bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of transplant urgency and benefit via multiple imputation
Authors: Xiang Fang , Murray Susan , Liu Xiaohong
Published: July 2014

Missing (censored) death times for lung candidates in urgent need of transplant are a signpost of success for allocation policy makers. However, statisticians analyzing these data must properly account for dependent censoring as the sickest patients are removed from the waitlist. Multiple imputation allows the creation of complete data sets that can be used for a variety of standard analyses in this setting. We propose an approach to multiply impute lung candidate outcomes that incorporates (i) time‐varying factors predicting removal from the waitlist and (ii) estimates of transplant urgency via restricted mean models. The measures of transplant urgency and benefit for individual patient profiles are discussed in the context of lung allocation score modeling in the USA. Marginal survival estimates in the event that a transplant does not occur are also provided. Simulations suggest that the proposed imputation method gives attractive results when compared with existing methods. Copyright © 2014 John Wiley & Sons, Ltd.
Quantitative Imaging of the Magnetic Configuration of Modulated Nanostructures by Electron Holography
Authors: Körner Michael , Röder Falk , Lenz Kilian , Fritzsche Monika , Lindner Jürgen , Lichte Hannes , Fassbender Jürgen
Published: July 2014

By means of off‐axis electron holography the local distribution of the magnetic induction within and around a poly‐crystalline Permalloy (Ni81Fe19) thin film is studied. In addition the stray field above the sample is measured by magnetic force microscopy on a larger area. The film is deposited on a periodically nanostructured (rippled) Si substrate, which was formed by Xe+ ion beam erosion. This introduces the periodical ripple shape to the Permalloy film. The created ripple morphology is expected to modify the magnetization distribution within the Permalloy and to induce dipolar stray fields. These stray fields play an important role in spinwave dynamics of periodic nanostructures like magnonic crystals. Micromagnetic simulations estimate those stray fields in the order of only 10 mT. Consequently, their experimental determination at nanometer spatial resolution is highly demanding and requires advanced acquisition and reconstruction techniques such as electron holography. The reconstructed magnetic phase images show the magnetized thin film, in which the magnetization direction follows mainly the given morphology. Furthermore, a closer look to the Permalloy/carbon interface reveals stray fields at the detection limit of the method in the order of 10 mT, which is in qualitative agreement with the micromagnetic simulations.
Inorganic–Organic Hybrid Nanoprobe for NIR‐Excited Imaging of Hydrogen Sulfide in Cell Cultures and Inflammation in a Mouse Model
Authors: Zhou Yi , Chen Wangqiao , Zhu Jixin , Pei Wenbo , Wang Chengyuan , Huang Ling , Yao Cheng , Yan Qinyu , Huang Wei , Loo Joachim Say Chye , Zhang Qichun
Published: July 2014

Hydrogen sulfide (H2S) is an important gaseous signaling agent mediated by many physiological processes and diseases. In order to explore its role in biological signaling, much effort has been focused on developing organic fluorescent probes to image H2S. However, these downconversion H2S probes are impractical for bio‐imaging beyond a certain depth because of the short tissue penetration of UV/visible light (as an excitation source). In most circumstance, these probes are also not suitable for long‐term assay due to photo‐bleaching. Herein, a new design to detect H2S based on the coumarin‐hemicyanine (CHC1)‐modified upconversion nanophosphors is reported. This inorganic–organic integrated nanoprobe is demonstrated to display a fast response time with a large ratiometric upconversion luminescence (UCL) enhancement, and extraordinary photo‐stability. CHC1‐UCNPs not only can be used for ratiometric UCL monitoring of pseudo‐enzymatic H2S production in living cells, but can also be used to identify the risk of endotoxic shock through ratiometric UCL imaging of tissue and measurement of endogenous H2S levels in plasma. The first ratiometric UCL H2S nanoprobe reported here may be further developed as the next‐generation diagnostic tool for the detection of inflammatory‐related diseases.
Noisy Chaos in a Large System of Decision‐Makers with Heterogeneous Beliefs with Application to Index Option Prices
Authors: Cadogan Godfrey
Published: July 2014

Decision‐makers (DMs) often exhibit preference reversal and phase transitions in their states of confidence. We show how those behaviors induce chaos in a large system of DMs with heterogeneous beliefs. We construct a behavioral matrix operator [from a DM's probability weighting function (PWF)] that characterizes a projective mapping of confidence in dual psychological spaces. Moreover, we prove that in a seemingly stable system of DMs, the empirical Lyapunov exponent process for the noisy orbit of DM deterministic PWFs admits tail event chaos controlled by risk attitude factors. We use reported results from rank‐dependent Standard & Poor's 500 index option prices and Chicago Board Options Exchange Volatility Index to illustrate our theory. Data show phase transitions in the state of DM confidence over time as PWFs change from skew S‐shape to inverted S‐shape. Our model identifies an instability criterion function for the distribution of critical values of risk attitude factors over a convex set of probabilities bounded from above by the fixed‐point probability for PWFs. In particular, we use the criterion function to estimate critical values for risk attitude factors in index option price data that predict market crash based on the orientation of the PWF implied by option data. Copyright © 2014 John Wiley & Sons, Ltd.
Simulation on Staffs Evacuation Behavior in Plant Fire Emergencies
Authors: Jia Liu , Yun Chen
Published: July 2014

This paper focuses on the evacuation behavior of staffs in plant fire emergencies. It first conducts an experiment, which simulates the scenarios of a plant fire emergency. The experiment confirms that the risk preference and stress ability of a staff have a significant impact on its evacuation behavior in plant fire emergencies. Then, the paper employs the multi‐agent system simulation platform to study the different evacuation decisions made by different types of staff groups in a plant fire emergency. The groups are distinguished by different risk preferences and stress abilities proportions of staffs. Afterwards, it simulates the optimal evacuation situation. Finally, the paper proposes several suggestions on optimizing the evacuation decision‐making of plant staffs in plant fire emergencies. Copyright © 2014 John Wiley & Sons, Ltd.
Supply Contracting with Risk‐Sensitive Retailers under Information Asymmetry: An Exploratory Behavioral Study
Authors: Chow Pui‐Sze , Choi Tsan‐Ming , Shen Bin , Zheng Jinhui
Published: July 2014

In this paper, we explore a two‐echelon supply chain with one upstream seller (supplier) and two downstream retailers selling a newsvendor type of fashion product. The retailers are the same except their degrees of risk sensitivity. In this supply chain, we examine the performance of the buyback contract via behavioral experiments in which the supplier is played by human subjects and the risk‐sensitive retailers are computerized. We study the effect of profit margin and also demand dispersion under different game scenarios. Our behavioral experiments reveal that the human suppliers can be classified into three types, namely type I (the highly consistent and rational players), type II (the highly strategic players), and type III (naïve and highly irrational players). We further generate a few insights: (i) Decision‐makers behave as type II players in the low profit margin scenarios but not in the high profit margin cases; (ii) there are no significant pieces of evidence on the existence of the demand dispersion effect and the game type effect on both type I and type III players; and (iii) the average profits earned by type I and type II decision‐makers are similar, whereas type III decision‐makers are the smallest in almost all cases. We believe that this paper provides many new insights on supply contracting with reference to the behavioral risk of human decision‐makers. Copyright © 2014 John Wiley & Sons, Ltd.
Mechanism of TiO2 nanoparticle‐induced neurotoxicity in zebrafish (Danio rerio)
Authors: Sheng Lei , Wang Ling , Su Mingyu , Zhao Xiaoyang , Hu Renping , Yu Xiaohong , Hong Jie , Liu Dong , Xu Bingqing , Zhu Yunting , Wang Han , Hong Fashui
Published: July 2014

Zebrafish (Danio rerio) has been used historically for evaluating the toxicity of environmental and aqueous toxicants, and there is an emerging literature reporting toxic effects of manufactured nanoparticles (NPs) in zebrafish embryos. Few researches, however, are focused on the neurotoxicity on adult zebrafish after subchronic exposure to TiO2 NPs. This study was designed to evaluate the morphological changes, alterations of neurochemical contents, and expressions of memory behavior‐related genes in zebrafish brains caused by exposures to 5, 10, 20, and 40 μg/L TiO2 NPs for 45 consecutive days. Our data indicated that spatial recognition memory and levels of norepinephrine, dopamine, and 5‐hydroxytryptamine were significantly decreased and NO levels were markedly elevated, and over proliferation of glial cells, neuron apoptosis, and TiO2 NP aggregation were observed after low dose exposures of TiO2 NPs. Furthermore, the low dose exposures of TiO2 NPs significantly activated expressions of C‐fos, C‐jun, and BDNF genes, and suppressed expressions of p38, NGF, CREB, NR1, NR2ab, and GluR2 genes. These findings imply that low dose exposures of TiO2 NPs may result in the brain damages in zebrafish, provide a developmental basis for evaluating the neurotoxicity of subchronic exposure, and raise the caution of aquatic application of TiO2 NPs. © 2014 Wiley Periodicals, Inc. Environ Toxicol 31: 163–175, 2016.
Mechanical and thermal properties of (acrylonitrile‐styrene‐acrylic)/(α‐methylstyrene‐acrylonitrile) binary blends
Authors: Zhu Wenqiang , Zhang Jun
Published: July 2014

In this work, (acrylonitrile‐styrene‐acrylic)/(α‐methylstyrene‐acrylonitrile) copolymer (ASA/α‐MSAN) binary alloy was prepared with different composition ratios via melt blending. This work mainly focused on improving the heat resistance of ASA. According to the results of dynamic mechanical thermal analysis, the binary blends exhibited three glass transition temperatures (Tgs) and the shift of the Tgs indicated the partial miscibility of binary blends. This partial miscibility maintained the high Tg of α‐MSAN, which led to the outstanding heat resistance of binary blends. Furthermore, heat distortion temperature also showed that the heat resistance of binary blends was significantly enhanced with the addition of α‐MSAN. However, the introduction of this highly rigid polymer also brought with it the sharp decrease of the impact strength and elongation at break, which is reflected in the morphologies of the blend system obtained via scanning electron microscopy. In addition, the incorporation of α‐MSAN increased the tensile strength, flexural strength, and modulus. There were no new groups observed from Fourier‐transform infrared spectra, which means no strong specific intermolecular interactions existed between ASA and α‐MSAN. Moreover, the processibility of the blend system was obviously improved from the results of melt flow rate. J. VINYL ADDIT. TECHNOL., 22:156–162, 2016. © 2014 Society of Plastics Engineers
Adhesion properties of (epoxidized natural rubber)/(ethylene‐propylene‐diene rubber) blend adhesive: Effect of blend ratio and testing rate
Authors: Poh B.T. , Teh Y.Y.
Published: July 2014

The adhesion properties of epoxidized natural rubber (ENR 25)/(ethylene‐propylene‐diene rubber) blend adhesive were investigated by using various blend ratios of the two rubbers and rate of testing. Coumarone‐indene resin was used as the tackifier. Results show that the loop tack and peel strength of adhesives increase steadily up to 60% ENR 25 before decreasing with further increase in % ENR 25. This observation is attributed to an increase in wettability and compatibility up to the optimum value of the ENR 25 blend ratio. However, shear strength increases continuously with increasing percentage of ENR 25, an observation that is ascribed to the increasing cohesive strength of the blend adhesive. In all cases, the adhesion properties increase with increasing coating thickness and testing rates. J. VINYL ADDIT. TECHNOL., 22:134–139, 2016. © 2014 Society of Plastics Engineers
Study on the physical and mechanical properties of electron‐beam‐irradiated Vinyl ester/TiO2 nanocomposites
Authors: Shahrajabian Hamzeh , Ahmadi‐Brooghani Seyed Yousef , Ahmadi Seyed Javad , Saeb Mohammad Reza , Moghri Mehdi
Published: July 2014

The effect of electron beam irradiation on the physical and mechanical properties of vinyl ester nanocomposites containing various amounts of TiO2 nanoparticles was investigated. The fracture toughness, surface hardness, and water uptake measurements were carried out to investigate alterations in the physical and mechanical properties owing to electron beam exposure. In this regard, it was attempted to infer the impact of TiO2 nanoparticles on the structural changes varying the irradiation dose. The results were then explained based on crosslinking and chain scission phenomena. Moreover, scanning electron microscopy was used to assess the degree of TiO2 dispersion within the polymer matrix. J. VINYL ADDIT. TECHNOL., 22:110–116, 2016. © 2014 Society of Plastics Engineers
Effect of chemical treatment on newspaper fibers reinforced polymer poly(vinyl chloride) composites
Authors: Nedjma Samira , Djidjelli Hocine , Boukerrou Amar , Grohens Yves , Chibani Nacera , Benachour Djafer , Pillin Isabelle
Published: July 2014

Natural fibers used as reinforcement in composite materials present specific mechanical properties, which are comparable to glass fibers. In addition, they have the advantage of being renewable and recyclable. However, their main drawback is their inherent susceptibility to moisture expansion, which has the effect of inducing a decrease in mechanical properties, and of debonding in the composite. In this study, lignocellulosic fibers from newspapers were modified with acetic anhydride, NaOH, and KMnO4 in order to enhance the interfacial adhesion between poly(viny lchloride) (PVC) matrix and the newspaper fibers. Composites samples were prepared with different treated fibers at the same loading (20 wt%). X‐ray and scanning electron microscopy (SEM) were used to characterize the fiber's surfaces. The mechanical, morphological, and thermal properties of PVC/newspaper composites were also studied. Moreover, the maximum improvement in the mechanical properties (tensile strength) was obtained for the permanganate treated PVC/newspaper composites. J. VINYL ADDIT. TECHNOL., 22:173–181, 2016. © 2014 Society of Plastics Engineers
Double‐hybrid density functionals
Authors: Goerigk Lars , Grimme Stefan
Published: July 2014

Double‐hybrid density functionals (DHDFs) are reviewed in this study. In DHDFs parts of conventional density functional theory (DFT) exchange and correlation are replaced by contributions from nonlocal Fock‐exchange and second‐order perturbative correlation. The latter portion is based on the well‐known MP2 wave‐function approach in which, however, Kohn–Sham orbitals are used to calculate its contribution. First, related methods preceding this idea are reviewed, followed by a thorough discussion of the first modern double‐hybrid B2‐PLYP. Parallels and differences between B2‐PLYP and its various successors are then outlined. This discussion is rounded off with representative thermochemical examples demonstrating that DHDFs belong to the most robust and accurate DFT approaches currently available. This analysis also presents hitherto unpublished results for recently developed DHDFs. Finally, how double‐hybrids can be combined with linear‐response time‐dependent DFT is also outlined and the value of this approach for electronically excited states is shown. WIREs Comput Mol Sci 2014, 4:576–600. doi: 10.1002/wcms.1193

This article is categorized under:

Electronic Structure Theory > Density Functional Theory
Computational finance: correlation, volatility, and markets
Authors: Ensor Katherine Bennett , Koev Ginger M.
Published: July 2014

Financial data by nature are inter‐related and should be analyzed using multivariate methods. Many models exist for the joint analysis of multiple financial instruments. Early models often assumed some type of constant behavior between the instruments over the time period of analysis. But today, time‐varying covariance models are a key component of financial time series analysis leading to a deeper understanding of changing market conditions. Models for covolatility of financial data quickly grow in their complexity and parameters, and 20 years of research offers a variety of solutions to this complexity. After a short introduction of univariate volatility models, this article begins with the basic multivariate formulation for time series covariance modeling and moves to leading time series tools that address this complexity. Coupling these models with regime switching via a Markov process extends the features that can be understood from market behavior. We ground this review in an example of modeling the covariance of securities within sectors and sectors within markets, with dynamics that allow for two different market regimes. Specifically, we simultaneously model individual daily stock data that belong to one of three market sectors and examine the behavior of the market as a whole as well as the behavior of the market sectors over time. A motivation for this characterization concerns portfolio diversification and stock anomalies, and we capture the changing comovement of stocks within and between sectors as market conditions change. For example, some of these market conditions include market crashes or collapses and common external influences. WIREs Comput Stat 2014, 6:326–340. doi: 10.1002/wics.1323

This article is categorized under:

Applications of Computational Statistics > Computational Finance

Statistical and Graphical Methods of Data Analysis > Multivariate Analysis

Data: Types and Structure > Time Series, Stochastic Processes, and Functional Data
Reinvestigation of Crystal Structure and Non‐Stoichiometry in Copper Hydride, CuH1–x (0 ≤ x ≤ 0.26)
Authors: Auer Henry , Kohlmann Holger
Published: July 2014

Copper hydride and deuteride were reinvestigated by X‐ray and neutron powder diffraction, revealing a pronounced phase width with respect to the hydrogen (deuterium) content. Synthesis from aqueous copper(II) sulfate with hypophosphoric acid solutions yields samples with a broad distribution of compositions and variations of up to 6.5 % in unit cell volume. The result is a metrical distortion with (hkl) dependent asymmetry and broadening of powder diffraction reflections. Patterns of such samples were described using a model with five copper hydride (deuteride) phases with different lattice parameters. A method for developing and refining reasonable multiphase models despite high correlation of parameters is described. Simultaneous refinement on X‐ray and neutron powder diffraction on a deuteride sample suggests a statistical occupation of deuterium on less than half of the tetrahedral voids of a hexagonal close packing of copper atoms [P63/mmc, a = 2.9024(5) Å, c = 4.632(2) Å, Cu in 2c, D in 4f with z = 0.6497(8), deuterium occupation 0.368(6)]. The reaction of aqueous copper(II) chloride with sodium boronate solutions yields copper hydride with a stoichiometric composition [P63/mmc, a = 2.8777(3) Å, c = 4.570(1) Å, Cu in 2c, H in 4f with z = 0.640(1), hydrogen occupation 1/2]. The structures are isotypic to ScD0.33 and reveal a surprising analogy to lanthanide hydrides.
Physiological and proteomic analysis of Lactobacillus casei in response to acid adaptation
Authors: Wu Chongde , He Guiqiang , Zhang Juan
Published: July 2014

The aim of this study was to investigate the acid tolerance response (ATR) in Lactobacillus casei by a combined physiological and proteomic analysis. To optimize the ATR induction, cells were acid adapted for 1 h at different pHs, and then acid challenged at pH 3.5. The result showed that acid adaptation improved acid tolerance, and the highest survival was observed in cells adapted at pH 4.5 for 1 h. Analysis of the physiological data showed that the acid-adapted cells exhibited higher intracellular pH (pHi), intracellular NH4+ content, and lower inner permeability compared with the cells without adaptation. Proteomic analysis was performed upon acid adaptation to different pHs (pH 6.5 vs. pH 4.5) using two-dimensional electrophoresis. A total of 24 proteins that exhibited at least 1.5-fold differential expression were identified. Four proteins (Pgk, LacD, Hpr, and Galm) involved in carbohydrate catabolism and five classic stress response proteins (GroEL, GrpE, Dnak, Hspl, and LCAZH_2811) were up-regulated after acid adaptation at pH 4.5 for 1 h. Validation of the proteomic data was performed by quantitative RT-PCR, and transcriptional regulation of all selected genes showed a positive correlation with the proteomic patterns of the identified proteins. Results presented in this study may be useful for further elucidating the acid tolerance mechanisms and may help in formulating new strategies to improve the industrial performance of this species during acid stress.
Valproic acid attenuates the suppression of acetyl histone H3 and CREB activity in an inducible cell model of Machado–Joseph disease
Authors: Lin X.P. , Feng L. , Xie C.G. , Chen D.B. , Pei Z. , Liang X.L. , Xie Q.Y. , Li X.H. , Pan S.Y.
Published: July 2014

Machado–Joseph disease (MJD) is caused by a (CAG)n trinucleotide repeat expansion that is translated into an abnormally long polyglutamine tract. This disease is considered the most common form of spinocerebellar ataxia (SCA). In the present study, we developed stable inducible cell lines (PC12Tet‐On‐Ataxin‐3‐Q28/84) expressing ataxin‐3 with either normal or abnormal CAG repeats under doxycycline control. The expression of acetyl histone H3 and the induction of c‐Fos in response to cAMP were strongly suppressed in cells expressing the protein with the expanded polyglutamine tract. Treatment with valproic acid, a histone deacetylase inhibitor (HDACi), attenuated mutant ataxin‐3‐induced cell toxicity and suppression of acetyl histone H3, phosphorylated cAMP‐responsive element binding protein (p‐CREB) as well as c‐Fos expression. These results indicate that VPA can stimulate the up‐regulation of gene transcription through hyperacetylation. Thus, VPA might have a therapeutic effect on MJD.
Characterization of long non‐coding RNA transcriptome in clear‐cell renal cell carcinoma by next‐generation deep sequencing
Authors: Malouf Gabriel G. , Zhang Jianping , Yuan Ying , Compérat Eva , Rouprêt Morgan , Cussenot Olivier , Chen Yunxin , Thompson Erika J. , Tannir Nizar M. , Weinstein John N. , Valero Vicente , Khayat David , Spano Jean-Philippe , Su Xiaoping
Published: July 2014

Introduction

Long non‐coding RNA (lncRNA) have proven to play key roles in cell physiology from nuclear organization and epigenetic remodeling to post‐transcriptional regulation. Last decade, gene expression based‐classifications have been developed in clear‐cell renal cell carcinoma (ccRCC) to identify distinct subtypes of disease and predict patient's outcome. However, there are no current lncRNA comprehensive characterizations in ccRCC.

Patients and methods

RNA‐sequencing profiles of 475 primary ccRCC samples from the Cancer Genome Atlas (TCGA) were used to assess expressed lncRNA and identify lncRNA‐based classification. In addition, integrative analysis was performed to correlate tumor subtypes with copy‐number alterations and somatic mutations.

Results

Using stringent criteria, we identified 1934 expressed lncRNA and assessed their chromatin marks. Unsupervised clustering unravels four lncRNA subclasses in ccRCC associated with distinct clinicopathological and genomic features of this disease. Cluster C2 (23.4%) defines the most aggressive tumours, with the highest Fuhrman grade and stage and the worst overall survival time. Furthermore, cluster C2 is enriched for 9p deletion and chromatin remodeler BAP1 somatic mutations. Interestingly, cluster C4 (7.8%) is related to a tumor subtype arising from the distal tubules of the nephron. Consistent with its distinct ontogeny, cluster C4 is devoid of classical alterations seen in ccRCC, bears frequent 1p deletion and 17q gain, and is enriched for MiTF/TFE translocations. In addition, reexaminations of copy‐number data from one side and tumor histology by pathologists from the other side reveal misclassified tumors within C4 cluster including chromophobe RCC and clear cell papillary RCC.

Conclusion

This study establishes a foundation for categorizing lncRNA subclasses, which may contribute to understand tumor ontogeny and help predicting patients' outcome in ccRCC.
Ubiquitous Computing in the Biology Laboratory
Authors: Arnstein Larry , Sigdursson Stefan , Franza Bob
Published: July 2014

Our objective is to eliminate the digital divide that persists between the physical and information spaces of wet-lab based enterprises by embedding computational resources into the shared laboratory environment. Our first challenge is to enable individual lab workers to contribute to a fine-grained formal representation of ongoing lab activities — to build the database by doing the work, without having to stop and write things down in a notebook or to enter information into a computer. By eliminating the redundancy of doing the work and then recording it, accuracy and completeness will be improved. And, by capturing information at a finer detail than is practical for manual entry systems, unanticipated applications can be supported.
Developing a Simple NMR Interface: WWNMR
Authors: Bach Alvin C. , Cochran David W.
Published: July 2014

We have designed and implemented an automated walkup NMR computer application for use by synthetic chemists. The Wyeth Walkup NMR (WWNMR) application is a TCL/TK graphical user interface front-end to Varian's NMR automation routines. The key feature of WWNMR is that the chemists are isolated from the spectrometer's control program (VNMR) and only enter information to WWNMR windows for a sample to be run. The resulting data can be printed out on paper, or stored on disk for easy access by all users at their desktops. Proton and carbon NMR experiments are available. An overview of the WWNMR application will be presented.
Automation of Serological Diagnosis for Herpes B Virus Infections Using Robot-Assisted Integrated Workstations
Authors: Katz David , Shi Wei , Wildes Marty , Hilliard Julia K.
Published: July 2014

A robot-assisted automated facility was established within a biosafety level 3 laboratory located on a university campus. A unique integration of a Genesis (TECAN) liquid handler into the SAGIAN Core System (Beckman-Coulter) enabled tube liquid handling and transfer of reagents from tubes to microplates. An automated enzyme immunoassay (ELISA) for detecting herpes B virus antibodies was developed. Repetition experiments of the automated ELISA and comparison to the manual ELISA demonstrated the efficacy and high reproducibility of the automated method. It is anticipated that research and education activities will benefit from the establishment of the automated diagnostic laboratory in an academic environment.
Automated High-Throughput Purification of PCR Products Using Wizard® MagneSil™ Paramagnetic Particles
Authors: Otto Paul , Larson Brad , Krueger Steve
Published: July 2014

Here we describe a reagent system and robotic methods for the purification of PCR(a) fragments from other contaminating amplification reaction components. The methods use the MagneSil™ paramagnetic particle chemistry(b) to isolate double stranded DNA fragments from 150bp to 23kbp. Purified fragments are eluted in water ready for downstream applications such as cloning, fluorescent DNA sequencing and microarray printing. This method has been adapted to a number of liquid handling robotic platforms, including the Biomek® FX and Biomek® 2000 Laboratory Automation Workstations, in both 96 and 384-well formats.
Spot-on™ Technology for Low Volume Liquid Handling
Authors: Shvets I.V. , Makarov S. , Franken C. , Shvets A. , Sweeney D. , Osing J.
Published: July 2014

The article describes the new proprietary spot-on™ technology developed by Allegro Technologies, Ltd., for nanolitre and microlitre dispensing of liquids for the drug discovery, genomics and proteomics industries. We analyze the requirements of the drug discovery industry for low volume liquid handling technologies and briefly summarize some the more common technologies currently available.

A detailed description is provided of the new spot-on™ technology in terms of function and operation as well as the relevant features and potential benefits to using this new method of nanolitre dispensing.
ACTUARIAL FAIRNESS AND SOLIDARITY IN POOLED ANNUITY FUNDS
Authors: Donnelly Catherine
Published: July 2014

Various types of structures that enable a group of individuals to pool their mortality risk have been proposed in the literature. Collectively, the structures are called pooled annuity funds. Since the pooled annuity funds propose different methods of pooling mortality risk, we investigate the connections between them and find that they are genuinely different for a finite heterogeneous membership profile. We discuss the importance of actuarial fairness, defined as the expected benefits equalling the contributions for each member, in the context of pooling mortality risk and comment on whether actuarial unfairness can be seen as solidarity between members. We show that, with a finite number of members in the fund, the group self-annuitization scheme is not actuarially fair: some members subsidize the other members. The implication is that the members who are subsidizing the others may obtain a higher expected benefit by joining a fund with a more favorable membership profile. However, we find that the subsidies are financially significant only for very small or highly heterogeneous membership profiles.
Wavefront measurement techniques used in high power lasers
Authors: Wang Haiyan , Liu Cheng , He Xiaoliang , Pan Xingchen , Zhou Shenlei , Wu Rong , Zhu Jianqiang
Published: July 2014

The properties of a series of phase measurement techniques, including interferometry, the Hartmann–Shack wavefront sensor, the knife-edge technique, and coherent diffraction imaging, are summarized and their performance in high power laser applications is compared. The advantages, disadvantages, and application ranges of each technique are discussed.
Cyclic homology, Serre's local factors and λ-operations
Authors: Connes Alain , Consani Caterina
Published: July 2014

We show that for a smooth, projective variety X defined over a number field K, cyclic homology with coefficients in the ring , provides the right theory to obtain, using λ-operations, Serre's archimedean local factors of the complex L-function of X as regularized determinants.
Effects of radiation in turbulent channel flow: analysis of coupled direct numerical simulations
Authors: Vicquelin R. , Zhang Y. F. , Gicquel O. , Taine J.
Published: July 2014

The role of radiative energy transfer in turbulent boundary layers is carefully analysed, focusing on the effect on temperature fluctuations and turbulent heat flux. The study is based on direct numerical simulations (DNS) of channel flows with hot and cold walls coupled to a Monte-Carlo method to compute the field of radiative power. In the conditions studied, the structure of the boundary layers is strongly modified by radiation. Temperature fluctuations and turbulent heat flux are reduced, and new radiative terms appear in their respective balance equations. It is shown that they counteract turbulence production terms. These effects are analysed under different conditions of Reynolds number and wall temperature. It is shown that collapsing of wall-scaled profiles is not efficient when radiation is considered. This drawback is corrected by the introduction of a radiation-based scaling. Finally, the significant impact of radiation on turbulent heat transfer is studied in terms of the turbulent Prandtl number. A model for this quantity, based on the new proposed scaling, is developed and validated.
Inertial wave dynamics in a rotating liquid metal
Authors: Vogt Tobias , Räbiger Dirk , Eckert Sven
Published: July 2014

The dynamics of free and forced inertial waves inside cylinders of different aspect ratios ($\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}A=H_0/2R_0$) were investigated experimentally in this study. The liquid metal GaInSn was chosen as the fluid in order to enable a contactless stimulation of the flow by means of alternating electromagnetic fields. A rotating magnetic field generates the rotating motion of the liquid, whereas periodic modulations of the field strength and short pulses excite specific wave modes. Ultrasound Doppler velocimetry was used to record the flow structure and to identify inertial waves in the set-up. Our experiments demonstrate selective excitation of different inertial wave modes by deliberate variation of the magnetic field parameters. Furthermore, it was found that turbulent perturbations in the boundary layers of the swirling flow are able to induce an inertial wave mode that survives over a long time. Experiments at the fundamental resonance have shown that multiple harmonic wave modes appeared simultaneously. The measured inertial wave frequencies were compared to the predictions of the linear inviscid theory.
Large-eddy simulation of turbulence and particle dispersion inside the canopy roughness sublayer
Authors: Pan Ying , Chamecki Marcelo , Isard Scott A.
Published: July 2014

Modelling the dispersion of small particles such as fungal spores, pollens and small seeds inside and above plant canopies is important for many applications. Transport of these particles is driven by strongly inhomogeneous and non-Gaussian turbulent flows inside the canopy roughness sublayer, the region that extends from the ground to approximately three canopy heights. A large-eddy simulation (LES) approach is refined to study particle dispersion within and above the canopy region. Effects of plant reconfiguration are parameterized through a velocity-dependent drag coefficient, which is shown to be critical for accurate reproduction of velocity statistics and mean spore concentrations. The model yields predictions of turbulence statistics that are in good agreement with measurements. This is particularly true of the stress fractions carried by strong events, as revealed by standard quadrant analysis of the resolved velocity fluctuations, which is a known weakness of earlier LES studies of canopy flow using a constant drag coefficient. Experimental data on spore dispersal inside and above a maize canopy are reproduced successfully as well. Characteristics of the particle plume are analysed using LES results, and a pre-existing theoretical framework is adapted to model particle dispersal above the canopy. The results suggest that the plume above the canopy can be approximated using a simple analytical solution if the fraction of spores that escape the canopy region is known. Source height and gravitational settling have strong effects on the plume inside the canopy region and consequently determine the escape fraction. These effects are parameterized in the theoretical model by using the escape fraction to rescale the source strength.
Flavonoids and saponins extracted from black bean (Phaseolus vulgarisL.) seed coats modulate lipid metabolism and biliary cholesterol secretion in C57BL/6 mice
Authors: Chavez-Santoscoy Rocio A. , Gutierrez-Uribe Janet A. , Granados Omar , Torre-Villalvazo Ivan , Serna-Saldivar Sergio O. , Torres Nimbe , Palacios-González Berenice , Tovar Armando R.
Published: July 2014

Black bean (Phaseolus vulgarisL.) seed coats are a rich source of natural compounds with potential beneficial effects on human health. Beans exert hypolipidaemic activity; however, this effect has not been attributed to any particular component, and the underlying mechanisms of action and protein targets remain unknown. The aim of the present study was to identify and quantify primary saponins and flavonoids extracted from black bean seed coats, and to study their effects on lipid metabolism in primary rat hepatocytes and C57BL/6 mice. The methanol extract of black bean seed coats, characterised by a HPLC system with a UV–visible detector and an evaporative light-scattering detector and HPLC–time-of-flight/MS, contained quercetin 3-O-glucoside and soyasaponin Af as the primary flavonoid and saponin, respectively. The extract significantly reduced the expression ofSREBP1c,FASandHMGCR, and stimulated the expression of the reverse cholesterol transportersABCG5/ABCG8andCYP7A1in the liver. In addition, there was an increase in the expression of hepaticPPAR-α. Consequently, there was a decrease in hepatic lipid depots and a significant increase in bile acid secretion. Furthermore, the ingestion of this extract modulated the proportion of lipids that was used as a substrate for energy generation. Thus, the results suggest that the extract of black bean seed coats may decrease hepatic lipogenesis and stimulate cholesterol excretion, in part, via bile acid synthesis.
Lifestyle patterns and dysglycaemic risk in urban Sri Lankan women
Authors: Waidyatilaka Indu , de Silva Angela , de Lanerolle-Dias Maduka , Wickremasinghe Rajitha , Atukorala Sunethra , Somasundaram Noel , Lanerolle Pulani
Published: July 2014

Specific dietary patterns are associated with the risk of chronic disease. An in-depth understanding more reflective of lifestyle would be possible when assessing the synergistic effects of both diet and physical activity in pattern analysis. In the present study, we examined the biochemical markers of dysglycaemia and cardiometabolic risk in relation to lifestyle patterns using principal component analysis (PCA). Urban women (n 2800) aged 30–45 years were screened for dysglycaemia using cluster sampling from the Colombo Municipal Council area. All the 272 dysglycaemic women detected through screening and 345 randomly selected normoglycaemic women were enrolled. The International Physical Activity Questionnaire and a quantitative FFQ were used to assess physical activity and diet, respectively. Anthropometric measurements, bioelectrical impedance analysis and biochemical estimations were carried out. Lifestyle patterns were identified based on dietary and physical activity data using exploratory factor analysis. PCA was used for the extraction of factors. A total of three lifestyle patterns were identified. Women who were predominantly physically inactive and consumed snacks and dairy products had the greatest cardiometabolic risk, with a higher likelihood of having unfavourable obesity indices (increased waist circumference, fat mass percentage and BMI and decreased fat-free mass percentage), glycaemic indices (increased glycosylated Hb (HbA1c) and fasting blood sugar concentrations) and lipid profile (increased total cholesterol/TAG and decreased HDL-cholesterol concentrations) and increased high-sensitivity C-reactive protein concentrations. For the first time, we report lifestyle patterns and demonstrate the synergistic effects of physical activity/inactivity and diet and their relative association with cardiometabolic risk in urban women. Lifestyle pattern analysis greatly increases our understanding of high-risk behaviours occurring within real-life complexities.
Diet quality score is a predictor of type 2 diabetes risk in women: The Australian Longitudinal Study on Women's Health
Authors: Alhazmi Amani , Stojanovski Elizabeth , McEvoy Mark , Brown Wendy , Garg Manohar L.
Published: July 2014

The present study aimed to determine the ability of two diet quality scores to predict the incidence of type 2 diabetes in women. The study population comprised a nationally representative sample of 8370 Australian middle-aged (45–50 years) women participating in the ALSWH (Australian Longitudinal Study on Women's Health), who were free of diabetes and completed FFQ at baseline. The associations between the Australian Recommended Food Score (ARFS) and Dietary Guideline Index (DGI) with type 2 diabetes risk were assessed using multiple logistic regression models, adjusting for sociodemographic characteristics, lifestyle factors and energy intake. During 6 years of follow-up, 311 incident cases of type 2 diabetes were reported. The DGI score was inversely associated with type 2 diabetes risk (OR comparing the highest with the lowest quintile of DGI was 0·51; 95 % CI 0·35, 0·76; P for trend = 0·01). There was no statistically significant association between the ARFS and type 2 diabetes risk (OR comparing the highest with the lowest quintile of ARFS was 0·99; 95 % CI 0·68, 1·43; P for trend = 0·42). The results of the present prospective study indicate that the DGI score, which assesses compliance with established dietary guidelines, is predictive of type 2 diabetes risk in Australian women. The risk of type 2 diabetes among women in the highest quintile of DGI was approximately 50 % lower than that in women in the lowest quintile. The ARFS was not significantly predictive of type 2 diabetes.
Dietary isoflavone intake is not statistically significantly associated with breast cancer risk in the Multiethnic Cohort
Authors: Morimoto Yukiko , Maskarinec Gertraud , Park Song-Yi , Ettienne Reynolette , Matsuno Rayna K. , Long Camonia , Steffen Alana D. , Henderson Brian E. , Kolonel Laurence N. , Le Marchand Loïc , Wilkens Lynne R.
Published: July 2014

Given the high intake levels of soya and low incidence rates of breast cancer in Asian countries, isoflavones, substances with an oestrogen-like structure occurring principally in soyabeans, are postulated to be cancer protective. In the present study, we examined the association of dietary isoflavone intake with breast cancer risk in 84 450 women (896 in situ and 3873 invasive cases) who were part of the Multiethnic Cohort (Japanese Americans, whites, Latinos, African Americans and Native Hawaiians) with a wide range of soya intake levels. The absolute levels of dietary isoflavone intake estimated from a baseline FFQ were categorised into quartiles, with the highest quartile being further subdivided to assess high dietary intake. The respective intake values for the quartiles (Q1, Q2, Q3, and lower and upper Q4) were 0– < 3·2, 3·2– < 6·7, 6·7– < 12·9, 12·9– < 20·3, and 20·3–178·7 mg/d. After a mean follow-up period of 13 years, hazard ratios (HR) and 95 % CI were calculated using Cox regression models stratified by age and adjusted for known confounders. Linear trends were tested by modelling continuous variables of interest assigned the median value within the corresponding quartile. No statistically significant association was observed between dietary isoflavone intake and overall breast cancer risk (HR for upper Q4 v. Q1: 0·96 (95 % CI 0·85, 1·08); P trend = 0·40). While the test for interaction was not significant (P= 0·14), stratified analyses suggested possible ethnic/racial differences in risk estimates, indicating that higher isoflavone intakes may be protective in Latina, African American and Japanese American women. These results are in agreement with those of previous meta-analyses showing no protection of isoflavones at low intake levels, but suggesting inverse associations in populations consuming high amounts of soya.
Nernst advection and the field-generating thermal instability revisited
Authors: Bissell J. J.
Published: July 2014

It is widely held that the Nernst effect can drive instability in un-magnetised laser-plasmas by laterally compressing seed B-fields arising from the field-generating thermal instability [Tidman & Shanny, Phys. Fluids, 12:1207 (1974)]. Indeed, for wavelike perturbations, differential compression by the Nernst mechanism is thought to be most pronounced in the limit of low wave-number k → 0, and is considered particularly important given that it can ostensibly lead to instability when the more usual field-generating mechanism is stable. However, as part of a recent article [Bissell et al., New J. Phys., 15:025017 (2013)] we noted some irregularities to the Nernst mechanism which obscure its operation. For example, by taking characteristic density and temperature length-scales ln and lT respectively, we observed that consistent analytical treatment of the instability requires kln,T ≫ 1, preventing the peak-growth limit k → 0. Furthermore, the Nernst term—which compresses magnetic field perturbations—does not couple to a corresponding term acting on thermal perturbations, and as such does not describe an unstable feedback mechanism. In this article we probe the origin of such ambiguities more formally, and in so doing argue (contrary to reports existing elsewhere in the literature) that the Nernst effect does not drive instability in un-magnetised conditions, at least not in the fashion typically cited.
Tashlhiyt Berber
Authors: Ridouane Rachid
Published: July 2014

Berber (or Tamazight) is an Afro-Asiatic language spoken by an estimated 15–25 million in North Africa. It is mainly spoken in Morocco, Algeria, and by the Touareg population in Niger and Mali. Berber is also a native language of populations living in Libya, Tunisia and Egypt, though their numbers are less significant. Large Berber communities also live in Diasporas mainly in France, Spain, Holland, and Belgium. Three varieties of Berber are spoken in Morocco: Tarifit, spoken in northern Morocco, Tamazight, spoken in the Middle-Atlas, and Tashlhiyt, spoken in southern Morocco. Tashlhiyt, the variety presented here, is sufficiently homogeneous for all native speakers, who number an estimated 7–9 million, to communicate without difficulties (Stroomer 2008). There is nonetheless a measure of sub-dialectal variation, which affects mainly the way some stop consonants are produced. Three subsystems, corresponding roughly to three distinct geographical locations, can be identified: the ‘occlusive’ subsystem spoken in Agadir and its suburbs, the ‘fricative’ subsystem spoken mainly in the High-Atlas area, which spirantizes noncoronal obstruents /bkg/ in some contexts, and the ‘sibilant’ subsystem spoken in the Anti-Atlas area, where /t/ and /d/ are realized in some contexts as [s] and [z], respectively (Boukous 1994). This study is based on the speech of Tashlhiyt speakers who originate from Agadir. The text of ‘The North Wind and the Sun’ was read by a 27-year-old female speaker.
Election of the IPA Council and PCICPhS representatives
Authors: Keating Patricia A.
Published: July 2014

As prescribed in the by-laws of the Association and the Permanent Council for the Organization of the International Congress of Phonetic Sciences, nominations to elect the new IPA Council, as well as the six IPA-elected representatives to the Permanent Council, for 2015–2019 will be open from 10 August 2014 to 10 October 2014. Elections for both the IPA Council and Permanent Council will be held in November–December 2014. Twenty members of the IPA Council will be elected; the Council-elect will then elect 10 additional members in March 2015. The new Council (30 members) will elect the Executive Committee in June 2015.