article, the compounds in the titles of Table 1 and Figure 9 have been mislabelled. The title of Table 1: “Zero-order kinetic parameters of X-3B degradation”. should read: “Zero-order kinetic parameters of Scarlet 3R degradation”.
A non-canonical binding interface in the crystal structure of HIV-1 gp120 core in complex with CD4
Authors: Duan Liang-Wei , Zhang Hui , Zhao Meng-Ting , Sun Ji-Xue , Chen Wen-Li , Lin Jian-Ping , Liu Xin-Qi
Published: April 2017

Numerous crystal structures of HIV gp120 have been reported, alone or with receptor CD4 and cognate antibodies; however, no sole gp120/CD4 complex without stabilization by an antibody is available. Here, we report a crystal structure of the gp120/CD4 complex without the aid of an antibody from HIV-1 CRF07_BC, a strain circulating in China. Interestingly, in addition to the canonical binding surface, a second interacting interface was identified. A mutagenesis study on critical residues revealed that the stability of this interface is important for the efficiency of Env-mediated membrane fusion. Furthermore, we found that a broad neutralizing antibody, ibalizumab, which targets CD4 in the absence of gp120, occupies the same binding surface as the second interface identified here on gp120. Therefore, we identified the possibility of the involvement of a second gp120-CD4 interaction interface during viral entry, and also provided a reasonable explanation for the broad activity of neutralizing antibody ibalizumab.
Interleukin-6 increases the expression and activity of insulin-degrading enzyme
Authors: Kurauti Mirian A. , Costa-Júnior José M. , Ferreira Sandra M. , Santos Gustavo J. , Sponton Carlos H. G. , Carneiro Everardo M. , Telles Guilherme D. , Chacon-Mikahil Mara P. T. , Cavaglieri Cláudia R. , Rezende Luiz F. , Boschero Antonio C.
Published: April 2017

Impairment of the insulin-degrading enzyme (IDE) is associated with obesity and type 2 diabetes mellitus (T2DM). Here, we used 4-mo-old male C57BL/6 interleukin-6 (IL-6) knockout mice (KO) to investigate the role of this cytokine on IDE expression and activity. IL-6 KO mice displayed lower insulin clearance in the liver and skeletal muscle, compared with wild type (WT), due to reduced IDE expression and activity. We also observed that after 3-h incubation, IL-6, 50 and 100 ng ml−1, increased the expression of IDE in HEPG2 and C2C12 cells, respectively. In addition, during acute exercise, the inhibition of IL-6 prevented an increase in insulin clearance and IDE expression and activity, mainly in the skeletal muscle. Finally, IL-6 and IDE concentrations were significantly increased in plasma from humans, after an acute exercise, compared to pre-exercise values. Although the increase in plasma IDE activity was only marginal, a positive correlation between IL-6 and IDE activity, and between IL-6 and IDE protein expression, was observed. Our outcomes indicate a novel function of IL-6 on the insulin metabolism expanding the possibilities for new potential therapeutic strategies, focused on insulin degradation, for the treatment and/or prevention of diseases related to hyperinsulinemia, such as obesity and T2DM.
Fucoxanthin provides neuroprotection in models of traumatic brain injury via the Nrf2-ARE and Nrf2-autophagy pathways
Authors: Zhang Li , Wang Handong , Fan Youwu , Gao Yongyue , Li Xiang , Hu Zhigang , Ding Ke , Wang Yujie , Wang Xiaoliang
Published: April 2017

Fucoxanthin is abundant in seaweed and is considered as a powerful antioxidant. It has been proposed to possess anti-cancer, anti-obesity and anti-diabetes effects. However, its roles in brain injury models have not been fully understood. The objective of this study was to investigate the neuroprotection of fucoxanthin in models of traumatic brain injury (TBI) and the role of the nuclear factor erythroid 2-related factor 2 (Nrf2)-antioxidant-response element (ARE) and Nrf2-autophagy pathways in the putative neuroprotection. We found that fucoxanthin alleviated TBI-induced secondary brain injury, including neurological deficits, cerebral edema, brain lesion and neuronal apoptosis. Moreover, the up-regulation of malondialdehyde (MDA) and the activity of glutathione peroxidase (GPx) were reversed by fucoxanthin treatment. Furthermore, our in vitro studies demonstrated that fucoxanthin increased the neuron survival and reduced the reactive oxygen species (ROS) level. In addition, fucoxanthin activated the Nrf2-ARE pathway and autophagy both in vivo and in vitro, which was proven by the results of immunohistochemistry, western blot and electrophoretic mobility shift assay (EMSA). However, fucoxanthin failed to provide neuroprotection and activated autophagy following TBI in Nrf2−/− mice. In conclusion, our studies indicated that fucoxanthin provided neuroprotective effects in models of TBI, potentially via regulation of the Nrf2-ARE and Nrf2-autophagy pathways.
Changes in arsenate bioaccumulation, subcellular distribution, depuration, and toxicity in Artemia salina nauplii in the presence of titanium dioxide nanoparticles
Authors: Yan Changzhou , Yang Fan , Wang Zaosheng , Wang Qiuquan , Seitz Frank , Luo Zhuanxi
Published: April 2017

The study provided a better understanding of arsenate bioavailability and toxicity associated with nano-TiO2in saltwater environments.
Generation and characterization of the blood transcriptome of Macaca thibetana and comparative analysis with M. mulatta
Authors: Li Peng , Du Lianming , Li Wujiao , Fan Zhenxin , Zeng Daiwen , Chen Hui , Zhou Liang , Yi Yong , Yang Na , Dou Kefeng , Yue Bisong , Li Jing
Published: April 2017

Transcriptome profiles provide a large transcript sequence data set for genomic study, particularly in organisms that have no accurate genome data published.
A label-free detection of diethylstilbestrol based on molecularly imprinted polymer-coated upconversion nanoparticles obtained by surface grafting
Authors: Wang Yu , Ren Shuyue , Jiang Huicong , Peng Yuan , Bai Jialei , Li Qiaofeng , Li Chao , Gao Zhixian , Ning Baoan
Published: April 2017

The novel MIPs-coated UCNPs fluorescent sensor could be used for on-field detection of diethylstilbestrol in real samples.
Development of emissive aminopentaazaphenalene derivatives employing a design strategy for obtaining luminescent conjugated molecules by modulating the symmetry of molecular orbitals with substituent effects
Authors: Watanabe Hiroyuki , Hirose Masataka , Tanaka Kazuo , Chujo Yoshiki
Published: April 2017

This communication describes the transformation of a non-emissive heterocycle into a luminophore via modulation of molecular orbitals by the introduction of dialkylamine group.
Targeting secondary protein complexes in drug discovery: studying the druggability and chemical biology of the HSP70/BAG1 complex
Authors: Evans Lindsay E. , Jones Keith , Cheeseman Matthew D.
Published: April 2017

A non-nucleotide FP-probe was designed to study the mechanism of action and druggability of the secondary HSP70/BAG1 complex.
A circulating electrolyte for a high performance carbon-based dye-sensitized solar cell
Authors: Gu Shuai , Bi Enbing , Fu Bitian , Dodbiba Gjergj , Fujita Toyohisa , Wilkinson David P. , Wei Yuezhou , Fang Baizeng
Published: April 2017

Novel Pt-free dye-sensitized solar cells with a circulating electrolyte demonstrate much better photovoltaic performance than those with a stationary one.
Stable (sila)difluoromethylboranes via C–F activation of fluoroform derivatives
Authors: Ito Shigekazu , Kato Naoto , Mikami Koichi
Published: April 2017

Lithium 1,3-bis(2,6-diisopropylphenyl)-2,3-dihydro-1H-1,3,2-diazaborol-2-uide activates the C–F linkage of CF3R (R = H, SiMe3) to provide difluoromethyl-substituted boranes as air-stable compounds.
Dynamical regimes of four oscillators with excitatory pulse coupling
Authors: Safonov Dmitry A. , Klinshov Vladimir V. , Vanag Vladimir K.
Published: April 2017

Dynamics of four almost identical chemical oscillators pulse coupled via excitatory coupling with time delays are systematically studied.
Molecular dynamics simulations of electric field induced water flow inside a carbon nanotorus: a molecular cyclotron
Authors: Sabzyan Hassan , Kowsar Maryam
Published: April 2017

A nano-flow is induced by applying gigahertz rotating electric fields (EFs) of different strengths and frequencies on a carbon nanotorus filled with water molecules, using molecular dynamics simulations.
Self-assembled core–polyethylene glycol–lipid shell nanoparticles demonstrate high stability in shear flow
Authors: Shen Zhiqiang , Ye Huilin , Kröger Martin , Li Ying
Published: April 2017

Core–polyethylene glycol–lipid shell (CPLS) nanoparticles demonstrate higher stability and less deformation in shear flow, in comparison with lipid vesicles.
Probing the role of excited states in ionization of acetylene
Authors: Dundas Daniel , Mulholland Peter , Wardlow Abigail , de la Calle Alejandro
Published: April 2017

Angularly-resolved photoelectron spectra for acetylene ionized by ultrashort laser pulses are calculated: these show how excited states influence electron emission.
Excitation wavelength dependence of the photoluminescence quantum yield and decay behavior of CdSe/CdS quantum dot/quantum rods with different aspect ratios
Authors: Geißler D. , Würth C. , Wolter C. , Weller H. , Resch-Genger U.
Published: April 2017

Our results reveal a strong λexc-dependence of PL quantum yields and decay times, particularly for longer quantum dot-quantum rods with high aspect ratios.
Probing covalency in halogen bonds through donor K-edge X-ray absorption spectroscopy: polyhalides as coordination complexes
Authors: Mustoe Chantal L. , Gunabalasingam Mathusan , Yu Darren , Patrick Brian O. , Kennepohl Pierre
Published: April 2017

The properties of halogen bonds (XBs) in solid-state I2X−and I4X−materials (where X = Cl, Br) are explored using donor K-edge X-ray absorption spectroscopy (XAS) to experimentally determine the degree of charge transfer in such XB interactions. The degree of covalency in these bonds is substantial, even in cases where significantly weaker secondary interactions are observed. These data, in concert with previous work in this area, suggests that certain halogen bonds have covalent contributions to bonding that are similar to, and even exceed, those observed in transition metal coordinate bonds. For this reason, we suggest that XB interactions of this type be denoted in a similar way to coordination bonds (X → Y) as opposed to using a representation that is the same as for significantly less covalent hydrogen bonds (X⋯Y).
Synthesis and magnetic and cytotoxic properties of copper(ii) halide complexes with 1,2,4-triazolo[1,5-a] benzimidazoles
Authors: Lavrenova L. G. , Kuz'menko T. A. , Ivanova A. D. , Smolentsev A. I. , Komarov V. Yu. , Bogomyakov A. S. , Sheludyakova L. A. , Vorontsova E. V.
Published: April 2017

Coordination compounds based on copper(ii) halides with 4H-1,2,4-triazolo[1,5-a]benzimidazole (L) and its derivatives with the compositions [CuL2Hal2]·nH2O.
An efficient charge separation and photocurrent generation in the carbon dot–zinc oxide nanoparticle composite
Authors: Barman Monoj Kumar , Mitra Piyali , Bera Rajesh , Das Somnath , Pramanik Amitava , Parta Amitava
Published: April 2017

The development of light harvesting systems based on heterostructures for efficient conversion of solar energy to renewable energy is an emerging area of research.
The application of perfluoroheteroaromatic reagents in the preparation of modified peptide systems
Authors: Gimenez Diana , Mooney Caitlin A. , Dose Anica , Sandford Graham , Coxon Christopher R. , Cobb Steven L.
Published: April 2017

A one-step peptide-modification using perfluoroheteroaromatics can deliver enhanced proteolytic stability in pharmaceutically relevant peptides such as oxytocin.
2,2,2-Trifluoroethanol as a solvent to control nucleophilic peptide arylation
Authors: Gimenez Diana , Dose Anica , Robson Nicholas L. , Sandford Graham , Cobb Steven L. , Coxon Christopher R.
Published: April 2017

Trifluoroethanol enables selective perfluoro-heteroaromatic peptide arylation of cysteine residues.
o,o-Difluorination of aromatic azide yields a fast-response fluorescent probe for H2S detection and for improved bioorthogonal reactions
Authors: Zhang Jie , Gao Yasi , Kang Xueying , Zhu Zhentao , Wang Zhiqian , Xi Zhen , Yi Long
Published: April 2017

Based on the o,o′-difluorinated aromatic azide, a new fluorescent probe was developed for the fast detection of H2S and for improved copper-free click and Staudinger reactions.
In situ synthesis of the Ag/poly(4-vinylpyridine)-block-polystyrene composite nanoparticles by dispersion RAFT polymerization
Authors: Liu Hui , Ding Mingdu , Ding Zhonglin , Gao Chengqiang , Zhang Wangqing
Published: April 2017

A new method for the synthesis of metal/block-copolymer nanocomposites of poly(4-vinylpyridine)-b-polystyrene (P4VP-b-PS) and Ag nanoparticles by dispersion RAFT polymerization is proposed.
Wholly biomass derivable sustainable polymers by ring-opening metathesis polymerisation of monomers obtained from furfuryl alcohol and itaconic anhydride
Authors: Bai Yinjuan , Clark James H. , Farmer Thomas J. , Ingram Ian D. V. , North Michael
Published: April 2017

Ring-opening metathesis polymerisation (ROMP) of oxanorbornene esters by Grubbs second generation catalyst is used to prepare a range of wholly biomass-derivable homo and copolymers.
Cisplatin combination drugs induce autophagy in HeLa cells and interact with HSA via electrostatic binding affinity
Authors: Chen Xuerui , Zhang Li , Ding Shiping , Lei Qunfang , Fang Wenjun
Published: April 2017

Cisplatin combination drugs induce autophagy in HeLa cells and interact with HSAviaelectrostatic binding affinity.
Iron phosphide nanocrystals decorated in situ on heteroatom-doped mesoporous carbon nanosheets used for an efficient oxygen reduction reaction in both alkaline and acidic media
Authors: Xu Xueyan , Shi Chengxiang , Chen Rui , Chen Tiehong
Published: April 2017

Oxygen reduction catalysts based on heteroatom-doped mesoporous carbon nanosheets loaded with highly crystalline FeP nanoparticles (FeP@FePNCs) were fabricated using a simple, one-step carbonization–phosphization methodology.
PHBV/bioglass composite scaffolds with co-cultures of endothelial cells and bone marrow stromal cells improve vascularization and osteogenesis for bone tissue engineering
Authors: Wu Jun , Wu Zhi , Xue Zhenqiang , Li Haiyan , Liu Jinbo
Published: April 2017

PHBV + 10% BG composite scaffolds stimulated osteogenic differentiation and angiogenic differentiation of co-cultures of HBMSCs and HUVECs by enhancing paracrine effects between the two types of cells.
Computational screening for high-activity MoS2 monolayer-based catalysts for the oxygen reduction reaction via substitutional doping with transition metal
Authors: Wang Zhongxu , Zhao Jingxiang , Cai Qinghai , Li Fengyu
Published: April 2017

By means of DFT computations we have proposed that Cu-doped MoS2 monolayer is a promising single-atom-catalyst with high efficiency for the ORR.
Benzophenone-based small molecular cathode interlayers with various polar groups for efficient polymer solar cells
Authors: Liu Zhiyang , Li Wang , Peng Ruixiang , Jiang Weigang , Guan Qian , Lei Tao , Yang Rongjuan , Islam Amjad , Wei Qiang , Ge Ziyi
Published: April 2017

A series of novel benzophenone-based molecules with different polar groups as cathode interfacial materials were synthesized for polymer solar cells.
The therapeutic potential of bacteriocins as protein antibiotics
Authors: Behrens Hannah M. , Six Anne , Walker Daniel , Kleanthous Colin
Published: April 2017

The growing incidence of antibiotic-resistant Gram-negative bacterial infections poses a serious threat to public health. Molecules that have yet to be exploited as antibiotics are potent protein toxins called bacteriocins that are produced by Gram-negative bacteria during competition for ecological niches. This review discusses the state of the art regarding the use for therapeutic purposes of two types of Gram-negative bacteriocins: colicin-like bacteriocins (CLBs) and tailocins. In addition to in vitro data, the potency of eight identified CLBs or tailocins has been demonstrated in diverse animal models of infection with no adverse effects for the host. Although the characteristics of bacteriocins will need further study, results obtained thus far regarding their in vivo potency, immunogenicity and low levels of resistance are encouraging. This leads the way for the development of novel treatments using bacteriocins as protein antibiotics.
Importance sampling with transformed weights
Authors: Vázquez M.A. , Míguez J.
Published: April 2017

The importance sampling (IS) method lies at the core of many Monte Carlo‐based techniques. IS allows the approximation of a target probability distribution by drawing samples from a proposal (or importance) distribution, different from the target, and computing importance weights (IWs) that account for the discrepancy between these two distributions. The main drawback of IS schemes is the degeneracy of the IWs, which significantly reduces the efficiency of the method. It has been recently proposed to use transformed IWs (TIWs) to alleviate the degeneracy problem in the context of population Monte Carlo, which is an iterative version of IS. However, the effectiveness of this technique for standard IS is yet to be investigated. The performance of IS when using TIWs is numerically assessed, and showed that the method can attain robustness to weight degeneracy thanks to a bias/variance trade‐off.
Compact InP spot‐size converter with vertically tapered core layer formed by micro‐loading effect
Authors: Ueda Y. , Ogiso Y. , Kashio N. , Hashizume Y. , Kikuchi N. , Ishikawa M. , Kohtoku M.
Published: April 2017

A compact (200 μm) spot‐size converter (SSC) with a vertically tapered core layer is developed, which is fabricated with a simple wafer process using the micro‐loading effect. It is confirmed that the vertical spot size of the SSC exceeded 2 μm, which was double that of the original waveguide. As a result, an InP waveguide integrated with the SSCs exhibited a coupling loss of <1 dB per facet for a lensed fibre with a 2.5 μm mode‐field diameter. The fluctuation in the total of coupling and excess losses of the SSC was <0.5 dB.
SSC strategy for SRG to achieve maximum power with minimum current ripple in battery charging
Authors: Roshandel Emad , Namazi Mohammad Masoud , Rashidi Amir , Saghaian‐Nejad Sayed Morteza , Ahn Jin‐Woo
Published: April 2017

Selection of electrical machine is a key issue in electrical and hybrid electrical vehicles (HEVs and EVs). As far as HEVs and EVs are concerned, mechanical ruggedness of electrical machine is of utmost importance. For these reasons, the application of switched reluctance (SR) machine in EVs and HEVs is a viable option. In this study, an SR generator (SRG) has been utilised to work as a battery charger in EVs. The current ripple of the SRG is the greatest issue when it works as a battery charger. Therefore, a power converter and a smart search control (SSC) approach are proposed in this study to decrease the current ripple when the output power has a maximum quantity. During the system operation, the SSC method determines the value of excitation angle, turn‐on and turn‐off angles for each phase of SRG. The simulation and experimental results demonstrate the eligibility of the SSC system and power converter to obtain the acceptable charging current in maximum generated power during battery charging.
Multicast middleware for performance and topology analysis of multimedia grids
Authors: Xie Jerry Z. , Chen Shaoli , Yang Zongkai
Published: April 2017

Since multicast reduces bandwidth consumption in multimedia grid computing, the middleware for monitoring the performance and topology of multicast communications is important to the design and management of multimedia grid applications. However, the current middleware technologies for multicast performance monitoring are still far from attaining the level of maturity and there lacks consistent approaches to obtain the evaluation data for multicast. In this study, to serve a clear guide for the design and implementation of the multicast middleware, two algorithms are developed for organising all constituents in multicast communications and analysing the multicast performance in two topologies – ‘multicast distribution tree’ and ‘clusters distribution’, and a definitive set of corresponding metrics that are comprehensive yet viable for evaluating multicast communications are also presented. Instead of using the inference data from unicast measurements, in the proposed middleware, the measuring data of multicast traffic are obtained directly from multicast protocols in real time. Moreover, this study makes a middleware implementation which is integrated into a real access grid multicast communication infrastructure. The results of the implementation demonstrate the substantial improvements in the accuracy and real time in evaluating the performance and topology of multicast network.
Distance estimates for state constrained trajectories of infinite dimensional differential inclusions
Authors: Frankowska Helene , Marchini Elsa M. , Mazzola Marco
Published: April 2017

This paper concerns estimates on the distance between a trajectory of a differential inclusion and the set of feasible trajectories of the same inclusion, feasible meaning confined to a given set of constraints. We apply these estimates to investigate Lipschitz continuity of the value functions arising in optimal control, and to variational inclusions, useful for proving non degenerate necessary optimality conditions. The main feature of our analysis is the infinite dimensional framework, which can be applied to models involving PDEs.
Role of the LF-SINE–Derived Distal ISL1 Enhancer in Patients with Classic Bladder Exstrophy
Authors: Zhang Rong , Knapp Michael , Kause Franziska , Reutter Heiko , Ludwig Michael
Published: April 2017

A genome-wide association study and meta-analysis identified ISL1 as the first genome-wide significant susceptibility gene for classic bladder exstrophy (CBE). A short interspersed repetitive element (SINE), first detected in lobe-finned fishes (LF-SINE), was shown to drive Isl1 expression in embryonic mouse genital eminence. Hence, we assumed this enhancer a conclusive target for mutations associated with CBE formation and analyzed a cohort of 200 CBE patients. Although we identified two enhancer variants in five CBE patients, their clinical significance seems unlikely, implying that sequence variants in the ISL1 LF-SINE enhancer are not frequently associated with CBE.
Comparison of Intact Parathyroid Hormone, Alkaline Phosphatase, Phosphate Levels for Diagnosing Severe Metabolic Bone Disease in Infants with Severe Bronchopulmonary Dysplasia
Authors: Tkach Erin , White Ammie , Dysart Kevin , Waber Brenda , Nawab Ursula , Zhang Huayan , Jensen Erik
Published: April 2017

Objective We compared the accuracy of serum intact parathyroid hormone (iPTH), alkaline phosphatase (ALP), and phosphate (phos) levels for diagnosing severe metabolic bone disease (MBD) in very low-birth-weight (VLBW) infants with severe bronchopulmonary dysplasia (BPD).

Study Design Retrospective analysis of VLBW infants with severe BPD admitted between 2010 and 2012 and with ≥ 1 iPTH, ALP, and phos level collected within a similar 72-hour period. MBD severity was classified by serial radiography.

Results Laboratory values were available for 65 infants, of whom 24 (36.9%) developed severe MBD. A maximum ALP > 660 IU/L was the most accurate for diagnosing severe MBD (area under the curve: 88.4%; 95% confidence interval [CI]: 77.2–94.5%). Maximum iPTH was the least accurate (optimal cut point > 130 pg/mL; area under the curve: 70.5%; 95% CI: 58.2–81.4).

Conclusion Maximum ALP was more accurate than iPTH or phos for diagnosing severe MBD among preterm infants with severe BPD.
A combined theoretical and experimental study of phenol-(acetylene)n (n ≤ 7) clusters
Authors: Singh Gurmeet , Nandi Apurba , Gadre Shridhar R. , Chiba Takashi , Fujii Asuka
Published: April 2017

Structures and vibrational spectra of phenol-(acetylene)n (Ph(Ac)n) clusters are studied by a combination of theoretical calculations and infrared (IR) spectroscopy. The molecular electrostatic potential features are utilized for generating trial geometries of the medium-sized Ph(Ac)n (n = 1, 2, 4, 6, and 7) clusters. These initial geometries are subjected to geometry optimization within the second-order Møller-Plesset (MP2) theory, employing correlation consistent aug-cc-pVDZ (aVDZ) basis set. Minimal nature of the reported structures is confirmed by doing vibrational frequency run at MP2/aVDZ level of theory using full calculations for n = 1 and 2 and employing grafting based molecular tailoring approach for the n = 4, 6, and 7. Several isomers for n ≥ 4 are found to lie in an energy window of 1 kcal mol−1 of each other. Considering the formidability of MP2 level investigation for the large number of isomers for n = 6 and 7, B97-D level theory is used for studying their energetics and IR spectra. It is seen that the number of energetically close isomers increases with increasing n. Moderately size-selected IR spectra of Ph(Ac)n (n = 4 and 7), prepared by a supersonic jet expansion, are measured for the acetylenic C–H and phenolic O–H stretch regions by infrared-ultraviolet (IR-UV) double resonance spectroscopy combined with time-of-flight mass spectrometry. Asymmetric line shape of the C–H stretch band and remarkable line broadening and weakening of the O–H stretch band are noteworthy features of the observed spectra. These findings of the experimental spectra are explained by the theoretical studies. The averaging of the vibrational spectrum of low-lying isomers of the Ph(Ac)n clusters lying in a narrow energy range is found to be responsible for the broadening and weakening of the O–H band.
About the nature of halogen bond interaction under the spatial confinement
Authors: Roztoczyńska Agnieszka , Lipkowski Paweł , Kozłowska Justyna , Bartkowiak Wojciech
Published: April 2017

Nowadays, much attention is put toward the description of noncovalent complexes exposed to the high pressure or embedded in confining environments. Such conditions may strongly modify the physical and chemical properties of molecular systems. This study focuses on the theoretical description of the confinement induced changes in geometry and energetic parameters of the halogen bonded FCl⋯CNF complex. A model analytical potential is applied to render the effect of orbital compression. In order to analyze the nature of halogen bond interaction, in the presence of spatial confinement, the supermolecular approach together with the symmetry-adapted perturbation theory is used. Furthermore, a thorough analysis of topological parameters, characterizing the halogen bond upon orbital compression, is performed within the quantum theory of atoms in molecules. The calculations are carried out using the ωB97x and CCSD(T) methods in connection with the aug-cc-pVTZ basis set. Among others, the obtained results indicate that the spatial confinement not only modifies the nature of halogen bond interaction but also induces the appearance of a completely new form of the studied FCl⋯CNF system.
IR spectral assignments for the hydrated excess proton in liquid water
Authors: Biswas Rajib , Carpenter William , Fournier Joseph A. , Voth Gregory A. , Tokmakoff Andrei
Published: April 2017

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm−1 for every local proton configuration, with the region 2000-2600 cm−1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H+⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H5O2+moiety.
Ramped-amplitude NOVEL
Authors: Can T. V. , Weber R. T. , Walish J. J. , Swager T. M. , Griffin R. G.
Published: April 2017

We present a pulsed dynamic nuclear polarization (DNP) study using a ramped-amplitude nuclear orientation via electron spin locking (RA-NOVEL) sequence that utilizes a fast arbitrary waveform generator (AWG) to modulate the microwave pulses together with samples doped with narrow-line radicals such as 1,3-bisdiphenylene-2-phenylallyl (BDPA), sulfonated-BDPA (SA-BDPA), and trityl-OX063. Similar to ramped-amplitude cross polarization in solid-state nuclear magnetic resonance, RA-NOVEL improves the DNP efficiency by a factor of up to 1.6 compared to constant-amplitude NOVEL (CA-NOVEL) but requires a longer mixing time. For example, at τmix = 8 μs, the DNP efficiency reaches a plateau at a ramp amplitude of ∼20 MHz for both SA-BDPA and trityl-OX063, regardless of the ramp profile (linear vs. tangent). At shorter mixing times (τmix = 0.8 μs), we found that the tangent ramp is superior to its linear counterpart and in both cases there exists an optimum ramp size and therefore ramp rate. Our results suggest that RA-NOVEL should be used instead of CA-NOVEL as long as the electronic spin lattice relaxation T1e is sufficiently long and/or the duty cycle of the microwave amplifier is not exceeded. To the best of our knowledge, this is the first example of a time domain DNP experiment that utilizes modulated microwave pulses. Our results also suggest that a precise modulation of the microwave pulses can play an important role in optimizing the efficiency of pulsed DNP experiments and an AWG is an elegant instrumental solution for this purpose.
Tests for, origins of, and corrections to non-Gaussian statistics. The dipole-flip model
Authors: Schile Addison J. , Thompson Ward H.
Published: April 2017

Linear response approximations are central to our understanding and simulations of nonequilibrium statistical mechanics. Despite the success of these approaches in predicting nonequilibrium dynamics, open questions remain. Laird and Thompson [J. Chem. Phys. 126, 211104 (2007)] previously formalized, in the context of solvation dynamics, the connection between the static linear-response approximation and the assumption of Gaussian statistics. The Gaussian statistics perspective is useful in understanding why linear response approximations are still accurate for perturbations much larger than thermal energies. In this paper, we use this approach to address three outstanding issues in the context of the “dipole-flip” model, which is known to exhibit nonlinear response. First, we demonstrate how non-Gaussian statistics can be predicted from purely equilibrium molecular dynamics (MD) simulations (i.e., without resort to a full nonequilibrium MD as is the current practice). Second, we show that the Gaussian statistics approximation may also be used to identify the physical origins of nonlinear response residing in a small number of coordinates. Third, we explore an approach for correcting the Gaussian statistics approximation for nonlinear response effects using the same equilibrium simulation. The results are discussed in the context of several other examples of nonlinear responses throughout the literature.
Correlation of the fragility of metallic liquids with the high temperature structure, volume, and cohesive energy
Authors: Gangopadhyay A. K. , Pueblo C. E. , Dai R. , Johnson M. L. , Ashcraft R. , Van Hoesen D. , Sellers M. , Kelton K. F.
Published: April 2017

The thermal expansion coefficients, structure factors, and viscosities of twenty-five equilibrium and supercooled metallic liquids have been measured using an electrostatic levitation (ESL) facility. The structure factor was measured at the Advanced Photon Source, Argonne, using the ESL. A clear connection between liquid fragility and structural and volumetric changes at high temperatures is established; the observed changes are larger for the more fragile liquids. It is also demonstrated that the fragility of metallic liquids is determined to a large extent by the cohesive energy and is, therefore, predictable. These results are expected to provide useful guidance in the future design of metallic glasses.
Path integral molecular dynamics with surface hopping for thermal equilibrium sampling of nonadiabatic systems
Authors: Lu Jianfeng , Zhou Zhennan
Published: April 2017

In this work, a novel ring polymer representation for a multi-level quantum system is proposed for thermal average calculations. The proposed representation keeps the discreteness of the electronic states: besides position and momentum, each bead in the ring polymer is also characterized by a surface index indicating the electronic energy surface. A path integral molecular dynamics with surface hopping (PIMD-SH) dynamics is also developed to sample the equilibrium distribution of the ring polymer configurational space. The PIMD-SH sampling method is validated theoretically and by numerical examples.
To kink or not: A search for long-chain cumulenones using microwave spectral taxonomy
Authors: McCarthy Michael C. , Zou Luyao , Martin-Drumel Marie-Aline
Published: April 2017

A systematic search for carbon-chain cumulenones beyond H2C4O has been undertaken using microwave spectral taxonomy in combination with a pulsed jet discharge source. No evidence was found for the C2υ isomer of H2C5O or its longer derivatives, but HC(O)C4H, the longer variant of propynal, HC(O)CCH, was identified instead. Its rotational and leading centrifugal distortion constants have been derived to high accuracy from detection of both a- and b-type lines; those below 40 GHz were measured using a Fabry-Perot cavity, while lines between 40 and 72 GHz were recorded by double resonance techniques. Overwhelming evidence for the identification is provided by detection of HC(O)C4D, DC(O)C4H, and HC(18O)C4H at the expected frequencies using isotopically enriched samples. Because HC(18O)C4H is produced with comparable abundance when using either 18O2 or C18O as the source of oxygen, and because H13C(O)C4H is not preferentially formed when starting from 13CO, atomic oxygen appears to be a key reactant in formation, plausibly via O insertion, e.g., H2CC2n+2H + O → HC(O)C2n+2H + H. Under the same experimental conditions, HC(O)CCH is more than 10 times more abundant than H2C3O, regardless of the source of oxygen, and no evidence is found for cyclopropenone, c-C3H2O. Taken together, these observations indicate that propynal and longer chains with an odd number of carbon atoms are either energetically more stable than cumulenones of the same size, are kinetically favored products, or both. On the basis of the HC(O)C4H discovery, searches for the isovalent sulfur species, HC(S)C4H, and HC(O)C6H have been conducted. Guided by new quantum chemical calculations, the rotational spectra of both were observed in the centimeter-wave band with the same spectrometer.
A high-precision digital integrator based on the Romberg algorithm
Authors: Li Zhen-Hua , Hu Wei-Zhong
Published: April 2017

An integrator is widely used for measurement in the field of power systems, and it is a key technology in signal processing. According to research on the digital integrator based on the traditional Newton–Cotes algorithm, the high-frequency response of the low-order Cotes formula is usually poor and the design of the transfer function introduced by the high-order Cotes formula is too complex. In this paper, we analyze the error between the composite Newton–Cotes algorithm and the ideal transfer function. One signal was sampled using the normal sampling frequency and the other signal was sampled using half the normal sampling frequency. The two signals were weighted based on the Romberg algorithm. Thus, the precision of the digital integrator was improved, and the design difficulty was reduced for algorithms of the same order. The simulation and test results show that the proposed digital integrator has better transient and steady performance, and also has a lower error, which is less than 0.01%.