bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and Physicochemical Characterization of Novel Organic–Inorganic Hybrids from Natural Aluminosilicate Nanotubes
Authors: Takahara A. , Higaki Y.
Published: November 2016

Surface functionalization of tubular nano-clays of imogolite and halloysite using the selective binding of organophosphonic acids and organosilane compounds, and the use of the surface modified nanotubes in polymer hybrids were studied. Surface modification of imogolite with alkyl phosphonic acid salt through the specific interaction of phosphonic acid and the exterior alumina sites of imogolite was presented. SI-ATRP was performed with the selectively adsorbed phosphonic acid functionalized ATRP-initiator to prepare polymer brushes on the imogolite surface. Selective modification of halloysite nanotube exterior and inner surfaces was demonstrated. Aqueous phosphonic acid binds to alumina sites at the tube lumen to make the lumen hydrophobic. Subsequent modification with organosilane affords bifunctionalized halloysites with both the lumen and exterior surface modified. Loading of hydrophobic organic compound to the modified lumen was confirmed. SI-ATRP was performed through the selectively adsorbed DOPA-functionalized ATRP-initiator to prepare polymer brushes on the nanotube lumen. Also, surface modified halloysite was applied for preparation of novel intelligent polyurethane nanocomposites with improved thermal stability and mechanical properties.
Halloysite and Related Mesoporous Carriers for Advanced Catalysis and Drug Delivery
Authors: Ariga Katsuhiko , Abe Hideki , Ji Qingmin , Lvov Yuri M.
Published: November 2016

For more precise structure control, bottom-up approaches have especially been paid much attention to control nanoscale structures on the basis of the organizing capabilities of the materials themselves. A more advanced concept, nanoarchitectonics, has recently been proposed to promote these nanotechnology flows. Among countless numbers of materials candidates, structurally defined inorganic materials can be nice hosts for development of functional materials structures according to nanoarchitectonics. In this chapter, we mainly focus on introduction of research examples on functionalization of the halloysite nanotubes for catalysis and antibacterial activities. In addition, several examples of hierarchic silica nanostructures for applications such as drug delivery are also briefly introduced.
Biocompatible Electrospun Polymer–Halloysite Nanofibers for Sustained Release
Authors: Zhao Yili , Wang Zhe , Shen Mingwu , Shi Xiangyang
Published: November 2016

Fabrication of nanofiber-based drug delivery systems with controlled release properties is of general interest in the biomedical sciences. The micro-nano scale organization and high porosity of electrospun membranes, which is similar to the natural extracellular matrix, is favorable for adhesion and proliferation of cells and decreases the immune response. The incorporation of drug-loaded halloysite within the electrospinning nanofibers is able to improve the tensile strength and maintain the three-dimensional structure of the nanofibrous mats. The “nano in nano” composite is a promising architectural approach for the design of a sustained drug delivery vehicle that combines the drug-loading capability of nanoparticles or nanotubes and electrospinning technology. With improved mechanical durability, sustained drug release profile, good cytocompatibility, and non-compromised therapeutic efficacy, the developed biocompatible electrospun polymer/halloysite nanofibers drug delivery system may be used as therapeutic scaffold materials for tissue engineering and drug delivery applications. In this chapter, we review the recent progress of biocompatible electrospun polymer–halloysite nanofibers for sustained release, and biomedical applications.
Determination of cadmium, chromium and copper in vegetables of the Solanaceae family using high-resolution continuum source graphite furnace atomic absorption spectrometry and direct solid sample analysis
Authors: Pozzatti Marianna , Borges Aline R. , Dessuy Morgana B. , Vale Maria Goreti R. , Welz Bernhard
Published: November 2016

Three methods have been developed for the determination of Cd, Cr, and Cu in vegetables of the Solanaceae family cultivated in different farming systems by HR-CS SS-GF AAS.
Electrochemical sensor for the facile detection of trace amounts of bisphenol A based on cyclodextrin-functionalized graphene/platinum nanoparticles
Authors: Zou Jinfeng , Liu Zhiguang , Guo Yujing , Dong Chuan
Published: November 2016

A sensitive electrochemical sensor for Bisphenol A is developed based on TM-β-CD-Gr/PtNPs. This method has wide linear range and low detection limit. Moreover, it is convenient and cost-effective.
Guanine-based chemiluminescence resonance energy transfer biosensing platform for the specific assay of uracil-DNA glycosylase activity
Authors: Dong Jingjing , Lian Jinyu , Jin Yan , Li Baoxin
Published: November 2016

Guanine-based chemiluminescence resonance energy transfer system was used to detect uracil-DNA glycosylase (UDG) activity. The proposed method is simple and rapid.
Influence of π-conjugation structural changes on intramolecular charge transfer and photoinduced electron transfer in donor–π–acceptor dyads
Authors: Kim So-Yoen , Cho Yang-Jin , Lee Ah-Rang , Son Ho-jin , Han Won-Sik , Cho Dae Won , Kang Sang Ook
Published: November 2016

Unit electron transfers (PET or PHT) were observed dominantly in the dyads having severed/twisted linkers in the π-conjugation and their mechanisms are also affected by whether selective excitation of the donor or acceptor moiety occurs.
Infrared dynamics study of thermally treated perfluoroimide acid proton exchange membranes
Authors: Puskar L. , Ritter E. , Schade U. , Yandrasits M. , Hamrock S. J. , Schaberg M. , Aziz E. F.
Published: November 2016

In situinfrared investigation of the water hydrogen-bonded network inside PFIA accounts for improved proton conductivity under hotter and dryer conditions.
Self-assembled Pt2L2 boxes strongly bind G-quadruplex DNA and influence gene expression in cancer cells
Authors: Domarco O. , Lötsch D. , Schreiber J. , Dinhof C. , Van Schoonhoven S. , García M. D. , Peinador C. , Keppler B. K. , Berger W. , Terenzi A.
Published: November 2016

Pt(ii) boxes bind native and G-quadruplex DNA motifs in a size-dependent fashion and influence the expression of G-quadruplex forming genes.
13C-Labeling the carbon-fixation pathway of a highly efficient artificial photosynthetic system
Authors: Liu Chong , Nangle Shannon N. , Colón Brendan C. , Silver Pamela A. , Nocera Daniel G.
Published: November 2016

Interfacing the CO2-fixing microorganism, Ralstonia eutropha, to the energy derived from hydrogen produced by water splitting is a viable approach to achieving renewable CO2 reduction at high efficiencies. We employ 13C-labeling to report on the nature of CO2 reduction in the inorganic water splitting|R. eutropha hybrid system. Accumulated biomass in a reactor under a 13C-enriched CO2 atmosphere may be sampled at different time points during CO2 reduction. Converting the sampled biomass into gaseous CO2 allows the 13C/12C ratio to be determined by gas chromatography-mass spectrometry. After 2 hours of inoculation and the initiation of water splitting, the microbes adapted and began to convert CO2 into biomass. The observed time evolution of the 13C/12C ratio in accumulated biomass is consistent with a Monod model for carbon fixation. Carbon dioxide produced by catabolism was found to be minimal. This rapid response of the bacteria to a hydrogen input and to subsequent CO2 reduction at high efficiency are beneficial to achieving artificial photosynthesis for the storage of renewable energy.
Electrochemical synthesis of ammonia directly from N2 and water over iron-based catalysts supported on activated carbon
Authors: Cui Baochen , Zhang Jianhua , Liu Shuzhi , Liu Xianjun , Xiang Wei , Liu Longfei , Xin Hongyu , Lefler Matthew J. , Licht Stuart
Published: November 2016

A CO2-free electrosynthesis of ammonia from air and water is presented with a solid Fe2O3 catalyst confined to activated charcoal.
Controlling the selectivity of catalytic oxidation of styrene over nanocluster catalysts
Authors: Chai Jinsong , Chong Hanbao , Wang Shuxin , Yang Sha , Wu Mingzai , Zhu Manzhou
Published: November 2016

The water is discovered to control the selectivity by changing the surface composition of Au nanocluster or the valence state of Ag nanocluster.
Preparation, characterization and oxygen reduction catalytic activities of nanocomposites of Co(ii)/montmorillonite containing polypyrrole, polyaniline or poly(ethylenedioxythiophene)
Authors: Senarathna K. G. C. , Randiligama H. M. S. P. , Rajapakse R. M. G.
Published: November 2016

Cobalt(ii)/conducting polymer/montmorillonite composites are synthesized through ion exchange of montmorillonite (MMT) followed by oxidative polymerization using Co(iii) as the oxidant. Composites are characterized and used as electrocatalysts.
Self assembly and hydrogelation of spermine functionalized aromatic peptidomimetics against planktonic and sessile methicillin resistant S. aureus
Authors: Dewangan Rikeshwer Prasad , Jain Aditi , Tanwar Swati , Yar Mohammad Shahar , Pasha Santosh
Published: November 2016

Novel spermine conjugated shortest nanofibres NF-3 and NF-4 showed potent activity against clinically relevant MRSA with a membrane disruptive mode of action.
Trypsin and chymotrypsin are necessary for in vitro enzymatic digestion of rice starch
Authors: Wang Shujun , Li Peiyan , Zhang Teng , Wang Shuo , Copeland Les
Published: November 2016

An appropriate in vitro starch digestion model is necessary to comparatively evaluate the digestibility of starch samples and to help predict the in vivo glycemic responses of starchy foods.
Development of a novel lysosome-targetable time-gated luminescence probe for ratiometric and luminescence lifetime detection of nitric oxide in vivo
Authors: Dai Zhichao , Tian Lu , Song Bo , Liu Xiangli , Yuan Jingli
Published: November 2016

A novel multifunctional probe based on the intramolecular LRET strategy, TRP-NO, was designed for ratiometric and luminescence lifetime detection of lysosomal NO.
Yolk–shell carbon microspheres with controlled yolk and void volumes and shell thickness and their application as a cathode material for Li–S batteries
Authors: Hong Young Jun , Lee Jung-Kul , Chan Kang Yun
Published: November 2016

A new strategy for the formation of yolk–shell structured carbon materials by a simple two-step process is introduced. The sulfur infiltrated carbon yolk–shell microspheres with a filled yolk showed good electrochemical properties as a cathode material for Li–S batteries.
Goodness and Accentedness Ratings of /hVt/ Tokens by Aware and Naive Listeners
Authors: Franklin Amber D. , Oksanen Kara A. , Gilfert Kaitlyn E.
Published: November 2016

Purpose

This study compares goodness and accentedness ratings of speech tokens rated by listeners who are naive to and aware of speakers' native language backgrounds. Listener responses to open-ended questions regarding goodness and accentedness ratings are also examined.

Method

Twenty-eight monolingual speakers of U.S. English served as listeners. Listeners were presented with 5 blocks of /hVt/ tokens. Each block represented a different vowel target and comprised correct and incorrect productions from English, Spanish, Korean, and Japanese speakers. Listeners rated goodness and accentedness using a 9-point Likert scale and explained their decision-making criteria when judging goodness versus accentedness.

Results

There is a high positive correlation between goodness and accentedness. Both naive and aware listeners assigned poorer ratings when judging goodness compared with accentedness, but results varied on the basis of target accuracy. Aware listeners assigned better goodness and accentedness ratings compared with naive listeners. This difference was highly statistically significant. Both accentedness and goodness ratings are susceptible to listener bias.

Conclusions

Goodness and accentedness are highly correlated yet distinct measures. Goodness is more reflective of target accuracy than is accentedness. Native English tokens were affected by listener bias to a greater extent than nonnative English tokens.
Spectral control of dispersion‐tuned wavelength‐swept laser
Authors: Takubo Yuya , Yamashita Shinji
Published: November 2016

Spectral profile control method of a dispersion‐tuned fibre laser is demonstrated. A dispersion‐tuned fibre laser is a fast and widely tunable wavelength‐swept laser without mechanical tunable filters. The lasing centre wavelength is tuned by changing the active mode‐locking modulation frequency to that of the corresponding operating wavelength matching the fundamental repetition rate of the cavity. The sweep spectra profile can be controlled by modulation frequency sweep. By applying a pre‐calculated modulation frequency sweep, the flatness of the wavelength‐swept spectral profile can be improved. We applied the dispersion‐tuned wavelength‐swept laser to a spectral‐domain optical coherence tomography system as a wideband light source and successfully obtained OCT images. The image resolution is enhanced by applying a nonlinear modulation frequency sweep to the laser instead of linear modulation frequency sweep. The potential of the proposed dispersion‐tuned wavelength‐swept laser as a spectrally flexible laser source is demonstrated.
Efficient grouping technique for low mutual‐coherence basis matrix in radar imaging
Authors: Alkhodary M.T. , Muqaibel A.H.
Published: November 2016

Sparse reconstruction has been recently proposed to overcome many challenges in radar imaging applications. In sparse reconstruction framework, the basis matrix of high‐resolution radar image demonstrates high mutual coherence, which is inversely proportional to the quality of the reconstructed image. The high mutual coherence, also, weakens the noise immunity in the sparse reconstruction. A technique for building a basis matrix with low mutual coherence is proposed which preserves the high quality of the resultant radar image. The proposed technique groups the columns of the original basis matrix that share the same range of time delay into one column with the average time delay of the group. The resultant basis matrix is used in a sparse reconstruction algorithm to reconstruct the pixel values of a radar image. The technique was validated over realistic and simulated radar measurements and was shown to be computationally efficient with improved noise immunity.
Duty‐cycle detection for noisy arbitrary waveforms using artificial neural networks
Authors: Khan F.N. , Tan M.C.
Published: November 2016

A novel technique for detecting duty cycles of noisy arbitrary waveforms by employing artificial neural networks trained with empirical moments of asynchronously sampled waveforms’ amplitudes is presented. The proposed technique is software‐based and hence can be applied flexibly to numerous waveform types without requiring any hardware changes. Furthermore, in contrast to existing duty‐cycle detection methods, this technique is capable of detecting duty cycles of noisy waveforms. Results obtained for square and sawtooth waveforms demonstrate wide duty‐cycle detection range of 10–95% with mean absolute percentage errors < 0.4%.
Method for improving the bank‐to‐turn missile manoeuvrability
Authors: Huang Di , Wang Qishao , Duan Zhisheng
Published: November 2016

This study addresses the autopilot design problem for a bank‐to‐turn missile to improve the manoeuvrability. A modified dynamic model is introduced by adding new reaction jet inputs to provide extra manouvrability. The H _ index, which is defined as the minimum singular value of the transfer function, is utilised to assess the manoeuvrability and the autopilot design problem is then transformed to a problem of H _ index controller design. An iterative linear matrix inequality algorithm is presented to obtain the control law. Simulation results illustrate the effectiveness of the proposed approach.
Stabilisation of Markov jump systems with input quantisation and general uncertain transition rates
Authors: Li Li‐Wei , Yang Guang‐Hong
Published: November 2016

This study addresses the problem of designing state feedback controllers for Markov jump systems subject to input quantisation mismatch, and general transition rates allowed to be uncertain and unknown. First, a non‐linear control law is constructed for eliminating the effect of input quantisation in the presence of mismatch between quantisation parameters. Then, a new method based on vertex separator algorithm is proposed for designing the controller. A sufficient condition is derived such that the stochastic stability and also the disturbance attenuation performance of the resulting closed‐loop system can be ensured. Moreover, it is proved that the obtained result is theoretically less conservative than previous results. Finally, numerical examples are presented to show the effectiveness and advantages of the proposed method.
Fault‐tolerant control for a dual‐winding fault‐tolerant permanent magnet motor drive based on SVPWM
Authors: Bai Hongfen , Zhu Jingwei , Qin Junfeng , Sun Junhao
Published: November 2016

The dual‐winding fault‐tolerant permanent magnet motor (FTPMM) drive can overcome the shortcomings of single FTPMM and dual‐redundant FTPMM drive and further improve the fault‐tolerant capability of motor drives. The vector control technique based on voltage space vector pulse width modulation (SVPWM) can reduce switching frequency and improve the dynamic performances of the motor drive. In this study, the structure and principle of vector control system based on SVPWM for a dual‐winding FTPMM drive was introduced. The distribution of voltage space vectors was analysed and the vector control strategies under healthy and one‐phase open‐circuit faulty conditions were proposed in which the magnetomotive force was kept constant with the minimum copper loss. The simulation and experimental results are provided to verify the validity of the proposed fault remedial strategy based on SVPWM technique.
Simultaneous determination of opioid drugs in urine with high‐performance liquid chromatography–ultraviolet after supramolecular based magnetic NP solid‐phase extraction
Authors: Zabardasti Abedien , Afrouzi Hossein , Kakanejadifard Ali , Amoli‐Diva Mitra
Published: November 2016

A simple and rapid extraction/preconcentration procedure using supramolecular based magnetic nanoparticle (MNP) solid‐phase extraction method by sodium dodecyl sulphate (SDS)‐coated MNPs has been developed for both removal and preconcentration of three important opioid drugs named morphine, codeine and methadone before their high‐performance liquid chromatography–ultraviolet determination. To get insight conﬁguration of SDS molecules on the surface of the MNPs, zeta potential measurements were performed in different SDS (mg)/mg of MNPs ratios. Parameters affecting the extraction and preconcentration efficiency of the opioids were optimised as recovery by one variable at‐a‐time methodology and the obtained recoveries were 91, 94 and 98% for morphine, codeine and methadone, respectively. Under optimum conditions (such as pH = 3.5; adsorbent amount = 60 mg; eluent solvent volume = 2 ml of acetonitrile, sample volume = 200 ml etc.), the method was linear in the range of 1–200 ng ml−1 with enrichment factors (EFs) of 91, 94 and 98 for morphine, codeine and methadone, respectively, and the limits of detection were <0.27 ng ml−1. Finally, the proposed method was successfully applied for both removal and trace determination of the targeted drugs in urine samples.
Primary Cervical Intradural Extramedullary Primitive Neuroectodermal Tumors Presented as Acute Transverse Myelitis: A Case Report and Review of Literature
Authors: Roy Kaushik , Bothra Sneha J. , B.V Sandeep , Ghosh Partha
Published: November 2016

Primary spinal cord presentation of primitive neuroectodermal tumors (PNET) is a rare occurrence and carries a poor prognosis. A 20-year-old female patient presented with pain in the neck region, bilateral upper and lower limb weakness, and bladder and bowel dysfunction. Neurological examination revealed the marked paresis with hyporeflexia of both the upper and hyperreflexia of lower extremities. Preoperative magnetic resonance imaging of the spine revealed an intradural mass at the C6–D1 level. A laminectomy of C5 to upper half D1 vertebra level and near-total removal of the tumor was performed. Pathological findings were consistent with PNET. The clinical, histopathological, and radiological findings of the patient are presented.
The Risk Factors of Postoperative Delirium after Total Knee Arthroplasty
Authors: Wang Lih , Kim Sungsoo , Kim Kyungtaek , Lee Seunghyun , Lee Kyungho , Seok Sangyun
Published: November 2016

We investigated the results of delirium which developed after total knee arthroplasty (TKA) and the risk factors for delirium in the patients who are older than 65 years. From March 2008 to March 2012, we performed a retrospective study on 296 knees of 265 patients who were treated with TKA. They were divided into two groups: 216 patients without delirium and 49 patients diagnosed with delirium by psychiatry. We analyzed the risk factors into three categories: First, the preoperative factors including gender, age, body mass index (BMI), clinical and functional knee joint score (Knee Society Knee Score and Knee Society Function Score) and the number of underlying diseases and associations with each disease; Second, the operative factors including the anesthesia method, amount of blood loss, operating time, laboratory factors, and transfusion count; Third, the postoperative factors such as start time of walking and duration of hospital stay were analyzed. There were significant statistical difference between two groups just in age, history of dementia, cerebrovascular disease, difference of hemoglobin and albumin, start time of walking, and duration of hospital stay. The delirium after TKA delays the postoperative ambulation and extends the hospital stay, which causes functional and socioeconomic loss of patients. Therefore, the risk factors for delirium should be assessed and proper prevention and management should be conducted.
Necrotizing Otitis Externa: A Disease Barely Known to Neurosurgeons
Authors: Cançado Sérgio Augusto Vieira , Souza Lucídio Duarte de , Faleiro Rodrigo Moreira , Siqueira José Maurício
Published: November 2016

Necrotizing otitis externa (NOE), also known as malignant otitis externa (MOE), is a severe and rare infectious disease of the external auditory canal (EAC). Without treatment, it may progress to skull base involvement. The bacteria Pseudomonas aeruginosa is the most common causative agent (∼ 90% of the cases), and affects immunocompromised subjects, particularly diabetic patients. Severe chronic otalgia, otorrhea, and cranial nerve palsy are the most common clinical presentations. Patients with NOE are frequently referred to neurosurgery because of the neurological impairment and skull base compromise. The definitive diagnosis is frequently elusive, requiring a high index of suspicion. Several laboratorial tests, imaging modalities, and the histologic exclusion of malignancy may be required. An early diagnosis and aggressive treatment reduce morbidity and mortality. We present four NOE cases to illustrate the spectrum of clinical presentation and complementary exams. According to the literature, more effort for early diagnosis and treatment is required, and neurosurgeons play an important role in this task.
A new bead-spring model for simulation of semi-flexible macromolecules
Authors: Saadat Amir , Khomami Bamin
Published: November 2016

A bead-spring model for semi-flexible macromolecules is developed to overcome the deficiencies of the current coarse-grained bead-spring models. Specifically, model improvements are achieved through incorporation of a bending potential. The new model is designed to accurately describe the correlation along the backbone of the chain, segmental length, and force-extension behavior of the macromolecule even at the limit of 1 Kuhn step per spring. The relaxation time of different Rouse modes is used to demonstrate the capabilities of the new model in predicting chain dynamics.
Persistence of atomic spectral line on laser-induced Cu plasma with spatial confinement
Authors: Wang Ying , Chen Anmin , Sui Laizhi , Li Suyu , Liu Dunli , Wang Xiaowei , Jiang Yuanfei , Huang Xuri , Jin Mingxing
Published: November 2016

This paper carries out the spatial confinement effect on laser-induced Cu breakdown spectroscopy in a cylindrical cavity via a nanosecond pulsed Q-switch Nd:YAG laser operating at a wavelength of 1064 nm. The temporal evolution of the laser-induced plasma spectroscopy is used to investigate the characteristics of spectral persistence. The atomic spectral persistence in plasma generated from Cu with spatial confinement is experimentally demonstrated, where the results indicate that the diameter of the confinement cavity plays a very important role in the persistence of an excited neutral Cu emission line, while the depth of the confinement cavity is almost independent of Cu (I) line persistence. As the diameter of the confinement cavity increases, the persistence of the Cu (I) line in the plasma grows longer under a certain limit. The likely reason for this phenomenon is that under spatial confinement, the reflected shockwave compresses the plasma and leads to an increase in the plasma temperature and density at a certain delay time, which causes further excitation of atomic population to higher excited levels. Finally, the collision rate between particles in the plasma plume is increased.
On the spatio-temporal behavior of magnetohydrodynamic turbulence in a magnetized plasma
Authors: Lugones R. , Dmitruk P. , Mininni P. D. , Wan M. , Matthaeus W. H.
Published: November 2016

Using direct numerical simulations of three-dimensional magnetohydrodynamic turbulence, the spatio-temporal behavior of magnetic field fluctuations is analyzed. Cases with relatively small, medium, and large values of a mean background magnetic field are considered. The (wavenumber) scale dependent time correlation function is directly computed for different simulations, varying the mean magnetic field value. From this correlation function, the time decorrelation is computed and compared with different theoretical times, namely, the local non-linear time, the random sweeping time, and the Alfvénic time, the latter being a wave effect. It is observed that time decorrelations are dominated by sweeping effects, and only at large values of the mean magnetic field and for wave vectors mainly aligned with this field time decorrelations are controlled by Alfvénic effects.
High-resolution acoustic imaging at low frequencies using 3D-printed metamaterials
Authors: Laureti S. , Hutchins D. A. , Davis L. A. J. , Leigh S. J. , Ricci M.
Published: November 2016

An acoustic metamaterial has been constructed using 3D printing. It contained an array of air-filled channels, whose size and shape could be varied within the design and manufacture process. In this paper we analyze both numerically and experimentally the properties of this polymer metamaterial structure, and demonstrate its use for the imaging of a sample with sub-wavelength dimensions in the audible frequency range.
Extracting fundamental transverse mode operation in broad area quantum cascade lasers
Authors: Kaspi R. , Luong S. , Yang C. , Lu C. , Newell T. C. , Bate T.
Published: November 2016

Power scaling in broad area quantum cascade lasers results in the operation of high order transverse modes with a far-field profile consisting of two lobes propagating at large angles relative to the optical axis. We report a method of suppressing the high order transverse modes that can extract the fundamental mode and provide emission along the optical axis. By generating a lateral constriction in the waveguide in the form of short trenches defined by the focused ion beam milling technique, we report broad area devices in which most of the power is contained in a near diffraction-limited beam that provides high brightness.
In-situ observation of self-cleansing phenomena during ultra-high vacuum anneal of transition metal nitride thin films: Prospects for non-destructive photoelectron spectroscopy
Authors: Greczynski G. , Hultman L.
Published: November 2016

Self-cleansing of transition metal nitrides is discovered to take place during ultra-high vacuum annealing of TiN, NbN, and VN thin films. Native oxide layers from air exposure disappear after isothermal anneal at 1000 °C. Also, for TiN, the Ti 2p and N 1s X-ray photoelectron spectra (XPS) recorded after the anneal are identical to those obtained from in-situ grown and analyzed epitaxial TiN(001). These unexpected effects are explained by oxide decomposition in combination with N-replenishing of the nitride during recrystallization. The finding opens up new possibilities for true bonding assignments through non-destructive XPS analyses, thus avoiding artefacts from Ar etching.
Lowest energy Frenkel and charge transfer exciton intermixing in one-dimensional copper phthalocyanine molecular lattice
Authors: Bondarev I. V. , Popescu A. , Younts R. A. , Hoffman B. , McAfee T. , Dougherty D. B. , Gundogdu K. , Ade H. W.
Published: November 2016

We report the results of the combined experimental and theoretical studies of the low-lying exciton states in crystalline copper phthalocyanine. We derive the eigen energy spectrum for the two lowest intramolecular Frenkel excitons coupled to the intermolecular charge transfer exciton state and compare it with temperature dependent optical absorption spectra measured experimentally, to obtain the parameters of the Frenkel-charge-transfer exciton intermixing. The two Frenkel exciton states are spaced apart by 0.26 eV, and the charge transfer exciton state is 50 meV above the lowest Frenkel exciton. Both Frenkel excitons are strongly mixed with the charge transfer exciton, showing the coupling constant 0.17 eV which agrees with earlier experimental measurements. These results can be used for the proper interpretation of the physical properties of crystalline phthalocyanines.
First-principles calculations of the near-edge optical properties of β-Ga2O3
Authors: Mengle Kelsey A. , Shi Guangsha , Bayerl Dylan , Kioupakis Emmanouil
Published: November 2016

We use first-principles calculations based on many-body perturbation theory to investigate the near-edge electronic and optical properties of β-Ga2O3. The fundamental band gap is indirect, but the minimum direct gap is only 29 meV higher in energy, which explains the strong near-edge absorption. Our calculations verify the anisotropy of the absorption onset and explain the range (4.4–5.0 eV) of experimentally reported band-gap values. Our results for the radiative recombination rate indicate that intrinsic light emission in the deep-ultra-violet (UV) range is possible in this indirect-gap semiconductor at high excitation. Our work demonstrates the applicability of β-Ga2O3 for deep-UV detection and emission.
High-throughput, sheathless, magnetophoretic separation of magnetic and non-magnetic particles with a groove-based channel
Authors: Yan S. , Zhang J. , Yuan D. , Zhao Q. , Ma J. , Li W. H.
Published: November 2016

The separation of target objects conjugated with magnetic particles is a significant application in biomedicine and clinical diagnosis. Conventional magnetophoresis-based devices use a sheath flow to pre-focus the particles into a single stream and typically operate at a low flow rate. We demonstrate in this work a high-throughput, sheathless, magnetophoretic separation of magnetic and non-magnetic beads in a groove-based channel, and also report on an interesting phenomenon where the same magnetic beads in the same microchannel, but with different setups, has a different particle tracing; a binary mixture of magnetic and non-magnetic beads in a diluted ferrofluid, is then fed into the channel. These magnetic beads are focused near the centreline of the channel by exploiting positive magnetophoresis and microvortices generated by grooves, whereas the non-magnetic beads are focused along the sidewalls of the channel by negative magnetophoresis and hydrophoresis. These magnetic and non-magnetic beads are separated in a wide range of flow rates (up to 80 μl min−1).
Rosmarinic acid reverses the effects of metronidazole-induced infertility in male albino rats
Authors: Al-Alami Zina M. , Shraideh Ziad A. , Taha Mutasem O.
Published: November 2016

Rosmarinic acid (RA) is a natural antioxidant that has many biological activities. In the present study we investigated the potential of RA to reverse the negative effects of the widely used antibiotic and antiprotozoal agent metronidazole (MTZ), which is known to induce reversible male infertility. Two doses of RA (5 and 15 mg kg–1) were studied in sexually mature rats with and without MTZ-induced infertility. Rats were intraperitoneally injected with 5 mg kg–1 RA or 15 mg kg–1 RA (in distilled water) and, 45 min later, they were intraperitoneally injected with 40 mg kg–1 MTZ (in distilled water). Cauda epididymidal sperm suspensions were used to assess sperm count, motility and morphology. Histological and ultrastructural studies were performed on the testes and cauda epididymidis. In rats in which infertility was not induced, neither dose of RA affected the parameters assessed. However, in sexually mature rats in which infertility was induced by 40 mg kg–1 MTZ, RA at both 5 and 15 mg kg–1 ameliorated the damaging effects of MTZ on final bodyweight (30 days later), sperm motility and morphology. Only 5 mg kg–1 RA, and not 15 mg kg–1 RA, improved the harmful effects of MTZ on the sperm count and testis ultrastructure. The findings of the present study have considerable clinical implications and suggest a possible use for RA to reverse the negative effects of MTZ on male fertility, the male reproductive system and spermatogenesis.
Optical magnetic detection of single-neuron action potentials using quantum defects in diamond
Authors: Barry John F. , Turner Matthew J. , Schloss Jennifer M. , Glenn David R. , Song Yuyu , Lukin Mikhail D. , Park Hongkun , Walsworth Ronald L.
Published: November 2016

Significance

We demonstrate noninvasive detection of action potentials with single-neuron sensitivity, including in whole organisms. Our sensor is composed of quantum defects within a diamond chip, which detect time-varying magnetic fields generated by action potentials. The sensor is biocompatible and can be brought into close proximity to the organism without adverse effect, allowing for long-term observation and superior resolution of neuron magnetic fields. Optical magnetic detection with quantum defects also provides information about action potential propagation that is not easily available with existing methods. The quantum diamond technique requires no labeling or genetic modification, allows submillisecond time resolution, does not bleach, and senses through opaque tissue. With further development, we expect micrometer-scale magnetic imaging of a variety of neuronal phenomena.
Rapid emergence and mechanisms of resistance by U87 glioblastoma cells to doxorubicin in an in vitro tumor microfluidic ecology
Authors: Han Jeonghun , Jun Yukyung , Kim So Hyun , Hoang Hong-Hoa , Jung Yeonjoo , Kim Suyeon , Kim Jaesang , Austin Robert H. , Lee Sanghyuk , Park Sungsu
Published: November 2016

Significance

Drug resistance is among the most critical problems in cancer treatment. This proof-of-principle study demonstrates that a combination of in vitro microecology and deep sequencing could provide an extremely efficient method to elucidate the in vivo resistance mechanisms of cancer drugs and predict if drug resistance is likely to occur. Remarkably, drug resistance was seen within 7 d in our microfluidic chip, enabling characterization of molecular mechanisms within a month. This would be of great value for clinicians in selecting drugs likely to be slow in drug resistance emergence, and choose therapies for resistant tumors more effectively. In principle, our microecology technology can be used for many combinations of cancer types and drugs.
High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing
Authors: Moffitt Jeffrey R. , Hao Junjie , Bambah-Mukku Dhananjay , Lu Tian , Dulac Catherine , Zhuang Xiaowei
Published: November 2016

Significance

Multiplexed single-molecule FISH allows spatially resolved gene-expression profiling in single cells. However, because of off-target binding of FISH probes and cellular autofluorescence, background can become limiting in multiplexed single-molecule FISH measurements, especially when tissue samples are imaged or when the degree of multiplexing is increased. Here we report a sample clearing approach for FISH that substantially reduced these background sources by anchoring RNAs to a polymer matrix and then removing proteins and lipids. This approach allows measurements with higher detection efficiency and sensitivity across more color channels in both cell culture and tissue with no detectable loss in RNA. We anticipate that this clearing approach will greatly facilitate applications of multiplexed FISH measurements in a wide variety of biological systems.
The content and distribution of steryl ferulates in wheat produced in Japan
Authors: Tsuzuki Wakako , Mogushi Hiroyuki , Kawahara Shuji , Kotake-Nara Eiichi , Komba Shiro , Kanai Yoshikazu , Yamada Sumiyo , Horigane Akira
Published: November 2016

Oryzanol contained in rice bran is a complex mixture of steryl ferulates (SFs) with many identified health benefits. Recently, SF has been shown to exist in other cereals such as wheat, rye, and corn. In this study, SFs in several wheats produced in Japan were analyzed. For instance, SF content of whole wheat grain, Yumekaori (Japan) was 15.2 ± 1.4 mg-oryzanol-equivalent/100 g grain, while that of the imported one, 1CW (Canada) was 11.4 ± 1.3 mg-oryzanol-equivalent/100 g grain. The main SF components in the examined wheats were campesteryl ferulate, campestanyl ferulate, and sitostanyl ferulate. SF distribution in whole wheat grain was investigated using 14 fractions produced by a conventional test milling machine. SF was intensively accumulated in the four bran fractions (24 − 95 mg-oryzanol-equivalent/100 g bran fraction). These results suggest that the wheat bran would be an important source of SF.
GTSE1 tunes microtubule stability for chromosome alignment and segregation by inhibiting the microtubule depolymerase MCAK
Authors: Bendre Shweta , Rondelet Arnaud , Hall Conrad , Schmidt Nadine , Lin Yu-Chih , Brouhard Gary J. , Bird Alexander W.
Published: November 2016

The dynamic regulation of microtubules (MTs) during mitosis is critical for accurate chromosome segregation and genome stability. Cancer cell lines with hyperstabilized kinetochore MTs have increased segregation errors and elevated chromosomal instability (CIN), but the genetic defects responsible remain largely unknown. The MT depolymerase MCAK (mitotic centromere-associated kinesin) can influence CIN through its impact on MT stability, but how its potent activity is controlled in cells remains unclear. In this study, we show that GTSE1, a protein found overexpressed in aneuploid cancer cell lines and tumors, regulates MT stability during mitosis by inhibiting MCAK MT depolymerase activity. Cells lacking GTSE1 have defects in chromosome alignment and spindle positioning as a result of MT instability caused by excess MCAK activity. Reducing GTSE1 levels in CIN cancer cell lines reduces chromosome missegregation defects, whereas artificially inducing GTSE1 levels in chromosomally stable cells elevates chromosome missegregation and CIN. Thus, GTSE1 inhibition of MCAK activity regulates the balance of MT stability that determines the fidelity of chromosome alignment, segregation, and chromosomal stability.
Astrocytic TLR4 at the crossroads of inflammation and seizure susceptibility
Authors: Henneberger Christian , Steinhäuser Christian
Published: November 2016

Astrocytes have been implicated in epilepsy development, but their contribution is under debate. In this issue, Shen et al. (2016. J. Cell Biol. https://doi.org/10.1083/jcb.201605046) demonstrate that early postnatal inflammatory stimuli activate toll-like receptor 4 signaling in astrocytes and promote excitatory synaptogenesis, thereby increasing seizure susceptibility in young and adult mice.
Cohomology of presheaves with oriented weak transfers
Authors: Ross Joseph
Published: November 2016

Over a field of characteristic zero, we establish the homotopy invariance of the Nisnevich cohomology of homotopy invariant presheaves with oriented weak transfers, and the agreement of Zariski and Nisnevich cohomology for such presheaves. This generalizes a foundational result in Voevodsky’s theory of motives. The main idea is to find explicit smooth representatives of the correspondences which provide the input for Voevodsky’s cohomological architecture.
DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter
Authors: Quach Bryan , Furey Terrence S
Published: November 2016

Motivation

Identifying the locations of transcription factor binding sites is critical for understanding how gene transcription is regulated across different cell types and conditions. Chromatin accessibility experiments such as DNaseI sequencing (DNase-seq) and Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) produce genome-wide data that include distinct ‘footprint’ patterns at binding sites. Nearly all existing computational methods to detect footprints from these data assume that footprint signals are highly homogeneous across footprint sites. Additionally, a comprehensive and systematic comparison of footprinting methods for specifically identifying which motif sites for a specific factor are bound has not been performed.

Results

Using DNase-seq data from the ENCODE project, we show that a large degree of previously uncharacterized site-to-site variability exists in footprint signal across motif sites for a transcription factor. To model this heterogeneity in the data, we introduce a novel, supervised learning footprinter called Detecting Footprints Containing Motifs (DeFCoM). We compare DeFCoM to nine existing methods using evaluation sets from four human cell-lines and eighteen transcription factors and show that DeFCoM outperforms current methods in determining bound and unbound motif sites. We also analyze the impact of several biological and technical factors on the quality of footprint predictions to highlight important considerations when conducting footprint analyses and assessing the performance of footprint prediction methods. Finally, we show that DeFCoM can detect footprints using ATAC-seq data with similar accuracy as when using DNase-seq data.

Availability and Implementation

Python code available at https://bitbucket.org/bryancquach/defcom

Supplementary information

Supplementary data are available at Bioinformatics online.
Improved VCF normalization for accurate VCF comparison
Authors: Bayat Arash , Gaëta Bruno , Ignjatovic Aleksandar , Parameswaran Sri
Published: November 2016

Motivation

The Variant Call Format (VCF) is widely used to store data about genetic variation. Variant calling workflows detect potential variants in large numbers of short sequence reads generated by DNA sequencing and report them in VCF format. To evaluate the accuracy of variant callers, it is critical to correctly compare their output against a reference VCF file containing a gold standard set of variants. However, comparing VCF files is a complicated task as an individual genomic variant can be represented in several different ways and is therefore not necessarily reported in a unique way by different software.

Results

We introduce a VCF normalization method called Best Alignment Normalisation (BAN) that results in more accurate VCF file comparison. BAN applies all the variations in a VCF file to the reference genome to create a sample genome, and then recalls the variants by aligning this sample genome back with the reference genome. Since the purpose of BAN is to get an accurate result at the time of VCF comparison, we define a better normalization method as the one resulting in less disagreement between the outputs of different VCF comparators.

Availability and Implementation

The BAN Linux bash script along with required software are publicly available on https://sites.google.com/site/banadf16

Supplementary information

Supplementary data are available at Bioinformatics online.
Peidong Yang: cultivating ground-breaking research in China
Authors: Wang Ling , Poo Mu-ming
Published: November 2016

Opened in September 2013, ShanghaiTech University is a small-scale research university jointly established by Shanghai Municipal Government and the Chinese Academy of Sciences. As the founding dean of the newly launched School of Physical Science and Technology (SPST) of ShanghaiTech, Peidong Yang has been busy in drawing up the roadmap, initiating new programs and recruiting faculty members over the past two years. His mission at SPST is to make breakthroughs in interdisciplinary areas and promote cutting-edge original research, which he refers to as research ‘from 0 to 1’. In a recent interview with NSR, Yang pointed out that many research programs in China are incremental or just simple optimization of ground-breaking work by others, leading to duplication and fragmentation of research programs. And lack of differentiation and signature contribution is a major problem for the science community in China. He hopes to wriggle out of this situation through training the young generation to be independent and innovative.
Wilt, Crown, and Root Rot of Common Rose Mallow (Hibiscus moscheutos) Caused by a Novel Fusarium sp.
Authors: Lupien S. L. , Dugan F. M. , Ward K. M. , O’Donnell K.
Published: November 2016

A new crown and root rot disease of landscape plantings of the malvaceous ornamental common rose mallow (Hibiscus moscheutos) was first detected in Washington State in 2012. The main objectives of this study were to complete Koch’s postulates, document the disease symptoms photographically, and identify the causal agent using multilocus molecular phylogenetics. Results of the pathogenicity experiments demonstrated that the Fusarium sp. could induce vascular wilt and root and crown rot symptoms on H. moscheutos ‘Luna Rose’. Maximum-likelihood and maximum-parsimony phylogenetic analyses of portions of translation elongation factor 1-α and DNA-directed RNA polymerase II largest and second-largest subunit indicated that the Hibiscus pathogen represents a novel, undescribed Fusarium sp. nested within the Fusarium buharicum species complex.
Swimming Upstream: Creating a Culture of High-Value Care
Authors: Gupta Reshma , Moriates Christopher
Published: November 2016

As health system leaders strategize the best ways to encourage the transition toward value-based health care, the underlying culture—defined as a system of shared assumptions, values, beliefs, and norms existing within an environment—continues to shape clinician practice patterns. The current prevailing medical culture contributes to overtesting, overtreatment, and health care waste. Choosing Wisely lists, appropriateness criteria, and guidelines codify best practices, but academic medicine as a whole must recognize that faculty and trainees are all largely still operating within the same cultural climate. Addressing this culture, on both local and national levels, is imperative for engaging clinicians in reforms and creating sustained changes that will deliver on the promise of better health care value. This Perspective outlines four steps for health system leaders to understand, cultivate, and maintain cultural changes toward value-based care: (1) Build the will for change through engaging frontline providers and communicating patient-centered motivations for health care value; (2) create necessary infrastructure to support value improvement efforts; (3) expose physicians to value-based payment structures; and (4) demonstrate leadership commitment and visibility to shared goals. The authors support their recommendations with concrete examples from emerging models and leaders across the country.