bluuebunny/crossref_metadata_2025 huggingface dataset:
NMR spectroscopy study of local correlations in water
Authors: Mallamace Francesco , Corsaro Carmelo , Mallamace Domenico , Vasi Sebastiano , Stanley H. Eugene
Published: December 2016

Using nuclear magnetic resonance we study the dynamics of the hydrogen bond (HB) sub-domains in bulk and emulsified water across a wide temperature range that includes the supercooled regime. We measure the proton spin-lattice T1 and spin-spin T2 relaxation times to understand the hydrophilic interactions that determine the properties of water. We use (i) the Bloembergen, Purcell, and Pound approach that focuses on a single characteristic correlation time τc, and (ii) the Powles and Hubbard approach that measures the proton rotational time τθ. We find that when the temperature is low both relaxation times are strongly correlated when the HB lifetime is long, and that when the temperature is high a decrease in the HB lifetime destroys the water clusters and decouples the dynamic modes of the system.
Moving charged particles in lattice Boltzmann-based electrokinetics
Authors: Kuron Michael , Rempfer Georg , Schornbaum Florian , Bauer Martin , Godenschwager Christian , Holm Christian , de Graaf Joost
Published: December 2016

The motion of ionic solutes and charged particles under the influence of an electric field and the ensuing hydrodynamic flow of the underlying solvent is ubiquitous in aqueous colloidal suspensions. The physics of such systems is described by a coupled set of differential equations, along with boundary conditions, collectively referred to as the electrokinetic equations. Capuani et al. [J. Chem. Phys. 121, 973 (2004)] introduced a lattice-based method for solving this system of equations, which builds upon the lattice Boltzmann algorithm for the simulation of hydrodynamic flow and exploits computational locality. However, thus far, a description of how to incorporate moving boundary conditions into the Capuani scheme has been lacking. Moving boundary conditions are needed to simulate multiple arbitrarily moving colloids. In this paper, we detail how to introduce such a particle coupling scheme, based on an analogue to the moving boundary method for the pure lattice Boltzmann solver. The key ingredients in our method are mass and charge conservation for the solute species and a partial-volume smoothing of the solute fluxes to minimize discretization artifacts. We demonstrate our algorithm’s effectiveness by simulating the electrophoresis of charged spheres in an external field; for a single sphere we compare to the equivalent electro-osmotic (co-moving) problem. Our method’s efficiency and ease of implementation should prove beneficial to future simulations of the dynamics in a wide range of complex nanoscopic and colloidal systems that were previously inaccessible to lattice-based continuum algorithms.
Dynamical quantum tomography
Authors: Kech Michael
Published: December 2016

We consider quantum state tomography with measurement procedures of the following type: First, we subject the quantum state we aim to identify to a known time evolution for a desired period of time. Afterwards we perform a measurement with a fixed measurement setup. This procedure can then be repeated for other periods of time, the measurement setup however remains unaltered. Given an n-dimensional system with suitable unitary dynamics, we show that any two states can be discriminated by performing a measurement with a setup that has n outcomes at n + 1 points in time. Furthermore, we consider scenarios where prior information restricts the set of states to a subset of lower dimensionality. Given an n-dimensional system with suitable unitary dynamics and a semi-algebraic subset R of its state space, we show that any two states of the subset can be discriminated by performing a measurement with a setup that has n outcomes at l steps of the time evolution if (n−1)l≥2dimR. In addition, by going beyond unitary dynamics, we show that one can in fact reduce to a setup with the minimal number of two outcomes.
Modeling and simulation of the zinc-nickel single flow batteries based on MATLAB/Simulink
Authors: Yao Shouguang , Liao Peng , Xiao Min , Cheng Jie , He Ke
Published: December 2016

Based on the working principle of the zinc-nickel single flow batteries (ZNBs), this paper builds the electrochemical model and mechanical model, analyzes the effect of electrolyte flux on the battery performance and obtains a single cell with a 216 Ah charge-discharge capacity as an example, and thereafter conducts a simulation to obtain several results under the condition of constant current charge and discharge. The simulation results are well matched in comparison with the experimental results. An optimal flux exists during the charge and discharge, which indicates that the model can well simulate the charge and discharge characteristics of the ZNBs under the condition of constant current.
Determining the vibrations between sensor and sample in SQUID microscopy
Authors: Schiessl Daniel , Kirtley John R. , Paulius Lisa , Rosenberg Aaron J. , Palmstrom Johanna C. , Ullah Rahim R. , Holland Connor M. , Fung Y.-K.-K. , Ketchen Mark B. , Gibson Gerald W. , Moler Kathryn A.
Published: December 2016

Vibrations can cause noise in scanning probe microscopies. Relative vibrations between the scanning sensor and the sample are important but can be more difficult to determine than absolute vibrations or vibrations relative to the laboratory. We measure the noise spectral density in a scanning SQUID microscope as a function of position near a localized source of magnetic field and show that we can determine the spectra of all three components of the relative sensor-sample vibrations. This method is a powerful tool for diagnosing vibrational noise in scanning microscopies.
A multiple-field coupled resistive transition model for superconducting Nb3Sn
Authors: Yang Lin , Ding He , Zhang Xin , Qiao Li
Published: December 2016

A study on the superconducting transition width as functions of the applied magnetic field and strain is performed in superconducting Nb3Sn. A quantitative, yet universal phenomenological resistivity model is proposed. The numerical simulation by the proposed model shows predicted resistive transition characteristics under variable magnetic fields and strain, which in good agreement with the experimental observations. Furthermore, a temperature-modulated magnetoresistance transition behavior in filamentary Nb3Sn conductors can also be well described by the given model. The multiple-field coupled resistive transition model is helpful for making objective determinations of the high-dimensional critical surface of Nb3Sn in the multi-parameter space, offering some preliminary information about the basic vortex-pinning mechanisms, and guiding the design of the quench protection system of Nb3Sn superconducting magnets.
Molecular dynamics simulations of the effect of shape and size of SiO2 nanoparticle dopants on insulation paper cellulose
Authors: Tang Chao , Zhang Song , Li Xu , Zhou Qu
Published: December 2016

The effect of silica nanoparticle (Nano-SiO2) dopants on insulation paper cellulose, and the interaction between them, was investigated using molecular dynamics simulations. The mechanical properties, interactions, and cellulose-Nano-SiO2 compatibility of composite models of cellulose doped with Nano-SiO2 were studied. An increase in Nano-SiO2 size leads to a decrease in the mechanical properties, and a decrease in the anti-deformation ability of the composite model. The binding energies and bond energies per surface area of the composite models indicate that the bonding interaction between spherical Nano-SiO2 and cellulose is the strongest among the four different Nano-SiO2 shapes that are investigated. The solubilities of the four composite models decrease with increasing Nano-SiO2 size, and the difference between the solubility of pure cellulose and those of the composite models increases with increasing Nano-SiO2 size. Good doping effects with the highest cellulose-Nano-SiO2 compatibility are achieved for the cellulose model doped with spherical Nano-SiO2 of 10 Å in diameter. These findings provide a method for modifying the mechanical properties of cellulose by doping, perhaps for improving insulation dielectrics.
Power characteristics of planar index-antiguided waveguide lasers with transverse mode competition
Authors: Wang Chaofan , Liu Yuanye , Casperson Lee W. , Her Tsing-Hua
Published: December 2016

We report comprehensive analysis of output characteristics of homogeneously broadened index-antiguided slab lasers with transverse mode competition. Robust single fundamental mode operation is achieved when the distributive modal loss due to index antiguiding dominates the output coupling loss. Maximal laser efficiency under single fundamental mode operation is investigated numerically for various combinations of single-pass gains and losses. We show analytically that an asymptotic limit of such efficiency exists that is solely determined by the loss ratio between the fundamental and 1st higher-order modes, which equals 66.7% for planar index antiguided lasers.
Simultaneous enhancement of conductivity and Seebeck coefficient in an organic Mott transistor
Authors: Kawasugi Yoshitaka , Seki Kazuhiro , Edagawa Yusuke , Sato Yoshiaki , Pu Jiang , Takenobu Taishi , Yunoki Seiji , Yamamoto Hiroshi M. , Kato Reizo
Published: December 2016

We report on the electrical conductivity and Seebeck coefficient of an electric-double-layer transistor based on an organic Mott insulator. The measurements were performed along the two in-plane crystallographic axes (a and c) of the same device. While the Seebeck coefficient along the a-axis was decreased by electron or hole doping, the value along the c-axis was increased by hole doping. This is in contrast to the general trade-off relation between the conductivity and the Seebeck coefficient. The simultaneous enhancement of the conductivity and the Seebeck coefficient is attributed to pseudogap formation in the hole-doped state, where a steep slope of the density of states emerges at the chemical potential because of the electron interaction.
Theoretical insights into kesterite and stannite phases of Cu2(Sn1–XGeX)ZnSe4 based alloys: A prospective photovoltaic material
Authors: Kumar S. , Sharma Durgesh Kumar , Joshi Bipin , Auluck S.
Published: December 2016

A comparative study of kesterite (KS) and stannite (ST) phases of Cu2(Sn1−xGex)ZnSe4 (CTGZSe) alloys has been carried out using a hybrid functional within the framework of density functional theory (DFT). Our calculations suggest that KS phase is energetically more stable. We find that the total energy of the KS phase decreases with increasing concentration (x) of Ge. The calculated positive binding energies suggest that the alloy systems are stable. The formation enthalpy clearly indicates that CTGZSe alloys are thermodynamically stable and its growth can be achieved by following the route of an exothermic reaction. The calculated energy band gaps of the alloys agree well with the experimental data for the KS phase. The band offsets of KS and ST phases as a function of Ge concentration (x) can be explained on the basis of the calculated energy band gaps. We find a slight upshift in the conduction band edges while the valence band edges remain almost the same on varying the concentration (x) of Ge. Our results could be useful for the development of CTGZSe alloys based solar cells.
Platinum (II) azatetrabenzoporphyrins for near-infrared organic light emitting diodes
Authors: Huang L. , Park C. D. , Fleetham T. , Li J.
Published: December 2016

This article describes a series of platinum (II) azatetrabenzoporphyrin emitters for near-infrared (NIR) organic light emitting diode (OLED) applications. Platinum (II) aza-triphenyltetrabenzoporphyrin (PtNTBP) results in a 72 nm shift in the photoluminescent (PL) emission spectrum to 842 nm compared to 770 nm of the platinum (II) tetraphenyltetrabenzoporphyrin (PtTPTBP). Also, the full width at half maximum of the emission spectrum of PtNTBP was significantly narrowed to 27 nm compared to 40 nm for PtTPTBP. The multilayer devices fabricated by thermal vacuum evaporation process employing PtTPTBP, PtNTBP, and cis-PtN2TBP exhibit electroluminescent (EL) emission peak at 770 nm, 848 nm, and 846 nm with the peak external quantum efficiency (EQE) of 8.0%, 2.8%, and 1.5%, respectively. Even with the decrease in EQE of devices employing PtNTBP and cis-PtN2TBP compared with those employing PtTPTBP, the combination of the spectral narrowing and the bathochromic shift to lower energy EL emission demonstrates the promise of PtNTBP for NIR applications. In the meanwhile, the solution-processed single-layer device using PtNTBP demonstrates the EQE of 0.33% and the peak EL emission at 844 nm.
Local carrier recombination and associated dynamics in m-plane InGaN/GaN quantum wells probed by picosecond cathodoluminescence
Authors: Zhu Tongtong , Gachet David , Tang Fengzai , Fu Wai Yuen , Oehler Fabrice , Kappers Menno J. , Dawson Phil , Humphreys Colin J. , Oliver Rachel A.
Published: December 2016

We report on spatially resolved and time-resolved cathodoluminescence (CL) studies of the recombination mechanisms of InGaN/GaN quantum wells (QWs) grown by metal-organic vapour phase epitaxy on bulk m-plane Ammono GaN substrates. As a result of the 2° miscut of the GaN substrate, the sample surface exhibits step bunches, where semi-polar QWs with a higher indium concentration than the planar m-plane QWs form during the QW growth. Spatially resolved time-integrated CL maps under both continuous and pulsed excitation show a broad emission band originating from the m-plane QWs and a distinct low energy emission originating from the semi-polar QWs at the step bunches. High resolution time-resolved CL maps reveal that when the m-QWs are excited well away from the step bunches the emission from the m-plane QWs decays with a time constant of 350 ps, whereas the emission originating semi-polar QWs decays with a longer time constant of 489 ps. The time constant of the decay from the semi-polar QWs is longer due to the separation of the carrier wavefunctions caused by the electric field across the semi-polar QWs.
CO2 adsorption on Fe-doped graphene nanoribbons: First principles electronic transport calculations
Authors: Berdiyorov G. R. , Abdullah H. , Al Ezzi M. , Rakhmatullaeva G. V. , Bahlouli H. , Tit N.
Published: December 2016

Decoration of graphene with metals and metal-oxides is known to be one of the effective methods to enhance gas sensing and catalytic properties of graphene. We use density functional theory in combination with the nonequilibrium Green’s function formalism to study the conductance response of Fe-doped graphene nanoribbons to CO2 gas adsorption. A single Fe atom is either adsorbed on graphene’s surface (aFe-graphene) or it substitutes the carbon atom (sFe-graphene). Metal atom doping reduces the electronic transmission of pristine graphene due to the localization of electronic states near the impurities. The reduction in the transmission is more pronounced in the case of aFe-graphene. In addition, the aFe-graphene is found to be less sensitive to the CO2 molecule attachment as compared to the sFe-graphene system. Pristine graphene is also found to be less sensitive to the molecular adsorption. Since the change in the conductivity is one of the main outputs of sensors, our findings will be useful in developing graphene-based solid-state gas sensors.
Experimental and numerical studies of microwave-plasma interaction in a MWPECVD reactor
Authors: Massaro A. , Velardi L. , Taccogna F. , Cicala G.
Published: December 2016

This work deals with and proposes a simple and compact diagnostic method able to characterize the interaction between microwave and plasma without the necessity of using an external diagnostic tool. The interaction between 2.45 GHz microwave and plasma, in a typical ASTeX-type reactor, is investigated from experimental and numerical view points. The experiments are performed by considering plasmas of three different gas mixtures: H2, CH4-H2 and CH4-H2-N2. The two latter are used to deposit synthetic undoped and n-doped diamond films. The experimental setup equipped with a matching network enables the measurements of very low reflected power. The reflected powers show ripples due to the mismatching between wave and plasma impedance. Specifically, the three types of plasma exhibit reflected power values related to the variation of electron-neutral collision frequency among the species by changing the gas mixture. The different gas mixtures studied are also useful to test the sensitivity of the reflected power measurements to the change of plasma composition. By means of a numerical model, only the interaction of microwave and H2 plasma is examined allowing the estimation of plasma and matching network impedances and of reflected power that is found about eighteen times higher than that measured.
Control of femtosecond multi-filamentation in glass by designable patterned optical fields
Authors: Li Ping-Ping , Cai Meng-Qiang , Lü Jia-Qi , Wang Dan , Liu Gui-Geng , Qian Sheng-Xia , Li Yongnan , Tu Chenghou , Wang Hui-Tian
Published: December 2016

We present a scheme for realizing femtosecond multi-filamentation with designable quantity and locations of filaments, based on the control of multi-focal spots formed by patterned optical fields (POFs) composed of multiple individual optical fields (IOFs). A computer-controlled spatial light modulator is used to engineer the POFs. In particular, we introduce a blazed phase grating in any IOF, which increases a degree of freedom, making the engineering of multi-focal spots becomes more flexible. We achieve experimentally the aim controlling femtosecond multi-filamentation in a K9 glass. Our scheme has great flexibility and convenience in controlling the multi-filamentation in quantity and locations of filaments and strength of interaction between filaments.
Maternal body composition in seedstock herds. 4. Genetic parameters for body composition of Angus and Hereford cows
Authors: Donoghue K. A. , Lee S. J. , Parnell P. F. , Pitchford W. S.
Published: December 2016

The genetics of body composition traits measured before calving and at weaning in the first and second parities were evaluated in 5975 Angus and 1785 Hereford cows. Traits measured were liveweight, body condition score and hip height and ultrasound scanned measurements of subcutaneous P8 and 12/13th rib fat depth, loin eye muscle area and intramuscular fat percentage. Corresponding yearling measures on these animals were obtained for analyses of relationships between yearling information with later-in-life traits. There was moderate genetic variation in all body composition traits measured at pre-calving and weaning in Angus (h2 = 0.14–0.59) and Hereford (h2 = 0.14–0.64) cows. Genetic correlations between measurements of the same trait at pre-calving and weaning were consistently positive and high in both parities for both breeds, indicating animals were ranking similarly for the same trait measured over time. Genetic correlations between measurements of different traits were generally consistent over time (pre-calving and weaning) in both breeds, indicating genetic relationships between traits were not changing significantly over time. Genetic correlations with corresponding yearling measures of body composition were consistently positive and high for the first parity, and lower for the second parity. The results of this study indicate that genetic improvement in body composition traits in cows is possible, and that body composition information recorded at yearling age is a reasonably good predictor of later in life performance for these traits.
Dead organic matter and the dynamics of carbon and greenhouse gas emissions in frequently burnt savannas
Authors: Cook Garry D. , Meyer C. P. (Mick) , Muepu Maëlys , Liedloff Adam C.
Published: December 2016

We developed a gain–loss approach to estimating the dynamics of the dead organic matter pool in northern Australian savannas consistent with the Intergovernmental Panel on Climate Change 2006 guidance. Previously, only emissions of methane and nitrous oxide were accounted in greenhouse gas budgets. The new approach is based on a modification of the Olson fuel accumulation equation. This modification includes the mean post-fire residue and accounts for losses from both fire and decomposition and for gains from grass production, tree litter fall and the death of trees. We apply the approach to a case study in western Arnhem Land, Northern Territory, Australia, in which the fire regime has been changed and the project has achieved recognised abatement of methane and nitrous oxide emissions. The carbon sequestration in the dead organic matter is ~85 times the annual emissions abatement in this project area and when expressed as an annual rate is ~3.5 times the abatement. We also show that the emissions abatement has previously been underestimated owing to an inability to fully account for dead organic matter dynamics. Future work could refine the models of dead organic matter to include seasonal dynamics in inputs.
The United States of wealth
Authors: Jayachandiran Chenthuran , Harrison Kathryn E. , Afifi Tamara D. , Davis Sharde M.
Published: December 2016

During the Great Recession, discourses of what constituted prosperity flooded the global landscape. The concept of prosperity
became a prominent master narrative that dictated the ways families operated and made decisions. The goal of this study was to
examine how 82 married couples experiencing economic uncertainty in California (re)negotiated their family narratives of wealth
and prosperity in the wake of the Great Recession. The findings revealed that few, if any, couples were able to communicatively
re-define prosperity in a way that wholly resisted or rejected the master narrative of material wealth. The narratives
demonstrated how this master narrative held many of these families captive by restricting their ability to reconstitute their
understanding of prosperity in productive ways even when the taken-for-granted meaning of prosperity-as-wealth was challenged
during the Great Recession. The families who successfully re-defined prosperity depended on other dominant discourses such as
health, faith, family quality and relationships to refuse or repudiate the master narrative of wealth as prosperity. The findings
support Lindemann-Nelson’s (2001) argument that successfully overcoming a master narrative often requires a patchwork of
resistance strategies that permeate daily discourse, before they begin to chip away at the larger dominant discourse.
‘I sort of did stuff to him’
Authors: Jackson Clare
Published: December 2016

This article presents a conversation analytic examination of a telephone call in which a teenage girl updates her friend about developments in a relationship. The telling is in three phases, from initial reluctance, through first kiss to first sexual contact. Drawing on the notion of lower and upper bounded tellability, I analyse the talk for what is constructed as tellable and as taboo. Eminently tellable, the kiss is a directly named activity, details are sought, and it is assessed in a delighted way. In contrast, the sexual activity is not named and instead is referred to as ‘stuff’. The details of ‘stuff’ are not pursued, and the activity is assessed with (playful) disapproval. The telling speaks to normative gendered sexual expectations for teenage girls in the UK. In talking about personal experience of sexual conduct but without talking in any detail, these speakers position themselves as morally respectable.
The effect of exposure to fluid intelligence components on learning sentence connectors of foreign language learners
Authors: Kamelifar Leila , Salimi Esmaeel Ali
Published: December 2016

Fluid intelligence (Gf) is the ability to solve novel problems without resorting to information obtained from previous training (Cattell, 1987: Horn & Cattell, 1966). However, several research studies (Au et al., 2015; Jaeggi et al., 2008; Kundu et al., 2013) have shown that Gf may be responsive to training if it is decomposed to its components, which are working memory capacity (WMC), fluid reasoning and visuospatial ability. Nonetheless, there are some counterarguments proposed by some researchers saying that Gf may not be improved through training (Chooi & Thompson, 2012; Harrison et al., 2013; Redick et al., 2013). In this study 60 Iranian intermediate students majoring in Psychology were randomly assigned into two groups of control (Gco) and experimental (Gex). Both groups had 6 sessions of writing treatment. Besides, Gex was exposed to n-back task, Cattell’s test and Raven’s test for 12 more sessions,4 sessions for each task. The results showed that the exposure to Gf components could significantly affect learning connectors.
Homozygosity mapping and CDH23 mutation analysis in Iranian deaf families
Authors: Davoudi-Dehaghani Elham , Bagherian Hamideh , DabbaghBagheri Samira , Mahdieh Nejat , Shirkavand Atefeh , Zeinali Sirous
Published: December 2016

Objective:

Cadherin-related 23 (CDH23) gene encodes a cell–cell adhesion protein which is required for the proper development of hair cells. Previous studies have shown that different mutations in this gene are associated with Usher syndrome, autosomal recessive nonsyndromic deafness (DFNB12) and age-related hearing loss. In this study the contribution of CDH23 mutations in hearing loss has been investigated.

Study design:

The homosygosity mapping, using microsatellite markers linked to DFNB12 locus was performed for a population of 45 GJB2 negative Iranian families with autosomal recessive non-syndromic form of hearing loss. Coding region and exon-intron boundaries of all 69 exons of the CDH23 gene were investigated using Sanger sequencing.

Results:

The homozygosity mapping showed co-segregation of the hearing loss with four STR markers linked to the DFNB12 locus in one family. Assessing pathogenicity of identified variations in this gene showed that previously reported mutation c.2968G > A (p.Asp990Asn) can be the cause of hearing loss in this family.

Conclusion:

This study suggests that CDH23 mutations may have a significant role in causing hearing loss in Iran. More studies should be performed to determine frequency of this gene in the Iranian population.
MOZART1 and γ-tubulin complex receptors are both required to turn γ-TuSC into an active microtubule nucleation template
Authors: Lin Tien-chen , Neuner Annett , Flemming Dirk , Liu Peng , Chinen Takumi , Jäkle Ursula , Arkowitz Robert , Schiebel Elmar
Published: December 2016

MOZART1/Mzt1 is required for the localization of γ-tubulin complexes to microtubule (MT)–organizing centers from yeast to human cells. Nevertheless, the molecular function of MOZART1/Mzt1 is largely unknown. Taking advantage of the minimal MT nucleation system of Candida albicans, we reconstituted the interactions of Mzt1, γ-tubulin small complex (γ-TuSC), and γ-tubulin complex receptors (γ-TuCRs) Spc72 and Spc110 in vitro. With affinity measurements, domain deletion, and swapping, we show that Spc110 and Mzt1 bind to distinct regions of the γ-TuSC. In contrast, both Mzt1 and γ-TuSC interact with the conserved CM1 motif of Spc110/Spc72. Spc110/Spc72 and Mzt1 constitute “oligomerization chaperones,” cooperatively promoting and directing γ-TuSC oligomerization into MT nucleation-competent rings. Consistent with the functions of Mzt1, human MOZART1 directly interacts with the CM1-containing region of the γ-TuCR CEP215. MOZART1 depletion in human cells destabilizes the large γ-tubulin ring complex and abolishes CEP215CM1-induced ectopic MT nucleation. Together, we reveal conserved functions of MOZART1/Mzt1 through interactions with γ-tubulin complex subunits and γ-TuCRs.
Navigating challenges in the application of superresolution microscopy
Authors: Lambert Talley J. , Waters Jennifer C.
Published: December 2016

In 2014, the Nobel Prize in Chemistry was awarded to three scientists who have made groundbreaking contributions to the field of superresolution (SR) microscopy (SRM). The first commercial SR microscope came to market a decade earlier, and many other commercial options have followed. As commercialization has lowered the barrier to using SRM and the awarding of the Nobel Prize has drawn attention to these methods, biologists have begun adopting SRM to address a wide range of questions in many types of specimens. There is no shortage of reviews on the fundamental principles of SRM and the remarkable achievements made with these methods. We approach SRM from another direction: we focus on the current practical limitations and compromises that must be made when designing an SRM experiment. We provide information and resources to help biologists navigate through common pitfalls in SRM specimen preparation and optimization of image acquisition as well as errors and artifacts that may compromise the reproducibility of SRM data.
TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes
Authors: Jung Inuk , Jo Kyuri , Kang Hyejin , Ahn Hongryul , Yu Youngjae , Kim Sun
Published: December 2016

Motivation

Identifying biologically meaningful gene expression patterns from time series gene expression data is important to understand the underlying biological mechanisms. To identify significantly perturbed gene sets between different phenotypes, analysis of time series transcriptome data requires consideration of time and sample dimensions. Thus, the analysis of such time series data seeks to search gene sets that exhibit similar or different expression patterns between two or more sample conditions, constituting the three-dimensional data, i.e. gene-time-condition. Computational complexity for analyzing such data is very high, compared to the already difficult NP-hard two dimensional biclustering algorithms. Because of this challenge, traditional time series clustering algorithms are designed to capture co-expressed genes with similar expression pattern in two sample conditions.

Results

We present a triclustering algorithm, TimesVector, specifically designed for clustering three-dimensional time series data to capture distinctively similar or different gene expression patterns between two or more sample conditions. TimesVector identifies clusters with distinctive expression patterns in three steps: (i) dimension reduction and clustering of time-condition concatenated vectors, (ii) post-processing clusters for detecting similar and distinct expression patterns and (iii) rescuing genes from unclassified clusters. Using four sets of time series gene expression data, generated by both microarray and high throughput sequencing platforms, we demonstrated that TimesVector successfully detected biologically meaningful clusters of high quality. TimesVector improved the clustering quality compared to existing triclustering tools and only TimesVector detected clusters with differential expression patterns across conditions successfully.

Availability and Implementation

The TimesVector software is available at http://biohealth.snu.ac.kr/software/TimesVector/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Effect of Bran Extract from Pigmented Rice Superjami on the Lipid and Glucose Metabolisms in a Postmenopause‐Like Model of Ovariectomized Rats
Authors: Nam Su Jin , Chung Soo Im , Ryu Su Noh , Kang Mi Young
Published: December 2016

The effect of rice bran ethanolic extract from Superjami, a new blackish‐purple pigmented cultivar, on the lipid and glucose metabolisms in a postmenopausal‐like model of ovariectomized rats was investigated. Sprague‐Dawley female rats were subjected to either bilateral ovariectomy or a sham operation and randomly divided into three dietary groups (n = 6): sham‐operated fed with normal diet (SHAM), ovariectomized fed with normal diet (OVX‐AIN76), and ovariectomized fed with normal diet supplemented with Superjami bran extract (OVX‐SJ). The OVX‐AIN76 group showed significantly higher body weight, triglyceride, total cholesterol, blood glucose, and insulin than the SHAM group. On the other hand, supplementation of Superjami bran extract markedly reduced the body weight gain and improved the lipid and glucose profiles in ovariectomized rats through inhibition of hepatic lipogenesis and adipokine production and modulation of glucose‐regulating enzyme activities. These findings demonstrate that extracts from Superjami bran may be useful in the prevention and management of postmenopause‐induced hyperlipidemia and hyperglycemia.
Accumulation of High‐Molecular‐Weight Glutenin Subunits in Superior and Inferior Grains of a Winter Wheat, Yangmai 158
Authors: Hoang Kimtoan , Li Xiangnan , Bo Yun , Zhou Qin , Cai Jian , Wang Xiao , Cai Hua , Dai Tingbo , Cao Weixing , Jiang Dong
Published: December 2016

The difference in accumulation of high‐molecular‐weight glutenin subunits (HMW‐GS) in superior (basal) and inferior (distal) grains results in the nonuniformity of grain quality in a winter wheat (Triticum aestivum L. ‘Yangmai 158’). The HMW‐GS accumulation and glutenin macropolymer (GMP) content were studied in superior and inferior grains during the grain‐filling period. Compared with inferior grains, HMW‐GS was formed earlier and total accumulation amount was higher in superior grains. The total HMW‐GS content was higher in superior grain than inferior grain, except at maturity. For individual HMW‐GS types, the accumulation and content of subunit 7 were the highest, followed by subunit 12, and those of subunit 8 were the lowest, followed by subunit 2 in superior grain. In contrast, the accumulation and content of subunit 7 at maturity were significantly higher than subunit 8 but similar between subunit 2 and subunit 12 in inferior grain. Moreover, the accumulation of subunit 7 and 12 in superior grain was significantly higher than in inferior grain. However, compared with the inferior grain, the GMP accumulation was higher but content was lower in superior grain at maturity.
Pearling Affects the Lipid Content and Composition and Lipase Activity Levels of Wheat (Triticum aestivum L.) Roller Milling Fractions
Authors: De Brier Niels , Delcour Jan A.
Published: December 2016

Wheat bran contains most of the dietary fiber, vitamins, minerals, and antioxidants of the grain. Unfortunately, it readily deteriorates upon storage because it has high lipid contents and lipase activity levels, which can cause rancidity and, hence, when used in food systems, inferior product quality. We here examined the lipid composition and the lipase activities of wheat bran and the impact of pearling prior to milling thereupon. The lipid content of the outer bran layers (2.31% on a dry matter [dm] basis) is lower than that of regular bran (3.81% dm). Nevertheless, these layers have the highest concentration of free fatty acids (FFA, 0.56% dm), which is ascribed to lipid hydrolysis. Indeed, the lipase activity levels in the peripheral layers were three times higher than in the bran itself. Abrading these tissues by pearling prior to milling yielded a bran fraction with about 30% lower FFA content and 30% lower lipase activity level. Pearling offers opportunities to lower the FFA content and lipase activity levels in wheat bran and, hence, to contribute to an improved storage stability of bran.
Rice Leaf Transcriptional Profiling Suggests a Functional Interplay Between Xanthomonas oryzae pv. oryzae Lipopolysaccharide and Extracellular Polysaccharide in Modulation of Defense Responses During Infection
Authors: Girija Anil Madhusoodana , Kinathi Bipin Kumar , Madhavi Mylavarapu B. , Ramesh Palaparthi , Vungarala Sridivya , Patel Hitendra Kumar , Sonti Ramesh V.
Published: December 2016

Treatment of rice leaves with isolated Xanthomonas oryzae pv. oryzae lipopolysaccharide (LPS) induces the production of callose deposits, reactive oxygen species, and enhanced resistance against subsequent bacterial infection. Expression profiling of X. oryzae pv. oryzae LPS-treated rice (Oryza sativa subsp. indica) leaves showed that genes involved in the biosynthetic pathways for lignins, phenylpropanoids, chorismate, phenylalanine, salicylic acid, and ethylene, as well as a number of pathogenesis-related proteins are up-regulated. Gene ontology categories like cell-wall organization, defense response, stress response, and protein phosphorylation/kinases were found to be upregulated, while genes involved in photosynthesis were down-regulated. Coinfiltration with xanthan gum, the xanthomonas extracellular polysaccharide (EPS), suppressed LPS-induced callose deposition. Gene expression analysis of rice leaves that are treated with an EPS-deficient mutant of X. oryzae pv. oryzae indicated that a number of defense-regulated functions are up-regulated during infection. These transcriptional responses are attenuated in rice leaves treated with an EPS-deficient mutant that is also deficient in the O-antigen component of LPS. Overall, these results suggest that the O-antigen component of X. oryzae pv. oryzae LPS induces rice defense responses during infection and that these are suppressed by bacterial EPS.
Identification and Characterization of Rhizoctonia Species Associated with Soybean Seedling Disease
Authors: Ajayi-Oyetunde Olutoyosi O. , Bradley Carl A.
Published: December 2016

In an effort to identify the Rhizoctonia spp. associated with seedling diseases of soybean, Rhizoctonia isolates were recovered from soybean seedlings with damping off and root and hypocotyl rot symptoms from Arkansas, Illinois, Kansas, Michigan, Minnesota, and the Canadian province of Ontario between 2012 and 2014. Based on cultural morphology, polymerase chain reaction restriction fragment length polymorphism, and phylogenetic analysis of the internal transcribed spacer (ITS) region of the ribosomal RNA genes, 80 isolates were confirmed to be Rhizoctonia solani, 24 were binucleate Rhizoctonia spp., and 10 were R. zeae. Of the 80 R. solani isolates, one belonged to anastomosis group (AG) 2-1, 52 belonged to AG-2-2IIIB, five belonged to AG-3 PT, three belonged to AG-4 HGI, two belonged to AG-4 HGIII, nine belonged to AG-7, and eight belonged to AG-11. Bayesian inference of phylogeny using the ITS region revealed two clades of R. solani AG-7 that possibly correspond to different AG-7 subgroups. Phylogenetic analysis also provided evidence for genetic relatedness between certain binucleate Rhizoctonia and some R. solani isolates. On ‘Williams 82’ soybean, isolates of AG-2-2IIIB were the most aggressive, followed by isolates of AG-7, AG-4, and AG-11. On ‘Jubilee’, a sweet corn cultivar, AG-2-2IIIB and AG-4 isolates caused significant stunting and root damage, whereas the damage caused by the AG-11 isolates was mostly restricted to the mesocotyl. Isolates of R. zeae and the binucleate Rhizoctonia spp. were not pathogenic on soybean or corn. Our results indicate that soybean and corn are hosts to the predominant and aggressive AG of R. solani, implying that rotation between these two crops may not be an effective management practice.
Detection of Oil Palm Root Penetration by Agrobacterium-Mediated Transformed Ganoderma boninense, Expressing Green Fluorescent Protein
Authors: Govender Nisha , Wong Mui-Yun
Published: December 2016

A highly efficient and reproducible Agrobacterium-mediated transformation protocol for Ganoderma boninense was developed to facilitate observation of the early stage infection of basal stem rot (BSR). The method was proven amenable to different explants (basidiospore, protoplast, and mycelium) of G. boninense. The transformation efficiency was highest (62%) under a treatment combination of protoplast explant and Agrobacterium strain LBA4404, with successful expression of an hyg marker gene and gus-gfp fusion gene under the control of heterologous p416 glyceraldehyde 3-phosphate dehydrogenase promoter. Optimal transformation conditions included a 1:100 Agrobacterium/explant ratio, induction of Agrobacterium virulence genes in the presence of 250 μm acetosyringone, co-cultivation at 22°C for 2 days on nitrocellulose membrane overlaid on an induction medium, and regeneration of transformants on potato glucose agar prepared with 0.6 M sucrose and 20 mM phosphate buffer. Evaluated transformants were able to infect root tissues of oil palm plantlets with needle-like microhyphae during the penetration event. The availability of this model pathogen system for BSR may lead to a better understanding of the pathogenicity factors associated with G. boninense penetration into oil palm roots.
Cross Interaction Between Ilyonectria mors-panacis Isolates Infecting Korean Ginseng and Ginseng Saponins in Correlation with Their Pathogenicity
Authors: Farh Mohamed El-Agamy , Kim Yeon-Ju , Singh Priyanka , Yang Deok-Chun
Published: December 2016

Ilyonectria mors-panacis belongs to I. radicicola species complex and causes root rot and replant failure of ginseng in Asia and North America. The aims of this work were to identify I. mors-panacis that infect Korean ginseng using molecular approaches and to investigate whether their aggressiveness depends on their ability to metabolize ginseng saponins (ginsenosides) by their β-glucosidases, in comparison with other identified Ilyonectria species. Fourteen isolates were collected from culture collections or directly isolated from infected roots and mainly identified based on histone H3 (HIS H3) sequence. Among them, six isolates were identified as I. mors-panacis while others were identified as I. robusta and I. leucospermi. The pathogenicity tests confirmed that the isolates of I. mors-panacis were significantly more aggressive than I. robusta and I. leucospermi. The major ginsenosides in I. mors-panacis-infected roots were significantly reduced while significantly increased in those infected with other species. In vitro, the isolates were tested for their sensitivity and ability to metabolize the total major ginsenosides (Total MaG), protopanaxadiol-type major ginsenosides (PPD-type MaG), and protopanaxatriol-type major ginsenosides (PPT-type MaG). Unexpectedly, the growth rate and metabolic ability of I. mors-panacis isolates were significantly low on the three different ginsenoside fractions while those of I. robusta and I. leucospermi were significantly reduced on PPT-type MaG and Total MaG fractions and not affected on PPD-type MaG fraction. Our results indicate that major ginsenosides, especially PPT-type, have an antifungal effect and may intervene in ginseng defense during Ilyonectria species invasion, in particular the weak species. Also, the pathogenicity of I. mors-panacis may rely on its ability to reduce saponin content; however, whether this reduction is caused by detoxification or another method remains unclear.
Diagnostic difficulty identifying Apophysomyces trapeziformis septic arthritis in a patient with multiple myeloma
Authors: Bertumen J. Bradford , Schell Wiley A. , Joyce Maria , Alley Christopher , Woods Christopher W.
Published: December 2016

Introduction:

Mucormycosis is a rare fungal infection, but can cause substantial morbidity and mortality in both immunocompromised and immunocompetent patients. Apophysomyces is a mucormycetes species ubiquitous in nature, particularly in soil, decaying wood and other organic matter. Apophysomyces is known to cause cutaneous fungal infections, particularly after penetrating trauma. Septic arthritis is a rare clinical manifestation.

Case presentation:

We describe a case of Apophysomyces trapeziformis causing septic arthritis of the knee of a patient with multiple myeloma. He was treated multiple times for bacterial septic arthritis with minimal improvement. Surgical tissue specimens finally grew mucoraceous mould, and DNA sequencing and morphological assessment of spores identified the mould as A. trapeziformis. The patient was treated with amphotericin B and posaconazole, but ultimately required an above-the-knee amputation for definitive treatment.

Conclusion:

This case illustrates the need to evaluate for fungal infection in a persistent septic arthritis that is culture negative and refractory to empiric antibiotics, particularly in an immunocompromised individual. It also shows the importance of a thorough social history and adequate tissue specimens for culture.
Acute influenza virus-associated encephalitis and encephalopathy in adults: a challenging diagnosis
Authors: Meijer Wouter J. , Linn Francisca H. H. , Wensing Anne M. J. , Leavis Helen L. , van Riel Debby , GeurtsvanKessel Corine H. , Wattjes Mike P. , Murk Jean-Luc
Published: December 2016

Background: Acute influenza-associated encephalopathy/encephalitis (IAE) in adults is a rare but well-known complication of influenza virus infection. The diagnosis is difficult to make due to the absence of distinctive clinical symptoms and validated diagnostic criteria. We present an illustrative case and a case review on acute IAE in adults.

Methods: We performed a Medline search of the English literature using the terms influenz*, encephal* and adult, and constructed a database of detailed descriptions of patients with influenza virus infection with influenza-like symptoms at the onset of neurological symptoms.

Results: A total of 44 patients were included. Confusion and seizures were the most prevalent neurological symptoms, present in 12 (27 %) and 10 (23 %) patients, respectively. Magnetic resonance imaging (MRI) was performed in 21 patients and anomalies were found in 13 (62 %), with lesions located throughout the brain. Influenza virus RNA was detected in cerebrospinal fluid (CSF) in 5 (16 %) of 32 patients. Eight (18 %) of the forty-four patients died. The benefits of antiviral and immunomodulatory therapy have not been well studied.

Discussion: Our results show that many different neurological symptoms can be present in patients with acute onset IAE. Therefore, the diagnosis should be considered in patients with fever and neurological symptoms, especially during the influenza season. Laboratory diagnosis consists of demonstration of influenza virus RNA in brain tissue, CSF or respiratory samples, and demonstration of intrathecal antibody production against influenza virus. The presence of brain lesions in MRI and influenza virus in CSF appear to be of prognostic value.