bluuebunny/crossref_metadata_2025 huggingface dataset:
CenH3 evolution reflects meiotic symmetry as predicted by the centromere drive model
Authors: Zedek František , Bureš Petr
Published: September 2016

The centromere drive model explaining rapid evolution of eukaryotic centromeres predicts higher frequency of positive selection acting on centromeric histone H3 (CenH3) in clades with asymmetric meiosis compared to the clades with only symmetric meiosis. However, despite the impression one might get from the literature, this key prediction of the centromere drive model has not only never been confirmed, but it has never been tested, because all the previous studies dealt only with the presence or absence instead of the frequency of positive selection. To provide evidence for or against different frequencies of positively selected CenH3 in asymmetrics and symmetrics, we have inferred the selective pressures acting on CenH3 in seventeen eukaryotic clades, including plants, animals, fungi, ciliates and apicomplexa, using codon-substitution models, and compared the inferred frequencies between asymmetrics and symmetrics in a quantitative manner. We have found that CenH3 has been evolving adaptively much more frequently in clades with asymmetric meiosis compared with clades displaying only symmetric meiosis which confirms the prediction of centromere drive model. Our findings indicate that the evolution of asymmetric meiosis required CenH3 to evolve adaptively more often to counterbalance the negative consequences of centromere drive.
Comparative DNA Methylation Profiling Reveals an Immunoepigenetic Signature of HIV-related Cognitive Impairment
Authors: Corley Michael J. , Dye Christian , D’Antoni Michelle L. , Byron Mary Margaret , Yo Kaahukane Leite-Ah , Lum-Jones Annette , Nakamoto Beau , Valcour Victor , SahBandar Ivo , Shikuma Cecilia M. , Ndhlovu Lishomwa C. , Maunakea Alika K.
Published: September 2016

Monocytes/macrophages contribute to the neuropathogenesis of HIV-related cognitive impairment (CI); however, considerable gaps in our understanding of the precise mechanisms driving this relationship remain. Furthermore, whether a distinct biological profile associated with HIV-related CI resides in immune cell populations remains unknown. Here, we profiled DNA methylomes and transcriptomes of monocytes derived from HIV-infected individuals with and without CI using genome-wide DNA methylation and gene expression profiling. We identified 1,032 CI-associated differentially methylated loci in monocytes. These loci related to gene networks linked to the central nervous system (CNS) and interactions with HIV. Most (70.6%) of these loci exhibited higher DNA methylation states in the CI group and were preferentially distributed over gene bodies and intergenic regions of the genome. CI-associated DNA methylation states at 12 CpG sites associated with neuropsychological testing performance scores. CI-associated DNA methylation also associated with gene expression differences including CNS genes CSRNP1 (P = 0.017), DISC1 (P = 0.012), and NR4A2 (P = 0.005); and a gene known to relate to HIV viremia, THBS1 (P = 0.003). This discovery cohort data unveils cell type-specific DNA methylation patterns related to HIV-associated CI and provide an immunoepigenetic DNA methylation “signature” potentially useful for corroborating clinical assessments, informing pathogenic mechanisms, and revealing new therapeutic targets against CI.
Long-term adaptation of the influenza A virus by escaping cytotoxic T-cell recognition
Authors: Woolthuis Rutger G. , van Dorp Christiaan H. , Keşmir Can , de Boer Rob J. , van Boven Michiel
Published: September 2016

The evolutionary adaptation of the influenza A virus (IAV) to human antibodies is well characterised. Much less is known about the long-term evolution of cytotoxic T lymphocyte (CTL) epitopes, which are important antigens for clearance of infection. We construct an antigenic map of IAVs of all human subtypes using a compendium of 142 confirmed CTL epitopes, and show that IAV evolved gradually in the period 1932–2015, with infrequent antigenic jumps in the H3N2 subtype. Intriguingly, the number of CTL epitopes per virus decreases with more than one epitope per three years in the H3N2 subtype (from 84 epitopes per virus in 1968 to 64 in 2015), mostly attributed to the loss of HLA-B epitopes. We confirm these observations with epitope predictions. Our findings indicate that selection pressures imposed by CTL immunity shape the long-term evolution of IAV.
Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane
Authors: Zhang Mingzhen , Zheng Jie , Nussinov Ruth , Ma Buyong
Published: September 2016

Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.
SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics
Authors: Chen Dana , Orenstein Yaron , Golodnitsky Rada , Pellach Michal , Avrahami Dorit , Wachtel Chaim , Ovadia-Shochat Avital , Shir-Shapira Hila , Kedmi Adi , Juven-Gershon Tamar , Shamir Ron , Gerber Doron
Published: September 2016

Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression.
Charge transport mechanism in lead oxide revealed by CELIV technique
Authors: Semeniuk O. , Juska G. , Oelerich J.-O. , Wiemer M. , Baranovskii S. D. , Reznik A.
Published: September 2016

Although polycrystalline lead oxide (PbO) belongs to the most promising photoconductors for optoelectronic and large area detectors applications, the charge transport mechanism in this material still remains unclear. Combining the conventional time-of-flight and the photo-generated charge extraction by linear increasing voltage (photo-CELIV) techniques, we investigate the transport of holes which are shown to be the faster carriers in poly-PbO. Experimentally measured temperature and electric field dependences of the hole mobility suggest a highly dispersive transport. In order to analyze the transport features quantitatively, the theory of the photo-CELIV is extended to account for the dispersive nature of charge transport. While in other materials with dispersive transport the amount of dispersion usually depends on temperature, this is not the case in poly-PbO, which evidences that dispersive transport is caused by the spatial inhomogeneity of the material and not by the energy disorder.
Y chromosome haplogroups based genome-wide association study pinpoints revelation for interactions on non-obstructive azoospermia
Authors: Lu Chuncheng , Wen Yang , Hu Weiyue , Lu Feng , Qin Yufeng , Wang Ying , Li Shilin , Yang Shuping , Lin Yuan , Wang Cheng , Jin Li , Shen Hongbing , Sha Jiahao , Wang Xinru , Hu Zhibin , Xia Yankai
Published: September 2016

The Y chromosome has high genetic variability with low rates of parallel and back mutations, which make up the most informative haplotyping system. To examine whether Y chromosome haplogroups (Y-hgs) could modify the effects of autosomal variants on non-obstructive azoospermia (NOA), based on our previous genome-wide association study (GWAS), we conducted a genetic interaction analysis in GWAS subjects. Logistic regression analysis demonstrated a protective effect of Y-hg O3e* on NOA. Then, we explored the potential interaction between Y-hg O3e* and autosomal variants. Our results demonstrated that there was a suggestively significant interaction between Y-hg O3e* and rs11135484 on NOA (Pinter = 9.89 × 10−5). Bioinformatic analysis revealed that genes annotated by significant single nucleotide polymorphisms (SNPs) were mainly enriched in immunological pathways. This is the first study of interactions between Y-hgs and autosomal variants on a genome-wide scale, which addresses the missing heritability in spermatogenic impairment and sheds new light on the pathogenesis of male infertility.
Molecular Dynamics Simulations of the Permeation of Bisphenol A and Pore Formation in a Lipid Membrane
Authors: Chen Liang , Chen Junlang , Zhou Guoquan , Wang Yu , Xu Can , Wang Xiaogang
Published: September 2016

Bisphenol A (BPA) is particularly considered as one of the most suspicious endocrine disruptors. Exposure to BPA may bring about possible human toxicities, such as cancerous tumors, birth defects and neoteny. One of the key issues to understand its toxicities is how BPA enters cells. In this paper, we perform molecular dynamics simulations to explore the interactions between BPA and a phospholipid membrane (dipalmitoylphosphatidylcholine, DPPC bilayer). The simulation results show that BPA can easily enter the membrane from the aqueous phase. With the increasing concentrations of BPA in the membrane, BPA tends to aggregate and form into cluster. Meanwhile, several DPPC lipids are pulled out from each leaflet and adsorbed on the cluster surface, leading to pore formation. Detailed observations indicate that the lipid extraction results mainly from the dispersion interactions between BPA cluster and lipid tails, as well as weak electrostatic attractions between lipid headgroups and the two hydroxyl groups on BPA. The lipid extraction and pore formation may cause cell membrane damage and are of great importance to uncover BPA’s cytotoxicity.
Solar-rechargeable battery based on photoelectrochemical water oxidation: Solar water battery
Authors: Kim Gonu , Oh Misol , Park Yiseul
Published: September 2016

As an alternative to the photoelectrochemical water splitting for use in the fuel cells used to generate electrical power, this study set out to develop a solar energy rechargeable battery system based on photoelectrochemical water oxidation. We refer to this design as a “solar water battery”. The solar water battery integrates a photoelectrochemical cell and battery into a single device. It uses a water oxidation reaction to simultaneously convert and store solar energy. With the solar water battery, light striking the photoelectrode causes the water to be photo-oxidized, thus charging the battery. During the discharge process, the solar water battery reduces oxygen to water with a high coulombic efficiency (>90%) and a high average output voltage (0.6 V). Because the reduction potential of oxygen is more positive [E0 (O2/H2O) = 1.23 V vs. NHE] than common catholytes (e.g., iodide, sulfur), a high discharge voltage is produced. The solar water battery also exhibits a superior storage ability, maintaining 99% of its specific discharge capacitance after 10 h of storage, without any evidence of self-discharge. The optimization of the cell design and configuration, taking the presence of oxygen in the cell into account, was critical to achieving an efficient photocharge/discharge.
Time-dependent effects of ultraviolet and nonthermal atmospheric pressure plasma on the biological activity of titanium
Authors: Choi Sung-Hwan , Jeong Won-Seok , Cha Jung-Yul , Lee Jae-Hoon , Yu Hyung-Seog , Choi Eun-Ha , Kim Kwang-Mahn , Hwang Chung-Ju
Published: September 2016

Here, we evaluated time-dependent changes in the effects of ultraviolet (UV) and nonthermal atmospheric pressure plasma (NTAPPJ) on the biological activity of titanium compared with that of untreated titanium. Grade IV machined surface titanium discs (12-mm diameter) were used immediately and stored up to 28 days after 15-min UV or 10-min NTAPPJ treatment. Changes of surface characteristics over time were evaluated using scanning electron microscopy, surface profiling, contact angle analysis, X-ray photoelectron spectroscopy, and surface zeta-potential. Changes in biological activity over time were as determined by analysing bovine serum albumin adsorption, MC3T3-E1 early adhesion and morphometry, and alkaline phosphatase (ALP) activity between groups. We found no differences in the effects of treatment on titanium between UV or NTAPPJ over time; both treatments resulted in changes from negatively charged hydrophobic (bioinert) to positively charged hydrophilic (bioactive) surfaces, allowing enhancement of albumin adsorption, osteoblastic cell attachment, and cytoskeleton development. Although this effect may not be prolonged for promotion of cell adhesion until 4 weeks, the effects were sufficient to maintain ALP activity after 7 days of incubation. This positive effect of UV and NTAPPJ treatment can enhance the biological activity of titanium over time.
The coiled-coil domain of zebrafish TRPM7 regulates Mg·nucleotide sensitivity
Authors: Jansen Chad , Sahni Jaya , Suzuki Sayuri , Horgen F. David , Penner Reinhold , Fleig Andrea
Published: September 2016

TRPM7 is a member of the Transient-Receptor-Potential Melastatin ion channel family. TRPM7 is a unique fusion protein of an ion channel and an α-kinase. Although mammalian TRPM7 is well characterized biophysically and its pivotal role in cancer, ischemia and cardiovascular disease is becoming increasingly evident, the study of TRPM7 in mouse models has been hampered by embryonic lethality of transgenic ablations. In zebrafish, functional loss of TRPM7 (drTRPM7) manifests itself in an array of non-lethal physiological malfunctions. Here, we investigate the regulation of wild type drTRPM7 and multiple C-terminal truncation mutants. We find that the biophysical properties of drTRPM7 are very similar to mammalian TRPM7. However, pharmacological profiling reveals that drTRPM7 is facilitated rather than inhibited by 2-APB, and that the TRPM7 inhibitor waixenicin A has no effect. This is reminiscent of the pharmacological profile of human TRPM6, the sister channel kinase of TRPM7. Furthermore, using truncation mutations, we show that the coiled-coil domain of drTRPM7 is involved in the channel’s regulation by magnesium (Mg) and Mg·adenosine triphosphate (Mg·ATP). We propose that drTRPM7 has two protein domains that regulate inhibition by intracellular magnesium and nucleotides, and one domain that is concerned with sensing magnesium only.
Global Ionospheric Modelling using Multi-GNSS: BeiDou, Galileo, GLONASS and GPS
Authors: Ren Xiaodong , Zhang Xiaohong , Xie Weiliang , Zhang Keke , Yuan Yongqiang , Li Xingxing
Published: September 2016

The emergence of China’s Beidou, Europe’s Galileo and Russia’s GLONASS satellites has multiplied the number of ionospheric piercing points (IPP) offered by GPS alone. This provides great opportunities for deriving precise global ionospheric maps (GIMs) with high resolution to improve positioning accuracy and ionospheric monitoring capabilities. In this paper, the GIM is developed based on multi-GNSS (GPS, GLONASS, BeiDou and Galileo) observations in the current multi-constellation condition. The performance and contribution of multi-GNSS for ionospheric modelling are carefully analysed and evaluated. Multi-GNSS observations of over 300 stations from the Multi-GNSS Experiment (MGEX) and International GNSS Service (IGS) networks for two months are processed. The results show that the multi-GNSS GIM products are better than those of GIM products based on GPS-only. Differential code biases (DCB) are by-products of the multi-GNSS ionosphere modelling, the corresponding standard deviations (STDs) are 0.06 ns, 0.10 ns, 0.18 ns and 0.15 ns for GPS, GLONASS, BeiDou and Galileo, respectively in satellite, and the STDs for the receiver are approximately 0.2~0.4 ns. The single-frequency precise point positioning (SF-PPP) results indicate that the ionospheric modelling accuracy of the proposed method based on multi-GNSS observations is better than that of the current dual-system GIM in specific areas.
Flat-Lens Focusing of Electron Beams in Graphene
Authors: Tang Yang , Cao Xiyuan , Guo Ran , Zhang Yanyan , Che Zhiyuan , Yannick Fouodji T. , Zhang Weiping , Du Junjie
Published: September 2016

Coupling electron beams carrying information into electronic units is fundamental in microelectronics. This requires precision manipulation of electron beams through a coupler with a good focusing ability. In graphene, the focusing of wide electron beams has been successfully demonstrated by a circular p-n junction. However, it is not favorable for information coupling since the focal length is so small that the focal spot locates inside the circular gated region, rather than in the background region. Here, we demonstrate that an array of gate-defined quantum dots, which has gradually changing lattice spacing in the direction transverse to propagation, can focus electrons outside itself, providing a possibility to make a coupler in graphene. The focusing effect can be understood as due to the gradient change of effective refractive indices, which are defined by the local energy band in a periodic potential. The strong focusing can be achieved by suitably choosing the lattice gradient and the layer number in the incident direction, offering an effective solution to precision manipulation of electron beams with wide electron energy range and high angular tolerance.
Crystal structures of the bifunctional tRNA methyltransferase Trm5a
Authors: Wang Caiyan , Jia Qian , Chen Ran , Wei Yuming , Li Juntao , Ma Jie , Xie Wei
Published: September 2016

tRNA methyltransferase Trm5 catalyses the transfer of a methyl group from S-adenosyl-L-methionine to G37 in eukaryotes and archaea. The N1-methylated guanosine is the product of the initial step of the wyosine hypermodification, which is essential for the maintenance of the reading frame during translation. As a unique member of this enzyme family, Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4-demethylwyosine at position 37 to produce isowyosine, but the mechanism for the double methylation is poorly understood. Here we report four crystal structures of PaTrm5a ranging from 1.7- to 2.3-Å, in the apo form or in complex with various SAM analogues. These structures reveal that Asp243 specifically recognises the base moiety of SAM at the active site. Interestingly, the protein in our structures all displays an extended conformation, quite different from the well-folded conformation of Trm5b from Methanocaldococcus jannaschii reported previously, despite their similar overall architectures. To rule out the possibilities of crystallisation artefacts, we conducted the fluorescence resonance energy transfer (FRET) experiments. The FRET data suggested that PaTrm5a adopts a naturally extended conformation in solution, and therefore the open conformation is a genuine state of PaTrm5a.
Methylcrotonoyl-CoA carboxylase 1 potentiates RLR-induced NF-κB signaling by targeting MAVS complex
Authors: Cao Zhongying , Xia Zhangchuan , Zhou Yaqin , Yang Xiaodan , Hao Hua , Peng Nanfang , Liu Shi , Zhu Ying
Published: September 2016

RNA virus infections are detected by the RIG-I family of receptors, which signal through the adaptor molecule mitochondrial antiviral signaling (MAVS). MAVS then recruits the adaptor’s tumor necrosis factor receptor-associated factor (TRAF) 3 and TRAF6, which in turn activate IRF3 and NF-κB, respectively, to induce interferons (IFNs) and inflammatory responses. Here we show that the biotin-containing enzyme methylcrotonoyl-CoA carboxylase 1 (MCCC1) enhances virus-induced, MAVS-mediated IFN and inflammatory cytokine expression through the NF-κB signaling pathway. MCCC1 knockdown strongly inhibits induction of IFNs and inflammatory cytokines. Furthermore, MCCC1 shows extensive antiviral activity toward RNA viruses, including influenza A virus, human enterovirus 71, and vesicular stomatitis virus. Here, we have elucidated the mechanism underlying MCCC1-mediated inhibition of viral replication. MCCC1 interacts with MAVS and components of the MAVS signalosome and contributes to enhanced production of type I IFNs and pro-inflammatory cytokines by promoting phosphorylation of the IκB kinase (IKK) complex and NF-κB inhibitor-α (IκBα), as well as NF-κB nuclear translocation. This process leads to activation of IFNs and cytokine expression and subsequent activation of IFN-stimulated genes, including double-stranded RNA-dependent protein kinase PKR and myxovirus resistance protein 1. These findings demonstrate that MCCC1 plays an essential role in virus-triggered, MAVS-mediated activation of NF-κB signaling.
Signal amplification of microRNAs with modified strand displacement-based cycling probe technology
Authors: Jia Huning , Bu Ying , Zou Bingjie , Wang Jianping , Kumar Shalen , Pitman Janet L. , Zhou Guohua , Song Qinxin
Published: September 2016

Micro ribose nucleic acids (miRNAs) play an important role in biological processes such as cell differentiation, proliferation and apoptosis.
Ultrasound-assisted micellar extraction of phenolic antioxidants from spices and antioxidant properties of the extracts based on coulometric titration data
Authors: Ziyatdinova Guzel , Ziganshina Endzhe , Cong Phuc Nguyen , Budnikov Herman
Published: September 2016

Ultrasound-assisted extraction of phenolic antioxidants from spices using surfactant-based micellar media.
Amide-functionalized pillar[5]arenes as a novel class of macrocyclic receptors for the sensing of H2PO4−anion
Authors: Yakimova L. S. , Shurpik D. N. , Stoikov I. I.
Published: September 2016

First, the “binding strength–selectivity” relationship has been decided for pillar[5]arene/anion systems.
Surface-independent one-pot chelation of copper ions onto filtration membranes to provide antibacterial properties
Authors: Liu Zhongyun , Hu Yunxia , Liu Caifeng , Zhou Zongyao
Published: September 2016

Surface-independent one-pot chelation of copper ions onto filtration membranes to provide antibacterial properties.
Microsecond and nanosecond polyproline II helix formation in aqueous nanodrops measured by mass spectrometry
Authors: Mortensen Daniel N. , Williams Evan R.
Published: September 2016

The 1.5 μs and <400 ns time constants for the formation of polyproline II helix structures in 21 and 16 residue peptides, respectively, are measured using rapid mixing from theta-glass emitters coupled with mass spectrometry.
Polycyclic aromatic hydrocarbons with orthogonal tetraimides as n-type semiconductors
Authors: Cui Xiaoping , Xiao Chengyi , Zhang Lei , Li Yan , Wang Zhaohui
Published: September 2016

We report two novel n-type polycyclic aromatic hydrocarbons bearing orthogonal tetraimides with high electron mobilities.
Near-infrared light-induced dissociation of zeolitic imidazole framework-8 (ZIF-8) with encapsulated CuS nanoparticles and their application as a therapeutic nanoplatform
Authors: Wang Zhifei , Tang Xuejiao , Wang Xiaoxiao , Yang Dandan , Yang Chao , Lou Yongbing , Chen Jinxi , He Nongyue
Published: September 2016

A new therapeutic nanoplatform based on CuS@ZIF-8NPs was developed, which could be disintegrated under NIR laser irradiation at pH 7.4.
Magnesium plasmonics for UV applications and chiral sensing
Authors: Jeong Hyeon-Ho , Mark Andrew G. , Fischer Peer
Published: September 2016

We demonstrate that chiral magnesium nanoparticles show remarkable plasmonic extinction- and chiroptical-effects in the ultraviolet region.
Triple-decker sandwich complexes with a bent cyclo-P5 middle-deck
Authors: Mädl Eric , Peresypkina Eugenia , Timoshkin Alexey Y. , Scheer Manfred
Published: September 2016

New types of triple-decker complexes with an organo-substituted P5 middle-deck were synthesized by the reaction of [Cp*Fe(η4-P5R)]− (1a: R = CH2SiMe3; 1b: R = NMe2) with halogeno-bridged transition metal dimers [Cp′′′MX]2 (M = Cr, Fe, Co, Ni; X = Cl, Br).
Reversible water activation driven by contraction and expansion of a 12-vertex-closo-12-vertex-nido biscarborane cluster
Authors: Wong Yuen Onn , Smith Mark D. , Peryshkov Dmitry V.
Published: September 2016

The metal-free reversible activation of H–OH bonds of water driven by the rearrangement of a boron cluster is presented.
Catalytic effects of silver plasmonic nanoparticles on the redox reaction leading to ABTS˙+formation studied using UV-visible and Raman spectroscopy
Authors: Garcia-Leis A. , Jancura D. , Antalik M. , Garcia-Ramos J. V. , Sanchez-Cortes S. , Jurasekova Z.
Published: September 2016

The strong effect of silver plasmonic nanoparticles on ABTS leading to the formation of ABTS radical cation is investigated by UV-visible, Raman and SERS spectroscopy.
Infrared spectrum of the cold ortho-fluorinated protonated neurotransmitter 2-phenylethylamine: competition between NH+⋯π and NH+⋯F interactions
Authors: Schütz Markus , Bouchet Aude , Dopfer Otto
Published: September 2016

IR spectra of cold rare-gas tagged ions reveal the switch of the preferred conformation of the highly flexible side chain of a prototypical protonated neurotransmitter induced by site-specific aromatic fluorination.
High yield production of HMF from carbohydrates over silica–alumina composite catalysts
Authors: Li Xiangcheng , Xia Qineng , Nguyen Van Chuc , Peng Kaihao , Liu Xiaohui , Essayem Nadine , Wang Yanqin
Published: September 2016

Mesoporous AlSiO catalysts have been prepared by a facile sol–gel method with tunable acidity for highly efficient production of HMF.
Fluorescent zinc(ii) complexes for gene delivery and simultaneous monitoring of protein expression
Authors: Rane Lalita B. , Kate Anup N. , Ramteke Shefali N. , Shravage Bhupendra V. , Kulkarni Prasad P. , Kumbhar Anupa A.
Published: September 2016

Two new fluorescent zinc(ii) complexes [Zn(l-His)(NIP)]+ (1) and [Zn(acac)2(NIP)] (2) with DNA condensation efficiency were used to deliver pCMV-tdTomato-N1 plasmid which express red fluorescent protein.
Ni-based bimetallic heterogeneous catalysts for energy and environmental applications
Authors: De Sudipta , Zhang Jiaguang , Luque Rafael , Yan Ning
Published: September 2016

This review provides a comprehensive overview of nickel based bimetallic catalysts for energy and environmental applications.
Highly efficient and stable planar perovskite solar cells by solution-processed tin oxide
Authors: Anaraki Elham Halvani , Kermanpur Ahmad , Steier Ludmilla , Domanski Konrad , Matsui Taisuke , Tress Wolfgang , Saliba Michael , Abate Antonio , Grätzel Michael , Hagfeldt Anders , Correa-Baena Juan-Pablo
Published: September 2016

Low temperature planar PSCs are fabricated by SnO2 yielding stable devices and efficiencies ca. 21%.
Anisotropic etching of rhodium and gold as the onset of nanoparticle formation by cathodic corrosion
Authors: Hersbach Thomas J. P. , Mints Vladislav A. , Calle-Vallejo Federico , Yanson Alexei I. , Koper Marc T. M.
Published: September 2016

Cathodic corrosion is a phenomenon in which negatively polarized metal electrodes are degraded by cathodic etching and nanoparticle formation. Though these changes are dramatic and sometimes even visible by eye, the exact mechanisms underlying cathodic corrosion are still unclear. This work aims to improve the understanding of cathodic corrosion by studying its onset on rhodium and gold electrodes, which are subjected to various constant cathodic potentials in 10 M NaOH. After this polarization, the electrodes are studied using cyclic voltammetry and scanning electron microscopy, allowing a corrosion onset potential of −1.3 Vvs.NHE for rhodium and −1.6 Vvs.NHE for gold to be defined. The mildness of the potentials on both metals suggests that cathodic corrosion is less extreme and more ubiquitous than expected. Furthermore, we are able to observe well-defined rectangular etch pits on rhodium. Combined with rhodium cyclic voltammetry, this indicates a strong preference for forming (100) sites during corrosion. In contrast, a (111) preference is indicated on gold by voltammetry and the presence of well-oriented quasi-octahedral nanoparticles. This different etching behavior is suggested to be caused by preferential adsorption of sodium ions to surface defects, as is confirmed by density functional theory calculations.
Valve interstitial cell contractile strength and metabolic state are dependent on its shape
Authors: Lam Ngoc Thien , Muldoon Timothy J. , Quinn Kyle P. , Rajaram Narasimhan , Balachandran Kartik
Published: September 2016

Valve interstitial cells with elongated shapes, representative of increased mechanical loading, demonstrated altered metabolism through a decreased optical redox ratio, and generated greater contractile force compared to cells with wider, shorter shapes.
Photo-extracellular synthesis of gold nanoparticles using Baker's yeast and their anticancer evaluation against Ehrlich ascites carcinoma cells
Authors: Attia Yasser A. , Farag Yassmeen E. , Mohamed Yasser M. A. , Hussien Akaber T. , Youssef Tareq
Published: September 2016

Novel gold nanoparticles capped by yeast extract, showing highly effective cytotoxicity towards cancer cells under visible light.
Correction: A systematic study of protein labeling by fluorogenic probes using cysteine targeting vinyl sulfone-cyclooctyne tags
Authors: Söveges B. , Imre T. , Szende T. , Póti Á. L. , Cserép G. B. , Hegedűs T. , Kele P. , Németh K.
Published: September 2016

Correction for ‘A systematic study of protein labeling by fluorogenic probes using cysteine targeting vinyl sulfone-cyclooctyne tags’ by B. Söveges, et al., Org. Biomol. Chem., 2016, 14, 6071–6078.
Tailored honeycomb-like polymeric films based on amphiphilic poly(urea/malonamide) dendrons
Authors: Wu Chien-Hsin , Ting Wei-Ho , Lai Yu-Wen , Dai Shenghong A. , Su Wen-Chiung , Tung Shih-Huang , Jeng Ru-Jong
Published: September 2016

A series of hydrogen bond-rich poly(urea/malonamide) dendrons were utilized as surfactants to facilitate the formation of honeycomb-like porous structures from the breath figure (BF) process.
A pillar[5]arene-containing cross-linked polymer: synthesis, characterization and adsorption of dihaloalkanes and n-alkylene dinitriles
Authors: Ye Fengqing , Wei Ruijin , Wang Lingyun , Meier Herbert , Cao Derong
Published: September 2016

A pillar[5]arene-containing cross-linked polymer was synthesized and utilized to adsorb dihaloalkanes andn-alkylene dinitriles.
Application of modified chitosan microspheres for nitrate and phosphate adsorption from aqueous solution
Authors: Zhao Tingting , Feng Tao
Published: September 2016

Modified chitosan microspheres were prepared by inverse suspension crosslinking and used for nitrate and phosphate adsorption from aqueous solution. Their surface was coarse and porous compared to pure chitosan microspheres and they were about 100 μm in size.
A new class of nanocomposites of Zn–Al–Bi layered double oxides: large reversible capacity and better cycle performance for alkaline secondary batteries
Authors: Long Jun , Yang Zhanhong , Zeng Xiao , Huang Jianhang
Published: September 2016

Zn–Al–Bi layered double oxide (Zn–Al–Bi-LDO) nanocomposites with a bilayer structure were prepared by calcining Zn–Al–Bi layered double hydroxides (Zn–Al–Bi LDHs) in an air atmosphere at 600 °C for 6 h.
A microwave-assisted highly practical chemoselective esterification and amidation of carboxylic acids
Authors: Pathak Gunindra , Das Diparjun , Rokhum Samuel Lalthazuala
Published: September 2016

The ubiquitousness of esters and amide functionalities makes their coupling reaction one of the most sought-after organic transformations.
A fused thieno[3,2-b]thiophene-dithiophene based donor molecule for organic photovoltaics: a structural comparative study with indacenodithiophene
Authors: Abe Yuichiro , Li Hairong , Yin Jun , Soci Cesare , Grimsdale Andrew C. , Lam Yeng Ming
Published: September 2016

A fused thieno[3,2-b]thiophene-dithiophene-based small molecular donor was synthesized and its properties were systematically compared with the corresponding indacenodithiophene-based molecule.
Copper iodide as a potential low-cost dopant for spiro-MeOTAD in perovskite solar cells
Authors: Wang Peng , Zhang Jing , Zeng Zhaobing , Chen Renjie , Huang Xiaokun , Wang Liming , Xu Jie , Hu Ziyang , Zhu Yuejin
Published: September 2016

Low-cost inorganic copper iodide (CuI) is introduced as a potential oxidizer for hole-transport material (HTM) in perovskite solar cells (PSCs).
Accurate dry etching technique for germanium waveguide by using CHF3 based inductively coupled plasma
Authors: Idris A.S. , Jiang H. , Hamamoto K.
Published: September 2016

A CHF3 inductively coupled plasma (ICP) based dry etching method is proposed for accurate etching of Ge waveguides. CHF3 ICP based dry etching produces excellent anisotropy along with good selectivity with regards to regular polymeric photoresist, which leads to the elimination of under‐cut. As a result, an almost vertical sidewall angle of 85° with an etching rate of 190 nm/min was realised with a relatively high selectivity ratio of 5:1 against regular photoresist.
Facial aging simulation via tensor completion and metric learning
Authors: Wang Heng , Huang Di , Wang Yunhong , Yang Hongyu
Published: September 2016

Facial aging simulation is one of the most challenging issues in automatic machine based face analysis, where the most essential requirements are (i) human identity should remain stable in texture synthesis and (ii) the texture synthesised is expected to accord with human cognitive perception in aging. In this study, the authors propose a tensor completion based method to transform the simulation task to a standard matrix completion one. To protect human dependent characteristics during texture synthesis, the proposed method processes the two major components, i.e. identity and age, in different channels. Furthermore, they incorporate prior information in such a process, assuming that the textures of different subjects in the same age group are similar and similar looking people tend to age in similar ways, and the metric learning technique is adopted to measure the similarity between identities so that the faces that have the highest similarities with the one in the test image are assigned bigger weights in texture generation. In addition, shape deformation is also considered to make the synthesised images more natural. Experimental results achieved on the FG‐NET database demonstrate the effectiveness of the proposed method.
Implementation of lossy FTRs for perfect risk hedging under the marginal loss pricing
Authors: Vaishya Shri Ram , Sarkar Vaskar
Published: September 2016

In this study, a market framework is proposed for the practical implementation of lossy financial transmission rights (FTRs). The advantage of lossy FTRs over conventional FTRs is that the lossy FTRs can be settled directly according to locational marginal prices (LMPs) without requiring any LMP decomposition. Therefore, the price risk for a forward contract can be perfectly hedged if the power transaction involved perfectly matches the corresponding FTR. Although proposed long back, lossy FTRs still did not find an entry to the market because of the prejudice of market complexity and inefficiency. The principal aim of this study is, thus, to create the necessary environment so as to make those fine risk‐hedging tools available in the market. First of all, a suitable format for forward contracts is prescribed to enable proper utilisation of lossy FTRs. The detailed lossy FTR auction model is prepared based upon a suitable optimal power flow (OPF) formulation. In addition, the implementation of lossy FTRs is shown for an AC–DC system by appropriately modelling the DC‐line power flow behaviour according to the chosen OPF framework. The lossy FTR auction model prepared is thoroughly verified for the FTR issuance as per the market expectations.
Wavelet denoising of multiframe optical coherence tomography data using similarity measures
Authors: Habib Wajiha , Sarwar Tabinda , Siddiqui Adil Masood , Touqir Imran
Published: September 2016

Speckle noise is the main cause of image degradation in optical coherence tomography, which makes denoising an essential process to obtain quality images. This study proposes a wavelet‐based denoising technique in which detail coefficients are assigned weights using similarity measures of Pearson's correlation coefficient and structural similarity index (SSIM). Stationary wavelet transform is used for SSIM which is an image quality measure is used as optimisation criterion to denoise images in this study. Procedure of weight computation is discussed in detail. Average of these detailed components is used to denoise the images. Comparison of proposed technique with the existing techniques has been carried out at length. Extensive qualitative and quantitative analysis reveal that the proposed technique is efficient and performs better in terms of noise reduction while maintaining the structural contents of the image.
Highly sensitive 10 Gb/s PAM‐4 optical receiver circuit for three‐dimensional optoelectronic integration
Authors: Vokić Nemanja , Milovančev Dinka , Goll Bernhard , Zimmermann Horst
Published: September 2016

This study presents a 0.35 µm silicon germanium bipolar complementary metal‐oxide‐semiconductor 10 Gb/s receiver circuit optimised for photonic–electronic three‐dimensional integration. Measurements were conducted on a test‐chip with a voltage‐input signal, which was converted to a current via a series resistor. On the basis of measurement results and using the expected value of the photodetector responsivity of 1 A/W, the PAM‐4 circuit consumes 145 mW, sensitivity is −21.8 dBm at 10 Gb/s, and at a bit error rate = 10−9.
Renal histopathological alterations induced by nanosilver toxicity: the size effect
Authors: Almansour Mansour , Jarrar Qais , Battah Abdelkader , Obeidat Fatima , Battah Khairat , Jarrar Bashir
Published: September 2016

Nanosilver is widely used in medicine, industry, and other applications where it poses a high potential risk for human health, even though little information is available on its toxicity to vital organs. This study was conducted to determine the histopathological changes induced in renal tissues by various sizes of silver nanoparticles (SNPs). Male BALB/C mice were exposed to various sizes of SNPs for 5 weeks. Renal tissue samples from all members of all experimental groups were subjected to histological processing and histopathological examination. SNPs caused glomerular and tubular alterations in the form of tubular degeneration, necrosis, eosinophilia, glomerular shrinkage, and Bowman's capsule thickening. Moreover, SNPs induced interstitial intertubular regeneration, mononuclear inflammatory cell infiltration, proteinaceous casting, and fibrocyte proliferation. These results indicated that smaller particles (10 and 20 nm) were more toxic than the larger ones (40, 60, and 100 nm). In addition, the cortex was more affected than the medulla, and the proximal tubules were more affected than the distal ones. The results of the current investigation reveal that SNPs induce histomorphological alterations in renal tissues, with size being a key factor in the toxicity of these particles.
Structure of ionic liquids with cationic silicon-substitutions
Authors: Wu Boning , Shirota Hideaki , Lall-Ramnarine Sharon , Castner Edward W.
Published: September 2016

Significantly lower viscosities result when a single alkyl carbon is replaced by a silicon atom on the side chain of an ionic liquid cation. To further explore this effect, we compare liquid structure factors measured using high-energy X-ray scattering and calculated using molecular dynamics simulations. Four ionic liquids are studied that each has a common anion, bis(trifluoromethylsulfonyl)amide (NTf2−). The four cations for this series of NTf2−-anion ionic liquids are 1-methyl-3-trimethylsilylmethylimidazolium (Si-mim+), 1-methyl-3-neopentylimidazolium (C-mim+), 1-methyl-3-pentamethyldisiloxymethylimidazolium (SiOSi-mim+), and 1-methyl-1-trimethylsilylmethylpyrrolidinium (Si-pyrr+). To achieve quantitative agreement between the structure factors measured using high-energy X-ray scattering and molecular dynamics simulations, new transferable parameters for silicon were calibrated and added to the existing force fields.
Micro-imaging of buried layers and interfaces in ultrathin films by X-ray reflectivity
Authors: Jiang Jinxing , Hirano Keiichi , Sakurai Kenji
Published: September 2016

X-ray reflectivity is a promising technique for characterizing buried layers and interfaces in ultrathin films because of its ability to probe the electron density profile along the depth in a non-destructive manner. While routine X-ray reflectivity assumes the in-plane uniformity of the sample to be measured, it is also quite important to see buried inhomogeneous/patterned layers and interfaces. The present paper describes the addition of spatial resolution and imaging capability to an X-ray reflectivity technique to visualize surfaces and buried interfaces. To visualize quite wide viewing area size quickly, the image reconstruction scheme has been employed instead of the scanning of microbeam. Though the mathematics is quite close to X-ray computer tomography, the technique gives the image contrast caused by the difference in reflectivity at each in-plane point in the thin film sample. By choosing a grazing angle, the image gives inhomogeneity of X-ray reflectivity at the specific wavevector transfer. With a collimated monochromatic synchrotron X-ray beam of 0.05 mm (H) × 8 mm (V), the intensity profiles of X-ray reflection projections have been taken at many different in-plane rotation angles, from 0° to 180°. We have succeeded in visualizing buried layers and interfaces of the 8 mm dia area with the spatial resolution of better than 20 μm. Because of the brilliance of synchrotron radiation, the typical measuring time is shorter than 1 min. Three analytical cases have been discussed: (i) imaging of a buried layer and an interface covered by a protection layer, (ii) distinguishing different local parts of different thicknesses in an ultrathin film, and (iii) selective imaging of a specific metal in the thin film form.
Local gap threshold for frustration-free spin systems
Authors: Gosset David , Mozgunov Evgeny
Published: September 2016

We improve Knabe’s spectral gap bound for frustration-free translation-invariant local Hamiltonians in 1D. The bound is based on a relationship between global and local gaps. The global gap is the spectral gap of a size-m chain with periodic boundary conditions, while the local gap is that of a subchain of size n < m with open boundary conditions. Knabe proved that if the local gap is larger than the threshold value 1/(n − 1) for some n > 2, then the global gap is lower bounded by a positive constant in the thermodynamic limit m → ∞. Here we improve the threshold to 6n(n+1), which is better (smaller) for all n > 3 and which is asymptotically optimal. As a corollary we establish a surprising fact about 1D translation-invariant frustration-free systems that are gapless in the thermodynamic limit: for any such system the spectral gap of a size-n chain with open boundary conditions is upper bounded as O(n−2). This contrasts with gapless frustrated systems where the gap can be Θ(n−1). It also limits the extent to which the area law is violated in these frustration-free systems, since it implies that the half-chain entanglement entropy is O(1/ϵ) as a function of spectral gap ϵ. We extend our results to frustration-free systems on a 2D square lattice.
Experimental research of high field pinning centers in 2% C doped MgB2 wires at 20 K and 25 K
Authors: Gajda D. , Morawski A. , Zaleski A. J. , Häßler W. , Nenkov K. , Małecka M. , Rindfleisch M. A. , Hossain M. S. A. , Tomsic M.
Published: September 2016

High field pinning centers in MgB2 doped with 2 at. % carbon under a low and a high hot isostatic pressures have been investigated by transport measurements. The field dependence of the transport critical current density was analyzed within the different pinning mechanisms: surface pinning, point pinning, and pinning due to spatial variation in the Ginzburg-Landau parameter (Δκ pinning). Research indicates that a pressure of 1 GPa allows similar pinning centers to Δκ pinning centers to be obtained. This pinning is very important, because it makes it possible to increase the critical current density in high magnetic fields at 20 K and 25 K. Our results indicate that the δTc and δl pinning mechanisms, which are due to a spatial variation in the critical temperature (Tc) and the mean free path, l, respectively, create dislocations. The high density of dislocations with inhomogeneous distribution in the structure of the superconducting material creates the δl pinning mechanism. The low density of dislocations with inhomogeneous distribution creates the δTc pinning mechanism. Research indicates that the hot isostatic pressure process makes it possible to obtain a high dislocation density with a homogeneous distribution. This allows us to obtain the δTc pinning mechanism in MgB2 wires. In addition, a high pressure increases the crossover field from the single vortex to the small vortex bundle regime (Bsb) and improves the δTc pinning mechanism. Our research has proved that a high pressure significantly increases the crossover field from the small bundle to the thermal regime (Bth), with only a modest decrease in Tc of 1.5 K, decreases the thermal fluctuations, increases the irreversibility magnetic field (Birr) and the upper critical field (Bc2) in the temperature range from 4.2 K to 25 K, and reduces Birr and Bc2 above 25 K.
Measurement of the lifetime of individual foam lamellae
Authors: Hofmann Matthias J. , Motschmann Hubert
Published: September 2016

Foams play a crucial role in a number of practical applications. Their analysis in terms of stability is subject to a large number of parameters. An automated, light reflection based device for the measurement of the lifetime of a single foam lamella of aqueous surfactant solutions in contact with the liquid and gas phases is proposed. The capability of the method is shown for the analysis of the cationic and anionic model surfactants hexadecyltrimethylammonium bromide (CTAB) and sodium dodecyl sulfate (SDS) with saturated humidity, respectively. A statistical approach for analysis of the individual foam lamella lifetimes is presented and a comparison to the foam stability parameters obtained from a foam column device is presented.