bluuebunny/crossref_metadata_2025 huggingface dataset:
Iodine vapor staining for atomic number contrast in backscattered electron and X‐ray imaging
Authors: Boyde Alan , Mccorkell Fergus A. , Taylor Graham K. , Bomphrey Richard J. , Doube Michael
Published: September 2014

Iodine imparts strong contrast to objects imaged with electrons and X‐rays due to its high atomic number (53), and is widely used in liquid form as a microscopic stain and clinical contrast agent. We have developed a simple technique which exploits elemental iodine's sublimation‐deposition state‐change equilibrium to vapor stain specimens with iodine gas. Specimens are enclosed in a gas‐tight container along with a small mass of solid I2. The bottle is left at ambient laboratory conditions while staining proceeds until empirically determined completion (typically days to weeks). We demonstrate the utility of iodine vapor staining by applying it to resin‐embedded tissue blocks and whole locusts and imaging them with backscattered electron scanning electron microscopy (BSE SEM) or X‐ray microtomography (XMT). Contrast is comparable to that achieved with liquid staining but without the consequent tissue shrinkage, stain pooling, or uneven coverage artefacts associated with immersing the specimen in iodine solutions. Unmineralized tissue histology can be read in BSE SEM images with good discrimination between tissue components. Organs within the locust head are readily distinguished in XMT images with particularly useful contrast in the chitin exoskeleton, muscle and nerves. Here, we have used iodine vapor staining for two imaging modalities in frequent use in our laboratories and on the specimen types with which we work. It is likely to be equally convenient for a wide range of specimens, and for other modalities which generate contrast from electron‐ and photon‐sample interactions, such as transmission electron microscopy and light microscopy. Microsc. Res. Tech. 77:1044–1051, 2014. © 2014 The Authors. Microscopy Research Technique published by Wiley Periodocals, Inc.
Immobilized palladium(II) ion affinity chromatography for recovery of recombinant proteins with peptide tags containing histidine and cysteine
Authors: Kikot Pamela , Polat Aise , Achilli Estefania , Fernandez Lahore Marcelo , Grasselli Mariano
Published: September 2014

Fusion of peptide‐based tags to recombinant proteins is currently one of the most used tools for protein production. Also, immobilized metal ion affinity chromatography (IMAC) has a huge application in protein purification, especially in research labs. The combination of expression systems of recombinant tagged proteins with this robust chromatographic system has become an efficient and rapid tool to produce milligram‐range amounts of proteins. IMAC‐Ni(II) columns have become the natural partners of 6xHis‐tagged proteins. The Ni(II) ion is considered as the best compromise of selectivity and affinity for purification of a recombinant His‐tagged protein. The palladium(II) ion is also able to bind to side chains of amino acids and form ternary complexes with iminodiacetic acid and free amino acids and other sulfur‐containing molecules. In this work, we evaluated two different cysteine‐ and histidine‐containing six amino acid tags linked to the N‐terminal group of green fluorescent protein (GFP) and studied the adsorption and elution conditions using novel eluents. Both cysteine‐containing tagged GFPs were able to bind to IMAC‐Pd(II) matrices and eluted successfully using a low concentration of thiourea solution. The IMAC‐Ni(II) system reaches less than 20% recovery of the cysteine‐containing tagged GFP from a crude homogenate of recombinant Escherichia coli, meanwhile the IMAC‐Pd(II) yields a recovery of 45% with a purification factor of 13. Copyright © 2014 John Wiley & Sons, Ltd.
Atomic force microscopy on plasma membranes from Xenopus laevis oocytes containing human aquaporin 4
Authors: Orsini Francesco , Santacroce Massimo , Cremona Andrea , Gosvami Nitya N. , Lascialfari Alessandro , Hoogenboom Bart W.
Published: September 2014

Atomic force microscopy (AFM) is a unique tool for imaging membrane proteins in near‐native environment (embedded in a membrane and in buffer solution) at ~1 nm spatial resolution. It has been most successful on membrane proteins reconstituted in 2D crystals and on some specialized and densely packed native membranes. Here, we report on AFM imaging of purified plasma membranes from Xenopus laevis oocytes, a commonly used system for the heterologous expression of membrane proteins. Isoform M23 of human aquaporin 4 (AQP4‐M23) was expressed in the X. laevis oocytes following their injection with AQP4‐M23 cRNA. AQP4‐M23 expression and incorporation in the plasma membrane were confirmed by the changes in oocyte volume in response to applied osmotic gradients. Oocyte plasma membranes were then purified by ultracentrifugation on a discontinuous sucrose gradient, and the presence of AQP4‐M23 proteins in the purified membranes was established by Western blotting analysis. Compared with membranes without over‐expressed AQP4‐M23, the membranes from AQP4‐M23 cRNA injected oocytes showed clusters of structures with lateral size of about 10 nm in the AFM topography images, with a tendency to a fourfold symmetry as may be expected for higher‐order arrays of AQP4‐M23. In addition, but only infrequently, AQP4‐M23 tetramers could be resolved in 2D arrays on top of the plasma membrane, in good quantitative agreement with transmission electron microscopy analysis and the current model of AQP4. Our results show the potential and the difficulties of AFM studies on cloned membrane proteins in native eukaryotic membranes. Copyright © 2014 John Wiley & Sons, Ltd.
Determination of sedative hypnotics in sewage sludge by pressurized liquid extraction with high‐performance liquid chromatography and tandem mass spectrometry
Authors: Arbeláez Paula , Granados Judith , Borrull Francesc , Marcé Rosa Maria , Pocurull Eva
Published: September 2014

This paper describes a method for the determination of eight sedative hypnotics (benzodiazepines and barbiturates) in sewage sludge using pressurized liquid extraction and liquid chromatography with tandem mass spectrometry. Pressurized liquid extraction operating conditions were optimized and maximum recoveries were reached using methanol under the following operational conditions: 100ºC, 1500 psi, extraction time of 5 min, one extraction cycle, flush volume of 60% and purge time of 120 s. Pressurized liquid extraction recoveries were higher than 88% for all the compounds except for carbamazepine (55%). The repeatability and reproducibility between days, expressed as relative standard deviation (n = 5), were lower than 6 and 10%, respectively. The detection limits for all compounds were lower than 12.5 μg/kg of dry weight. The method was applied to determine benzodiazepines and barbiturates in sewage sludge from urban sewage treatment plants, and carbamazepine showed the highest concentration (7.9–18.9 μg/kg dry weight).
Admission after sleep surgery is unnecessary in patients without cardiovascular disease
Authors: Rotenberg Brian , Theriault Jenna , Cheng Horace , Fuller John
Published: September 2014

Objective/Hypothesis

Evidence is lacking to guide whether patients with obstructive sleep apnea (OSA) require mandatory postoperative monitoring when undergoing multilevel sleep surgery. The purpose of this study was to examine the respiratory complication rate following OSA surgery and identify which patients benefit from monitoring after surgery.

Study Design

A prospective study was conducted.

Methods

Fifty patients (age 45.4 ± 12.4; male 39, female 11), with sleep study‐proven OSA (apnoea/hypopnoea index [AHI] 24.3 ± 22.2) underwent multilevel sleep surgery. All patients had the St. Joseph's OSA risk score calculated preoperatively and then again within the postanesthesia care unit (PACU). The patients were then stratified into two categories: safe for same‐day discharge and requiring admission for overnight O2 saturation monitoring. Groups were compared across age, sex, AHI, body mass index, mean O2 saturation, minimum O2 saturation, length of time in PACU, narcotic use, smoking, surgery type, and other comorbidities. The St. Joseph's OSA Risk Tool was applied.

Results

Seventy‐eight percent of patients met criteria for same‐day discharge, and 22% required admission. For the discharged patients, we had a 0.0% readmission or complication rate for OSA‐specific reasons. For the admitted patients, we had no OSA‐specific complications while admitted to hospital. No variables consistently predicted complications or need for admission.

Conclusions

The incidence of respiratory events requiring intervention following multilevel sleep surgery is very low. Most patients with OSA undergoing surgery can be safely discharged home without any subsequent respiratory complications. In addition, those patients admitted for monitoring after surgery do not benefit from their admission.

Level of Evidence: 2b.

Laryngoscope, 125:498–502, 2015
Hydrogenated styrene–isoprene–butadiene rubber: optimisation of hydrogenation conditions and performance evaluation as viscosity index improver
Authors: Li Wei
Published: September 2014

Hydrogenated styrene–isoprene–butadiene rubber (HSIBR) was prepared through the hydrogenation reaction of self‐prepared styrene–isoprene–butadiene rubber using a Ziegler–Natta type catalyst prepared with nickel naphthenate (Ni) and aluminum triisobutyl (Al). The precursors and corresponding hydrogenated polymers were characterised using size exclusion chromatography, proton nuclear magnetic resonance (1H NMR) spectroscopy, differential scanning calorimetry and thermal gravimetric analysis. The effects of various reaction parameters on the level of hydrogenation, calculated from 1H NMR spectroscopy, were investigated in the current paper. A maximum of 98% hydrogenation was obtained under the following conditions: Al/Ni molar ratio, 6; catalyst amount, 3 mg Ni per g of polymer; time, 3 h; temperature, 60°C; H2 pressure, 4 MPa and polymer concentration, 10 wt.%. Moreover, a different SAE 5W‐30 multigrade oil (5 CST hydroisomerisation dewax base oil) was formulated using HSIBR samples as viscosity index improvers (VII). The effect of butadiene/isoprene mass ratio in HSIBR on the performance of VII for lubricants was investigated here for the first time. HSIBR used as VII for lubricants integrated some advantages of hydrogenated styrene–butadiene rubber and hydrogenated styrene–isoprene rubber. Copyright © 2014 John Wiley & Sons, Ltd.
NLS approximation of time oscillatory long waves for equations with quasilinear quadratic terms
Authors: Chirilus‐Bruckner Martina , Düll Wolf‐Patrick , Schneider Guido
Published: September 2014

We consider a nonlinear wave equation with a quasilinear quadratic nonlinearity. Slow spatial and temporal modulations of the envelope of an underlying carrier wave can be described formally by an NLS equation. It is the purpose of this paper to present a method which allows to prove error estimates between this formal approximation and true solutions of the quasilinear wave equation in case . The paper contains the first validity proof of the NLS approximation for a nonlinear wave equation with quasilinear quadratic terms.
Using a Compromise Programming Framework to Integrating Spatially Specific Preference Information for Forest Management Problems
Authors: Eyvindson Kyle , Kangas Annika
Published: September 2014

The development of forest management plans is a multi‐criteria problem that usually involves multiple stakeholders. In forested recreational areas or natural parks, stakeholders could include government officials, forest companies and visitors to the area. With the progress of mobile phone technology, preference information (including aesthetic values) can be conveniently obtained from stakeholders while they are in the forest. This paper develops a methodological approach that incorporates place‐specific opinion preference into the development of alternative forest management plans. Through the use of a modified Compromise Programming approach, prospective alternatives are developed, which optimize the opinions of stakeholders and the quantity of timber over time depending on specified parameters. The analysis is based on a small simulated forest holding and place‐specific simulated opinion data. To allow for a comparison between potential stakeholder groups, the opinion data was generated by a method that produced three separate groups. The results indicate the practical use of place‐specific preferences and provide a means to incorporate the information to generate possible alternative plans. In addition, the analysis highlights that by segregating the preference information into groups, the planning of more specific courses of actions can be made. Copyright © 2015 John Wiley & Sons, Ltd.
Reduction of microvoids in composite laminates fabricated by bladder assisted composite manufacturing (BACM)
Authors: Anderson J.P. , Altan M.C.
Published: September 2014

Bladder Assisted Composite Manufacturing (BACM) is a recently developed out‐of‐autoclave process designed to fabricate geometrically complex, hollow composite parts. This paper assesses the ability of three new BACM process variations to fabricate parts with high fiber and low void contents. This was achieved by fabricating 4‐ply cylinders from a carbon/epoxy prepreg at cure pressures of 207 and 483 kPa. The fiber/void content, mechanical properties, and energy consumed during the curing of the cylinders are investigated and compared to the original BACM process. The fiber content of the cylinders were observed to be dependent on both bladder pressure and BACM variation used, reaching a maximum fiber content of 66% which is 5% greater than that obtained by the original BACM process. The elastic moduli and failure strength results for the cylinders were found to increase with fiber content and showed no preference to any of the studied BACM process variations. In addition, the void content of the cylinders were reduced by 94% with the utilization of a porous bleeder fabric when compared to the original BACM process. POLYM. COMPOS., 37:561–572, 2016. © 2014 Society of Plastics Engineers
The effect of atmospheric‐pressure air plasma discharge power on adhesive properties of aramid fibers
Authors: Jia Caixia , Chen Ping , Wang Qian , Wang Jing , Xiong Xuhai , Ma Keming
Published: September 2014

After exposure to the atmospheric‐pressure air plasma at different discharge powers, the adhesion characteristics of Twaron aramid fibers were investigated. For the 12 s‐300 W plasma treatment, the interlaminar shear strength of Twaron fiber reinforced thermoplastic poly(phthalazinone ether sulfone ketone) was increased from 46.0 to 61.7 MPa by 34.1%, and the diffusion of water molecule into the resulting composites was proved to be effectively prevented. These results showed that surface adhesive properties of the plasma‐treated aramid fibers were improved. At the power level of 300 W, X‐ray photoelectron spectroscopy analysis revealed the increases in concentrations of oxygen and nitrogen polar groups on the fiber surface, and atomic force microscopy observations led to the conclusion that the fiber surface morphology was changed and the surface roughness was greatly increased. These new polar and irregular surface structures accounted for the better adhesion between the fiber and the matrix, while due to the reasonability of this discharge power level applied to the surface modification, the measured fiber tensile strength only decreased by 2.0%. POLYM. COMPOS., 37:620–626, 2016. © 2014 Society of Plastics Engineers
A comparative analysis of woven jute/glass hybrid polymer composite with and without reinforcing of fly ash particles
Authors: Raghavendra G. , Ojha Shakuntala , Acharya S.K. , Pal S.K.
Published: September 2014

The objective of this research article is to compare the mechanical and tribological properties of jute‐glass‐fiber‐reinforced epoxy (J‐G‐E) hybrid composites with and without fly ash particulate filler. A dry hand lay‐up technique is used to fabricate all the laminates. The properties including flexural strength, tensile strength, flexural modulus, and erosion behavior of all the composites are evaluated as per American Society for Testing and Materials (ASTM) standards. The fly ash particulate‐filled hybrid composite shows a better mechanical and tribological property. The maximum flexural strength and flexural modulus are obtained for GJGJ+ 5 wt% fly ash filler epoxy composites. Whereas the maximum tensile strength is obtained for GJJG+ 10 wt% fly ash filler epoxy composites. Scanning Electron Microscopy (SEM) analysis also has been carried out to categorize mechanical and tribological behavior of composites. POLYM. COMPOS. 37:658–665, 2016. © 2014 Society of Plastics Engineers
Preparation, thermal, and flammability of halogen‐free flame retarding thermoplastic poly(ether‐ester) elastomer/montmorillonite nanocomposites
Authors: Zhong Yuhua , Jiang Chenchen , Ruan Mingzhu , Chen Yu , Wu Wei
Published: September 2014

In this article, the nanocomposites thermoplastic polyester‐ether elastomer (TPEE) with phosphorous–nitrogen (P–N) flame retardants and montmorillonite (MMT) was prepared by melt blending.The fire resistance of nanocomposites was analyzed by limiting oxygen index (LOI) and vertical burning (UL94) test. The result shows that the flame retardants containing P–N increased the LOI of the material from 17.3 to 27%. However, TPEE containing P–N flame retardants just got UL94 V‐2 ranking, which resulted in the flaming dripping phenomenon. On the other hand, TPEE containing P–N flame retardant and organic‐modified montmorillonite (o‐MMT) achieved UL94 V‐0 rating for the special microstructure. The XRD and TEM morphology has demonstrated that the formation of multi‐ordered structure regarding restricted segmental motions at the organic–inorganic interface and stronger interactions between the clay mineral layers and the polymer chains. The structure was supported by the results of rheological properties and DSC analysis. The thermal degradation and char residue characterization was studied by thermal gravimetric analysis (TGA) and SEM‐EDX measurements, respectively. The TGA and SEM‐EDX have demonstrated that o‐MMT results in the increase of char yield and the formation of the thermal stable carbonaceous char. POLYM. COMPOS., 37:700–708, 2016. © 2014 Society of Plastics Engineers
Maleic anhydride polypropylene modified cellulose nanofibril polypropylene nanocomposites with enhanced impact strength
Authors: Peng Yucheng , Gallegos Sergio A. , Gardner Douglas J. , Han Yousoo , Cai Zhiyong
Published: September 2014

Development of cellulose nanofibrils (CNFs) reinforced polypropylene (PP) nanocomposites using melt compounding processes has received considerable attention. The main challenges are to obtain well‐dispersed CNFs in the polymer matrix and to establish compatible linkages between the CNFs and PP. Manufacturing of CNF reinforced PP nanocomposites was conducted using a twin‐screw co‐rotating extruder with the masterbatch concept. Modifications of CNFs using maleic anhydride polypropylene were performed. The best mechanical properties of the nanocomposites are 1.94 GPa (tensile modulus), 32.8 MPa (tensile strength), 1.63 GPa (flexural modulus), 50.1 MPa (flexural strength), and 3.8 kJ m−2 (impact strength), which represents about 36, 11, 21, 7, and 23% improvement, respectively, compared to those of pure PP (1.43 GPa, 29.5 MPa, 1.35 GPa, 46.9 MPa, and 3.1 kJ m−2). Fracture morphology examination indicated good dispersion of CNFs in the PP matrix was achieved through this specific manufacturing process. MAPP treatments enhanced the interfacial adhesion between the CNFs and PP. POLYM. COMPOS., 37:782–793, 2016. © 2014 Society of Plastics Engineers
Controversial Therapeutics: The β‐Adrenergic Antagonist and Cocaine‐Associated Cardiovascular Complications Dilemma
Authors: Schurr James W. , Gitman Brenda , Belchikov Yuly
Published: September 2014

Cocaine abuse is associated with cardiovascular complications that include chest pain and myocardial infarction. Traditional therapy for these conditions includes a β‐adrenergic antagonist. However, guidelines released in 2008 recommended against this treatment option because of the prevailing theory that cocaine will potentiate vasospasm secondary to unopposed α‐adrenergic effects. Subsequently, further evidence and updated guidelines have become available, debunking this claim. Current literature is limited but suggests that β‐adrenergic antagonists are harmful. Although case reports support a detrimental effect of β‐adrenergic antagonists, the anecdotal data are inconsistent, and the conclusions from case studies are overruled by larger studies. The pharmacology, pathophysiology, and literature on the use of β‐adrenergic antagonists in association with cocaine are reviewed. Future studies that focus on outcomes and different pharmacologic profiles of β‐adrenergic antagonists are needed.
Stakeholder Management Strategies and Practices during a Project Course
Authors: Eskerod Pernille , Vaagaasar Anne Live
Published: September 2014

In stakeholder management, a key question is: How can an actor/organization (e.g., a project) under different contingencies apply strategies to develop the relationship with each stakeholder into a favorable one seen from the focal organization's perspective? Based on an in-depth longitudinal case study, we provide detailed descriptions of how a project management team worked with its stakeholder relationships. Applying a practice approach, we explore how stakeholder management practices emerged and evolved as embedded actions and interpretations related to perceptions of each stakeholder's harm and help potentials. We show how trust was both input to and outcomes of the managerial action.
A Comparison Study of Single‐Scale and Multiscale Approaches for Data‐Driven and Model‐Based Online Denoising
Authors: Rendall Ricardo R. , Reis Marco S.
Published: September 2014

Signal denoising is a pervasive operation in most online applications, such as engineering process control and online optimization, strongly affecting the outcome of these higher‐level tasks and impacting the overall variability exhibited by processes and products. Therefore, it plays a fundamental role in improving process capability, which is, however, often overlooked. In this work, we compare the performance of different types of currently available online denoising filters using a variety of test signals that represent the diversity of situations likely to be found in practice, properly corrupted with additive noise of varying magnitudes. Both single‐scale/multiscale, data‐driven/model‐based and time domain/frequency domain, online filtering approaches were contemplated, in what is, to the best of the authors knowledge, the more extensive comparison study conducted on online denoising (or filtering) methodologies. A new class of multiscale denoising algorithms is also considered in this study, based on the online wavelet multiresolution decomposition. In this context, we propose and test a new formulation, called the online multiscale hybrid Kalman filter. After proper tuning, the methods are tested and their performances compared. As a result of the comparison study, clear guidelines are provided for practitioners on the use of online denoising methodologies, which allow for a better management of the impact of the propagation of unstructured components of variability in the final outcome of the processes. Copyright © 2014 John Wiley & Sons, Ltd.
Promoting Holistic Well-Being in Chronic Stroke Patients Through Leisure Art-Based Creative Engagement
Authors: Sit Janet W. H. , Chan Amy W. H. , So Winnie K. W. , Chan Carmen W. H. , Chan Aileen W. K. , Chan Helen Y. L. , Fung Olivia W. M. , Wong Eliza M. L.
Published: September 2014

Purpose:

To examine the potential value of a creative art-based activity as a caring modality for promoting holistic well-being among chronic stroke patients, and to explore the feelings and meanings that stroke patients derived from their experience in leisure art-based creative engagement (LACE).

Design:

Qualitative design.

Method:

Participants were recruited through purposive and snowball sampling. Individual semi-structured interviews were conducted. Qualitative content analysis was performed. The design and implementation of LACE was guided by Watson’s theory of caring.

Findings:

Twenty-four participants completed the study. Four themes emerged from participants’ account of experiences with the LACE: (1) appreciation of opportunities, (2) appreciation of self, (3) appreciation of others, and (4) appreciation of life.

Conclusion:

From the perspective of the participants, engaging in LACE enhances their sense of enjoyment and self-expression. Furthermore, they perceived LACE as an affirmation of life and an empowering process strengthening their connection and appreciation with the self and others.

Clinical Relevance:

This study adds evidence to existing literature on Watson’s theory-guided design and implementation of caring initiatives for community rehabilitation and has laid the groundwork for developing further evidencebased research in leisure art-based caring occasions for promoting holistic well-being in stroke rehabilitation.
A distributed secret share update scheme with public verifiability for ad hoc network
Authors: Zhenhua Chen , Shundong Li , Qianhong Wu , Qiong Huang
Published: September 2014

In this paper, a distributed secret share update scheme with public verifiability for ad hoc network is proposed, in which the system secret key is collaboratively generated by k nodes or more, instead of by a centralized key generation center. To prevent a passive adversary from collecting other nodes' shares to compromise the system key over a long period, each node can periodically refresh its share without changing the system key. At the same time, to resist an active adversary to forge partial share and even to solve the accusation problem, any one can publicly verify the correctness of partial shares submitted by other nodes in the share update phase. To achieve our goals, we explore the technique of verifiable encryption with additive homomorphism and that of threshold cryptography. The analysis shows that the proposed scheme is more secure and efficient than the previous schemes for ad hoc networks. Copyright © 2014 John Wiley & Sons, Ltd.
A marginalized zero‐inflated Poisson regression model with overall exposure effects
Authors: Long D. Leann , Preisser John S. , Herring Amy H. , Golin Carol E.
Published: September 2014

The zero‐inflated Poisson (ZIP) regression model is often employed in public health research to examine the relationships between exposures of interest and a count outcome exhibiting many zeros, in excess of the amount expected under sampling from a Poisson distribution. The regression coefficients of the ZIP model have latent class interpretations, which correspond to a susceptible subpopulation at risk for the condition with counts generated from a Poisson distribution and a non‐susceptible subpopulation that provides the extra or excess zeros. The ZIP model parameters, however, are not well suited for inference targeted at marginal means, specifically, in quantifying the effect of an explanatory variable in the overall mixture population. We develop a marginalized ZIP model approach for independent responses to model the population mean count directly, allowing straightforward inference for overall exposure effects and empirical robust variance estimation for overall log‐incidence density ratios. Through simulation studies, the performance of maximum likelihood estimation of the marginalized ZIP model is assessed and compared with other methods of estimating overall exposure effects. The marginalized ZIP model is applied to a recent study of a motivational interviewing‐based safer sex counseling intervention, designed to reduce unprotected sexual act counts. Copyright © 2014 John Wiley & Sons, Ltd.
Mediation analysis when a continuous mediator is measured with error and the outcome follows a generalized linear model
Authors: Valeri Linda , Lin Xihong , VanderWeele Tyler J.
Published: September 2014

Mediation analysis is a popular approach to examine the extent to which the effect of an exposure on an outcome is through an intermediate variable (mediator) and the extent to which the effect is direct. When the mediator is mis‐measured, the validity of mediation analysis can be severely undermined. In this paper, we first study the bias of classical, non‐differential measurement error on a continuous mediator in the estimation of direct and indirect causal effects in generalized linear models when the outcome is either continuous or discrete and exposure–mediator interaction may be present. Our theoretical results as well as a numerical study demonstrate that in the presence of non‐linearities, the bias of naive estimators for direct and indirect effects that ignore measurement error can take unintuitive directions. We then develop methods to correct for measurement error. Three correction approaches using method of moments, regression calibration, and SIMEX are compared. We apply the proposed method to the Massachusetts General Hospital lung cancer study to evaluate the effect of genetic variants mediated through smoking on lung cancer risk. Copyright © 2014 John Wiley & Sons, Ltd.
A general framework for parametric survival analysis
Authors: Crowther Michael J. , Lambert Paul C.
Published: September 2014

Parametric survival models are being increasingly used as an alternative to the Cox model in biomedical research. Through direct modelling of the baseline hazard function, we can gain greater understanding of the risk profile of patients over time, obtaining absolute measures of risk. Commonly used parametric survival models, such as the Weibull, make restrictive assumptions of the baseline hazard function, such as monotonicity, which is often violated in clinical datasets. In this article, we extend the general framework of parametric survival models proposed by Crowther and Lambert (Journal of Statistical Software 53:12, 2013), to incorporate relative survival, and robust and cluster robust standard errors. We describe the general framework through three applications to clinical datasets, in particular, illustrating the use of restricted cubic splines, modelled on the log hazard scale, to provide a highly flexible survival modelling framework. Through the use of restricted cubic splines, we can derive the cumulative hazard function analytically beyond the boundary knots, resulting in a combined analytic/numerical approach, which substantially improves the estimation process compared with only using numerical integration. User‐friendly Stata software is provided, which significantly extends parametric survival models available in standard software. Copyright © 2014 John Wiley & Sons, Ltd.
A highly efficient design strategy for regression with outcome pooling
Authors: Mitchell Emily M. , Lyles Robert H. , Manatunga Amita K. , Perkins Neil J. , Schisterman Enrique F.
Published: September 2014

The potential for research involving biospecimens can be hindered by the prohibitive cost of performing laboratory assays on individual samples. To mitigate this cost, strategies such as randomly selecting a portion of specimens for analysis or randomly pooling specimens prior to performing laboratory assays may be employed. These techniques, while effective in reducing cost, are often accompanied by a considerable loss of statistical efficiency. We propose a novel pooling strategy based on the k‐means clustering algorithm to reduce laboratory costs while maintaining a high level of statistical efficiency when predictor variables are measured on all subjects, but the outcome of interest is assessed in pools. We perform simulations motivated by the BioCycle study to compare this k‐means pooling strategy with current pooling and selection techniques under simple and multiple linear regression models. While all of the methods considered produce unbiased estimates and confidence intervals with appropriate coverage, pooling under k‐means clustering provides the most precise estimates, closely approximating results from the full data and losing minimal precision as the total number of pools decreases. The benefits of k‐means clustering evident in the simulation study are then applied to an analysis of the BioCycle dataset. In conclusion, when the number of lab tests is limited by budget, pooling specimens based on k‐means clustering prior to performing lab assays can be an effective way to save money with minimal information loss in a regression setting. Copyright © 2014 John Wiley & Sons, Ltd.
Structural modeling from electron microscopy data
Authors: López‐Blanco José Ramón , Chacón Pablo
Published: September 2014

Cryo‐electron microscopy is a powerful technique for the determination of three‐dimensional (3D) structures of macromolecular machines, as it provides functional snapshots of biologically relevant complexes under near‐physiological in vitro conditions. In this study, we review the computational algorithms developed to build macromolecular models from the information encoded in cryo‐electron microscopy (EM) density maps. These modeling tools include fitting strategies to localize atomic structures into 3D maps, de novo methods to identify structural elements, and hybrid methods for the combination of multiple structural data from complementary biophysical techniques and other experimental sources. We also illustrate the power of EM‐derived models in the atomic‐level interpretation of the conformational changes of relevant macromolecular assemblies. WIREs Comput Mol Sci 2015, 5:62–81. doi: 10.1002/wcms.1199

This article is categorized under:

Structure and Mechanism > Computational Biochemistry and Biophysics
Secretome analysis of the thermophilic xylanase hyper-producerThermomyces lanuginosusSSBP cultivated on corn cobs
Authors: Winger A M , Heazlewood J L , Chan L J G , Petzold C J , Permaul K , Singh S
Published: September 2014

Thermomyces lanuginosus is a thermophilic fungus known for its ability to produce industrially important enzymes including large amounts of xylanase, the key enzyme in hemicellulose hydrolysis. The secretome of T. lanuginosus SSBP was profiled by shotgun proteomics to elucidate important enzymes involved in hemicellulose saccharification and to characterise the presence of other industrially interesting enzymes. This study reproducibly identified a total of 74 proteins in the supernatant following growth on corn cobs. An analysis of proteins revealed nine glycoside hydrolase (GH) enzymes including xylanase GH11, β-xylosidase GH43, β-glucosidase GH3, α-galactosidase GH36 and trehalose hydrolase GH65. Two commercially produced Thermomyces enzymes, lipase and amylase, were also identified. In addition, other industrially relevant enzymes not currently explored in Thermomyces were identified including glutaminase, fructose-bisphosphate aldolase and cyanate hydratase. Overall, these data provide insight into the novel ability of a cellulase-free fungus to utilise lignocellulosic material, ultimately producing a number of enzymes important to various industrial processes.
Creation of a Network to Promote Universal Screening for Lynch Syndrome: The Lynch Syndrome Screening Network
Authors: Mange Sarah , Bellcross Cecelia , Cragun Deborah , Duquette Deb , Gorman Lisa , Hampel Heather , Jasperson Kory
Published: September 2014

The Evaluation of Genomic Applications in Practice and Prevention Working Group published an evidence‐based recommendation stating that every newly diagnosed colorectal cancer (CRC) should undergo tumor screening for Lynch syndrome (LS). In 2011, leading cancer institutions and public health agencies created the Lynch Syndrome Screening Network (LSSN) in order to promote routine LS screening on all newly diagnosed CRCs and endometrial cancers (EC). The LSSN facilitates implementation of appropriate screening via shared resources, protocols and data through network collaboration. The LSSN website contains resources for institutions interested in initiating screening, including materials for program development, implementation and sustainability. The LSSN listserv gives providers access to experts in LS screening and implementation. The LSSN database will allow exploration of key gaps in implementation as a consortia‐wide endeavor. To date, the LSSN's membership includes 85 institutions involved in the care of CRC patients and nine official partners such as national and state public health entities and other non‐profit institutions. Nearly 80 % of the LSSN's members have already implemented routine or universal CRC and/or EC screening. LSSN serves to further the population health potential of universal LS screening through collaborative efforts and resources.
PORTFOLIO SELECTION BY MINIMIZING THE PRESENT VALUE OF CAPITAL INJECTION COSTS
Authors: Zhou Ming , Yuen Kam C.
Published: September 2014

This paper considers the portfolio selection and capital injection problem for a diffusion risk model within the classical Black–Scholes financial market. It is assumed that the original surplus process of an insurance portfolio is described by a drifted Brownian motion, and that the surplus can be invested in a risky asset and a risk-free asset. When the surplus hits zero, the company can inject capital to keep the surplus positive. In addition, it is assumed that both fixed and proportional costs are incurred upon each capital injection. Our objective is to minimize the expected value of the discounted capital injection costs by controlling the investment policy and the capital injection policy. We first prove the continuity of the value function and a verification theorem for the corresponding Hamilton–Jacobi–Bellman (HJB) equation. We then show that the optimal investment policy is a solution to a terminal value problem of an ordinary differential equation. In particular, explicit solutions are derived in some special cases and a series solution is obtained for the general case. Also, we propose a numerical method to solve the optimal investment and capital injection policies. Finally, a numerical study is carried out to illustrate the effect of the model parameters on the optimal policies.
Seep deposits from northern Istria, Croatia: a first glimpse into the Eocene seep fauna of the Tethys region
Authors: NATALICCHIO M. , PECKMANN J. , BIRGEL D. , KIEL S.
Published: September 2014

Three isolated limestone deposits and their fauna are described from a middle Eocene Flysch succession in northwestern Istria, Croatia. The limestones are identified as ancient methane-seep deposits based on fabrics and characteristic mineral phases, δ13Ccarbonatevalues as low as −42.2 ‰ and13C-depleted lipid biomarkers indicative of methane-oxidizing archaea. The faint bedding of the largest seep deposit, the great dominance of authigenic micrite over early diagenetic fibrous cement, as well as biomarker patterns indicate that seepage was diffusive rather than advective. Apart from methanotrophic archaea, aerobic methanotrophic bacteria were present at the Eocene seeps as revealed by13C-depleted lanostanes and hopanoids. The observed corrosion surfaces in the limestones probably reflect carbonate dissolution caused by aerobic methanotrophy. The macrofauna consists mainly of chemosymbiotic bivalves such as solemyids (Acharax), thyasirids (Thyasira) and lucinids (Amanocina). The middle Eocene marks the rise of the modern seep fauna, but so far the fossil record of seeps of this age is restricted to the North Pacific region. The taxa found at Buje originated during the Cretaceous Period, whereas taxa typical of the modern seep fauna such as bathymodiolin mussels and vesicomyid clams are absent. Although this is only a first palaeontological glimpse into the biogeography during the rise of the modern seep fauna, it agrees with biogeographic investigations based on the modern vent fauna indicating that the dominant taxa of the modern seep fauna first appeared in the Pacific Ocean.
The Binding Effect of a Customary Arbitration Award: Exorcizing the Ghost of Agu v Ikewibe
Authors: Ikeyi Nduka , Maduka Tochukwu
Published: September 2014

Agu v Ikewibe has been widely interpreted as holding that a customary arbitration award is binding only if none of the parties rejected the award after it was made; it has been widely criticized for this reason. However, the Nigerian Supreme Court has reached decisions, subsequent to though not as notorious as Agu v Ikewibe, to the effect that post-award consent is not necessary to found a binding customary arbitration award. This article contends that Agu v Ikewibe did not indeed decide what has been ascribed to it over the years, or that, even if it did, that decision is not supported by the previous judicial authorities upon which it claimed to have relied. Reference is also made to the current predominant indications from the Nigerian Supreme Court that post-award consent is not necessary to establish a binding customary arbitration award.
Sustainability of organic food production: challenges and innovations
Authors: Niggli Urs
Published: September 2014

The greatest challenge for agriculture is to reduce the trade-offs between productivity and long-term sustainability. Therefore, it is interesting to analyse organic agriculture which is a given set of farm practices that emphasise ecological sustainability. Organic agriculture can be characterised as being less driven by off-farm inputs and being better embedded in ecosystem functions. The literature on public goods and non-commodity outputs of organic farms is overwhelming. Most publications address the positive effects of organic farming on soil fertility, biodiversity maintenance and protection of the natural resources of soil, water and air. As a consequence of focusing on public goods, organic agriculture is less productive. Meta-analyses show that organic agriculture yields range between 0·75 and 0·8 of conventional agriculture. Best practice examples from disadvantaged sites and climate conditions show equal or, in the case of subsistence farming in Sub-Saharan Africa, higher productivity of organic agriculture. Hence, organic agriculture is likely to be a good model for productive and sustainable food production. Underfunding in R&D addressing specific bottlenecks of organic agriculture are the main cause for both crop and livestock yield gaps. Therefore, the potential for improving the performance of organic agriculture through agricultural research is huge. Although organic farming is a niche in most countries, it is at the verge of becoming mainstream in leading European countries. Consumer demand has grown over the past two decades and does not seem to be a limiting factor for the future development of organic agriculture.
Fragmented populations of the Vulnerable eastern hoolock gibbon Hoolock leuconedys in the Lower Dibang Valley district, Arunachal Pradesh, India
Authors: Sarma Kuladip , Krishna Murali , Kumar Awadhesh
Published: September 2014

We conducted a survey of the distribution and population status of the eastern hoolock gibbon Hoolock leuconedys in non-protected fragmented forest areas of the Lower Dibang Valley district of Arunachal Pradesh, India, during September 2010–June 2011. We estimated the minimum population density at seven study sites by direct observation and by counting the number of vocalizations heard from groups that were out of view. We used 1-ha belt transects (500 × 20 m) to estimate tree diversity in the study area. For two groups of gibbons we recorded their feeding patterns in forest fragments, using focal individual sampling, during May 2011. A total of 54 groups and three solitary individuals were recorded: 39 groups and three individuals through visual encounter and 15 groups through vocalization recognition. The mean group size recorded was 2.89 ± SE 0.11 (range 2–4). We counted a total of 289 trees, of 26 species and 17 families, in 18 belt transect surveys covering all non-protected fragments of the Lower Dibang Valley district. The gibbons' diet consisted of seasonal fruits and figs (29%), leaves (65%), seeds (2%) and flowers (0.5%). The major threats recorded at the study sites were habitat destruction and hunting. To protect the Vulnerable eastern hoolock gibbon, conservation measures will need to involve local communities.
A paradox of restoration: prey habitat engineering for an introduced, threatened carnivore can support native biodiversity
Authors: Remm Liina , Lõhmus Asko , Maran Tiit
Published: September 2014

Conservation of charismatic vertebrates in modern landscapes often includes habitat engineering, which is well supported by the public but lacks a consideration of wider conservation consequences. We analysed a pond management project for an introduced island population of captive-bred, Critically Endangered European mink Mustela lutreola. Ponds were excavated near watercourses in hydrologically impoverished forests to support the main prey of the mink (brown frogs Rana temporaria and Rana arvalis). A comparison of these ponds with other, natural, water bodies revealed that the (re)constructed ponds could reduce food shortages for the mink. Moreover, the ponds provided habitat for macroinvertebrates that were uncommon in the managed forests in the study area, including some species of conservation concern. The cost-effectiveness of the management of charismatic species can be increased by explicitly including wider conservation targets at both the planning and assessment stages.
National Versus Ethnic Identification in Africa: Modernization, Colonial Legacy, and the Origins of territorial Nationalism
Authors: Robinson Amanda Lea
Published: September 2014

Communal conflicts, civil wars, and state collapse have led many to portray the notion of African nation-states as an oxymoron. Some scholars of African politics—often referred to as second-generation modernization theorists—have argued that strong ethnic attachments across the continent resulted from rapid economic and political modernization, the very forces credited with reducing parochial ties and consolidating European nations in classic modernization theory. Others have argued that national consolidation in Africa is particularly unlikely due to high degrees of ethnic diversity, colonial rule that exacerbated that diversity, and the partition of cultural groups. Despite the ubiquity of these arguments, there has been very little comparative empirical research on territorial nationalism in Africa. Using individual-level data from sixteen countries, combined with a novel compilation of ethnic group and state characteristics, the author evaluates the observable implications of these long-respected theoretical traditions within a multilevel framework. She finds that attachment to the nation, relative to one's ethnic group, increases with education, urbanization, and formal employment at the individual level, and with economic development at the state level—patterns more consistent with classic modernization theory than with second-generation modernization theory. Thus, if modernization in Africa does indeed intensify ethnic attachment, the impact is overwhelmed by the concurrent increase in panethnic territorial nationalism. Similarly, the results show that ethnic diversity and the partition of ethnic groups by “artificial” state borders increase, rather than decrease, the degree to which individuals identify nationally. Taken together, these results reject pessimistic expectations of African exceptionalism and instead suggest that the emergence of widespread national identification within African states is not only possible but even increasingly likely with greater economic development.
NONSTATIONARY LOSS QUEUES VIA CUMULANT MOMENT APPROXIMATIONS
Authors: Pender Jamol
Published: September 2014

In this paper, we provide a new technique for analyzing the nonstationary Erlang loss queueing model with abandonment. Our method uniquely combines the use of the functional Kolmogorov forward equations with the well-known Gram-Charlier series expansion from the statistics literature. Using the Gram-Charlier series expansion, we show that we can estimate salient performance measures of the loss queue such as the mean, variance, skewness, kurtosis, and blocking probability. Lastly, we provide numerical examples to illustrate the effectiveness of our approximations.