bluuebunny/crossref_metadata_2025 huggingface dataset:
Separation of Peptides on HALO 2‐Micron Particles
Authors: Mant Colin T. , Hodges Robert S.
Published: August 2016

Reversed‐phase high‐performance liquid chromatography (RP‐HPLC) is of fundamental importance to the isolation and separation of peptides, proteins, and other biomolecules. Hence, there is a continuing high demand for the development of RP‐HPLC stationary‐phase materials with enhanced separation efficiency. HALO packing materials began the revolution in “core‐shell” technology with the advantages of faster separations, higher resolution and peak capacity, high temperature stability, and rugged reliable performance compared to traditional HPLC and UHPLC. These materials are characterized by a solid core surrounded by a thin layer of porous material, and represent a technology for the future with continuing refinements. Such refinements are aided via the use of designed synthetic peptide standards during stationary‐phase development. Concomitantly, such standards also enable the researcher to monitor RP‐HPLC column performance and develop optimized separation protocols for peptides from a wide array of sources. © 2016 by John Wiley & Sons, Inc.
Introduction to Atomic Force Microscopy (AFM) in Biology
Authors: Kreplak Laurent
Published: August 2016

The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution over a wide range of time scales from milliseconds to hours. In addition to providing topographical images of surfaces with nanometer‐ to angstrom‐scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nano‐scale to the micro‐scale. Importantly, the measurements are made in buffer solutions, allowing biological samples to “stay alive” within a physiological‐like environment while temporal changes in structure are measured—e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described. © 2016 by John Wiley & Sons, Inc.
Numerical characterization of nonlinear oscillatory waves in a composite right‐ and left‐handed traveling‐wave field‐effect transistor
Authors: Narahara Koichi
Published: August 2016

A specialized type of traveling‐wave field‐effect transistor, the gate and drain lines of which have composite right‐ and left‐handed structures, is considered as the platform to support nonlinear oscillatory waves. The cubic–quintic complex Ginzburg–Landau equation is obtained by application of the reductive perturbation method, by which we quantify the homogeneous oscillations including the property of the Andronov–Hopf bifurcation point, oscillation frequency, and amplitude. Several numerical calculations follow to validate the Ginzburg–Landau equation‐based analysis. Finally, the dynamics of numerically obtained stationary flat‐top pulses are discussed. Copyright © 2016 John Wiley & Sons, Ltd.
Numerical analysis of stochastic resonance in a bistable circuit
Authors: Djurhuus Torsten , Krozer Viktor
Published: August 2016

The paper documents the construction of a novel nonlinear model of a noise‐driven, multi‐dimensional, bistable circuit employing stochastic resonance. Simulations are performed in order to characterize the various relevant device performance measures and their sensitivity to parameter values. The numerical results are considered in the context of nonlinear energy harvesting, and it is explained how the developed simulation tools could prove useful for the development of such devices. The topic of reduced‐order modelling is discussed, and it is shown that this approach leads to incorrect results. Copyright © 2016 John Wiley & Sons, Ltd.
Cytomorphology and flow cytometry of brain biopsy rinse fluid enables faster and multidisciplinary diagnosis of large B‐cell lymphoma of the central nervous system
Authors: Debliquis Agathe , Voirin Jimmy , Harzallah Inès , Maurer Maxime , Lerintiu Felix , Drénou Bernard , Ahle Guido
Published: August 2016

Background

Central nervous system lymphomas are aggressive tumors requiring a prompt diagnosis for successful treatment. Stereotactic biopsy remains the standard procedure, but the time needed for histopathology is usually over 2 days. We evaluated the contribution of cytomorphology and flow cytometry to histopathology of the brain biopsy in particular on the rinse fluid usually removed.

Methods

Eighteen patients with suspected localized brain lymphoma underwent stereotactic brain biopsy. Brain biopsy tissue sample and/or brain biopsy rinse fluid were analyzed by cytomorphology combined with flow cytometry. Histopathology was used as a reference.

Results

Histopathology characterized ten diffuse large B‐cell lymphomas and eight other diseases. Cytomorphology and flow cytometry showed lymphoma cells in nine out of the ten lymphomas. Three cytomorphology or flow cytometry negative results were reported for lymphomas in tissue samples due to low cellularity and biopsy sample conditioning. No lymphomatous cells were found by cytomorphology or flow cytometry in the eight other diseases. Rinse fluid results were consistent with histology in all cases studied (sensitivity and specificity, 100%). The median time to result was 4.5 days (range, 2–10 days) for histopathology, while 5 h (range, 3–20 h) were required for both cytomorphology and flow cytometry.

Conclusions

Brain biopsy rinse fluid alleviates problems of tissue sample distribution compared to tissue sample. Its analysis performs the diagnosis of B‐cell lymphoma in a few hours and, associated with histopathology, allows a multidisciplinary diagnosis. This study shows that cytomorphology combined with flow cytometry on brain biopsy rinse fluid is a new, fast, and useful strategy. © 2016 International Clinical Cytometry Society
Protocol for a systematic review of effect sizes and statistical power in the rodent fear conditioning literature
Authors: Moulin T.C. , Carneiro C.F.D. , Macleod M.R. , Amaral O.B.
Published: August 2016

The concepts of effect size and statistical power are often disregarded in basic neuroscience, and most articles in the field draw their conclusions solely based on the arbitrary significance thresholds of statistical inference tests. Moreover, studies are often underpowered, making conclusions from significance tests less reliable. With this in mind, we present the protocol of a systematic review to study the distribution of effect sizes and statistical power in the rodent fear conditioning literature, and to analyse how these factors influence the description and publication of results. To do this, we will conduct a search in PubMed for “fear conditioning” AND “mouse” OR “mice” OR “rat” OR “rats” and obtain all articles published online in 2013. Experiments will be included if they: (1) describe the effect(s) of a single intervention on fear conditioning acquisition or consolidation; (2) have a control group to which the experimental group is compared; (3) use freezing as a measure of conditioned fear and (4) have available data on mean freezing, standard deviation and sample size of each group and on the statistical significance of the comparison. We will use the extracted data to calculate the distribution of effect sizes in these experiments as well as the distribution of statistical power curves for detecting a range of differences at a threshold of α = 0.05. We will assess correlations between these variables and (1) the chances of a result being statistically significant, (2) the way the result is described in the article text, (3) measures to reduce risk of bias in the article and (4) the impact factor of the journal and the number of citations of the article. We will also perform analyses to see whether effect sizes vary systematically across species, gender, conditioning protocols or intervention types.
The effect of demographic correlations on the stochastic population dynamics of perennial plants
Authors: Compagnoni Aldo , Bibian Andrew J. , Ochocki Brad M. , Rogers Haldre S. , Schultz Emily L. , Sneck Michelle E. , Elderd Bret D. , Iler Amy M. , Inouye David W. , Jacquemyn Hans , Miller Tom E. X.
Published: August 2016

Understanding the influence of environmental variability on population dynamics is a fundamental goal of ecology. Theory suggests that, for populations in variable environments, temporal correlations between demographic vital rates (e.g., growth, survival, reproduction) can increase (if positive) or decrease (if negative) the variability of year‐to‐year population growth. Because this variability generally decreases long‐term population viability, vital rate correlations may importantly affect population dynamics in stochastic environments. Despite long‐standing theoretical interest, it is unclear whether vital rate correlations are common in nature, whether their directions are predominantly negative or positive, and whether they are of sufficient magnitude to warrant broad consideration in studies of stochastic population dynamics. We used long‐term demographic data for three perennial plant species, hierarchical Bayesian parameterization of population projection models, and stochastic simulations to address the following questions: (1) What are the sign, magnitude, and uncertainty of temporal correlations between vital rates? (2) How do specific pairwise correlations affect the year‐to‐year variability of population growth? (3) Does the net effect of all vital rate correlations increase or decrease year‐to‐year variability? (4) What is the net effect of vital rate correlations on the long‐term stochastic population growth rate (λs)? We found only four moderate to strong correlations, both positive and negative in sign, across all species and vital rate pairs; otherwise, correlations were generally weak in magnitude and variable in sign. The net effect of vital rate correlations ranged from a slight decrease to an increase in the year‐to‐year variability of population growth, with average changes in variance ranging from −1% to +22%. However, vital rate correlations caused virtually no change in the estimates of λs(mean effects ranging from −0.01% to +0.17%). Therefore, the proportional changes in the variance of population growth caused by demographic correlations were too small on an absolute scale to importantly affect population growth and viability. We conclude that, in our three focal populations and perhaps more generally, vital rate correlations have little effect on stochastic population dynamics. This may be good news for population ecologists, because estimating vital rate correlations and incorporating them into population models can be data intensive and technically challenging.
MAIT be different–persisting dysfunction after DAA‐mediated clearance of chronic hepatitis C virus infection
Authors: Hofmann Maike , Thimme Robert
Published: August 2016

MAIT cells are an abundant innate‐like T‐cell subset that is defined by the invariant T‐cell receptor (iTCR) V‐alpha chain Vα7.2‐Jα33. Little is currently known about their frequency and function in chronic hepatitis C virus (HCV) infection and their fate after therapy‐mediated HCV elimination by direct acting antivirals (DAA). In this issue of the European Journal of Immunology, Hengst et al. [Eur. J. Immunol. 2016. 46: 2204‐2210] give important novel insights into the biological role of MAIT cells in a relevant human chronic viral infection by showing that first, MAIT cells are only present at low frequencies in chronic HCV infection; second, circulating MAIT cells in HCV patients also display an altered phenotype; third, they are impaired in their MR‐1‐dependent effector functions and finally, and maybe most importantly, MAIT‐cell frequency and function was not restored after HCV elimination by DAA therapy. These results suggest that MAIT cells are severely affected by a chronic human viral infection in their frequency and function and that this impairment is not reversed after HCV elimination. This is in contrast to rapid DAA‐mediated restorations of NK‐cell and CD8+ T‐cell functions, and indicates a differential impact of chronic infection and clearance on different immune cell subsets.
Environmental impact assessment of electricity production from lignite
Authors: Nanaki Evanthia A. , Koroneos Christopher J. , Xydis George A.
Published: August 2016

Lignite is by far the most used fuel in Greece for the production of electricity as there are large reserves in the country. The high emissions of global warming gases have led to the need for the adaptation of measures and initiatives to reduce emissions in the Greek energy system for the period up to 2030. It is imperative that an environmental policy and measures are implemented to limit CO2 emissions towards the Kyoto targets. The objective of this work is to analyze the environmental impacts associated with the atmospheric emissions and other wastes that are produced during the extraction, transportation, and use of lignite for electricity production in Greece using the methodology of life cycle assessment. The results presented here indicate that the most significant emission's reduction can be made from technology substitution. The introduction of advanced fossil fuel technologies can also lead to improvements in life‐cycle GHG emissions. NOx, SO2, and PM emissions from the lignite life cycle, contributing to the respiratory effects impact category (21.1–28.3%), have a bigger impact than the climate change (10–32.7%) and acidification/eutrophication effects (2.17–3.82%). As per Greece's National Renewable Energy Policy the penetration of renewable energy sources in country's energy mix is investigated. © 2016 American Institute of Chemical Engineers Environ Prog, 35: 1868–1875, 2016
Defining the floodplain in hydrologically‐variable settings: implications for flood risk management
Authors: Croke Jacky , Fryirs Kirstie , Thompson Chris
Published: August 2016

Flood risk management is an essential responsibility of state governments and local councils to ensure the protection of people residing on floodplains. Globally, floodplains are under increasing pressure from growing populations. Typically, the engineering‐type solutions that are used to predict local flood magnitude and frequency based on limited gauging data are inadequate, especially in settings which experience high hydrological variability. This study highlights the importance of incorporating geomorphological understanding into flood risk management in southeast Queensland (SEQ), an area badly affected by extreme flood events in 2011 and 2013. The major aim of this study is to outline the hydrological and sedimentological characteristics of various ‘inundation surfaces’ that are typical of catchments in the sub‐tropics. It identifies four major inundation surfaces; within‐channel bench [Q ~ 2.33 yr average recurrence interval (ARI)]; genetic floodplain (Q = 20 yr ARI); hydraulic floodplain (20 yr < Q ≤ 200 yr ARI) and terrace (Q > 1000 yr ARI). These surfaces are considered typical of inundation areas within, and adjacent to, the large macrochannels common to this region and others of similar hydrological variability. An additional area within genetic floodplains was identified where flood surfaces coalesce and produce an abrupt reduction in channel capacity. This is referred to here as a Spill‐out Zone (SOZ). The associated vulnerability and risk of these surfaces is reviewed and recommendations made based on incorporating this geomorphological understanding into flood risk assessments. These recommendations recognize the importance to manage for risks associated with flow inundation and sediment erosion, delivery and deposition. The increasing availability of high resolution topographic data opens up the possibility of more rapid and spatially extensive assessments of key geomorphic processes which can readily be used to predict flood risk. Copyright © 2016 John Wiley & Sons, Ltd.
Megafires: an emerging threat to old‐forest species
Authors: Jones Gavin M , Gutiérrez RJ , Tempel Douglas J , Whitmore Sheila A , Berigan William J , Peery M Zachariah
Published: August 2016

Increasingly frequent “megafires” in North America's dry forests have prompted proposals to restore historical fire regimes and ecosystem resilience. Restoration efforts that reduce tree densities (eg via logging) could have collateral impacts on declining old‐forest species, but whether these risks outweigh the potential effects of large, severe fires remains uncertain. We demonstrate the effects of a 2014 California megafire on an iconic old‐forest species, the spotted owl (Strix occidentalis). The probability of owl site extirpation was seven times higher after the fire (0.88) than before the fire (0.12) at severely burned sites, contributing to the greatest annual population decline observed during our 23‐year study. The fire also rendered large areas of forest unsuitable for owl foraging one year post‐fire. Our study suggests that megafires pose a threat to old‐forest species, and we conclude that restoring historical fire regimes could benefit both old‐forest species and the dry forest ecosystems they inhabit in this era of climate change.
Smokey comes of age: unmanned aerial systems for fire management
Authors: Twidwell Dirac , Allen Craig R , Detweiler Carrick , Higgins James , Laney Christian , Elbaum Sebastian
Published: August 2016

During the past century, fire management has focused on techniques both to protect human communities from catastrophic wildfire and to maintain fire‐dependent ecological systems. However, despite a large and increasing allocation of resources and personnel to achieve these goals, fire management objectives at regional to global scales are not being met. Current fire management techniques are clearly inadequate for the challenges faced by fire managers, and technological innovations are needed. Advances in unmanned aerial systems (UAS) technology provide opportunities for innovation in fire management and science. In many countries, fire management organizations are beginning to explore the potential of UAS for monitoring fires. We have taken the next step and developed a prototype that can precisely ignite fires as part of wildfire suppression tactics or prescribed fires (fire intentionally ignited within predetermined conditions to reduce hazardous fuels, improve habitat, or mitigate for large wildfires). We discuss the potential for these technologies to benefit fire management activities, while acknowledging the sizeable sociopolitical barriers that prevent their immediate broad application.
Natural variation in sensory‐motor white matter organization influences manifestations of Huntington's disease
Authors: Orth Michael , Gregory Sarah , Scahill Rachael I , Mayer Isabella SM , Minkova Lora , Klöppel Stefan , Seunarine Kiran K , Boyd Lara , Borowsky Beth , Reilmann Ralf , Bernhard Landwehrmeyer G. , Leavitt Blair R , Roos Raymund AC , Durr Alexandra , Rees Geraint , Rothwell John C , Langbehn Douglas , Tabrizi Sarah J ,   TRACK‐On Investigators
Published: August 2016

While the HTT CAG‐repeat expansion mutation causing Huntington's disease (HD) is highly correlated with the rate of pathogenesis leading to disease onset, considerable variance in age‐at‐onset remains unexplained. Therefore, other factors must influence the pathogenic process. We asked whether these factors were related to natural biological variation in the sensory‐motor system. In 243 participants (96 premanifest and 35 manifest HD; 112 controls), sensory‐motor structural MRI, tractography, resting‐state fMRI, electrophysiology (including SEP amplitudes), motor score ratings, and grip force as sensory‐motor performance were measured. Following individual modality analyses, we used principal component analysis (PCA) to identify patterns associated with sensory‐motor performance, and manifest versus premanifest HD discrimination. We did not detect longitudinal differences over 12 months. PCA showed a pattern of loss of caudate, grey and white matter volume, cortical thickness in premotor and sensory cortex, and disturbed diffusivity in sensory‐motor white matter tracts that was connected to CAG repeat length. Two further major principal components appeared in controls and HD individuals indicating that they represent natural biological variation unconnected to the HD mutation. One of these components did not influence HD while the other non‐CAG‐driven component of axial versus radial diffusivity contrast in white matter tracts were associated with sensory‐motor performance and manifest HD. The first component reflects the expected CAG expansion effects on HD pathogenesis. One non‐CAG‐driven component reveals an independent influence on pathogenesis of biological variation in white matter tracts and merits further investigation to delineate the underlying mechanism and the potential it offers for disease modification. Hum Brain Mapp 37:4615–4628, 2016. © 2016 Wiley Periodicals, Inc.
Multiwalled Carbon Nanotubes Supported Pd(II)‐Salen Complex: An Effective, Phosphorous‐Free, and Reusable Heterogeneous Precatalyst for the Synthesis of Diaryl Ketones
Authors: Mohammadi Elmira , Hajilou Zahra , Movassagh Barahman
Published: August 2016

The Suzuki–Miyaura cross‐coupling reaction of aroyl chlorides and arylboronic acids has been carried out efficiently in the presence of Pd(II)‐salen@MWCNTs as an air‐moisture stable precatalyst. The influence of various parameters, such as solvent, temperature, and base on the reaction system, was studied. Furthermore, the catalyst can be easily recovered quantitatively by a simple filtration and reused for three consecutive runs without significant loss of its activity.
Coarse‐grained and All‐atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation
Authors: Chiricotto Mara , Tran Thanh Thuy , Nguyen Phuong H. , Melchionna Simone , Sterpone Fabio , Derreumaux Philippe
Published: August 2016

Alzheimer's disease is the most common neurodegenerative disease. Experiments and computer simulations can complement one another to provide a full and in‐depth understanding of many aspects in the amyloid field at the atomistic level. Here, we review results of our coarse‐grained and all‐atom simulations in aqueous solution aimed at determining: 1) early aggregation steps of short linear peptides; 2) nucleation size number; 3) solution structure of the Aβ1–40/Aβ1–42 wild‐type dimers; 4) impact of FAD (familial forms of Alzheimer's disease) mutations on the structure of Aβ1–40/Aβ1–42 dimers; and 5) impact of protective mutations on the structure of Aβ1–40/Aβ1–42 dimers.
Situation, Strategies and BMPS to Control Agricultural NPS Pollution In The European Union
Authors: Provolo Giorgio , Sali Guido , Gandolfi Claudio , Jang Jeongryeol , Cho Youngkweon , Magette William
Published: August 2016

Although significant improvements in water quality have been achieved in Europe over the last two decades, water quality status is still below desirable levels in many locations. As in many other regions around the world, nonpoint source pollution from agricultural landscapes remains the key cause of water quality problems in many parts of Europe due to nitrogen surplus, and, in some countries, losses of phosphorus. A variety of physical, managerial, financial and political tools exist for addressing nonpoint source pollution from agricultural sources. However, water resource managers face difficulties in cajoling landowners to adopt the necessary actions, particularly if the effects of such actions to enhance productivity do not exist (or are not apparent). As shown by trends in groundwater quality data, there may be significant delays in observable water quality improvements after action has been taken. These delays in the response times of natural systems will further challenge the willpower of governments at all levels to provide the financial and human resources necessary to combat diffuse pollution. Consequently, there must be continued close cooperation between researchers seeking new control strategies, government agencies that fund such research and finance implementation and landowners who must adopt the measures. Copyright © 2016 John Wiley & Sons, Ltd.
“When Grief Breaks Your Heart”: A Case Study of Interpersonal Psychotherapy Delivered in a Primary Care Setting
Authors: Gomes Maria Fatima , Chowdhary Neerja , Vousoura Eleni , Verdeli Helen
Published: August 2016

Depression and anxiety, the so‐called common mental disorders (CMDs), are highly prevalent and disabling, yet remain largely untreated. This treatment gap is particularly true in low‐ and middle‐income settings, where there is significant scarcity of resources (including human resources) and treatment accessibility is complicated by stigma surrounding mental illness. To address these challenges, the MANAS trial, one of the largest to date randomized, controlled trials, aimed to test the effectiveness of a stepped care intervention led by lay health counselors in primary care settings in Goa, India. Six‐ and 12‐month follow‐up outcomes suggest that MANAS was a safe, feasible, effective, and cost‐effective intervention for CMDs in that context. This article demonstrates the use of culturally adapted IPT as an intervention to treat CMDs in a 54‐year‐old Indian primary care patient struggling with depression and heart‐related problems after his wife's death. A case formulation is presented based on core IPT principles, followed by detailed delineation of treatment from beginning through termination.
VIP Family Members Prevent Outer Blood Retinal Barrier Damage in a Model of Diabetic Macular Edema
Authors: Maugeri Grazia , D'Amico Agata Grazia , Gagliano Caterina , Saccone Salvatore , Federico Concetta , Cavallaro Sebastiano , D'Agata Velia
Published: August 2016

Diabetic macular edema (DME), characterized by an increase of thickness in the eye macular area, is due to breakdown of the blood‐retinal barrier (BRB). Hypoxia plays a key role in the progression of this pathology by activating the hypoxia‐inducible factors. In the last years, various studies have put their attention on the role of pituitary adenylate cyclase‐activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) in retinal dysfunction. However, until now, no study has investigated their protective role against the harmful combined effect of both hyperglycemia and hypoxia on outer BRB. Therefore, in the present study, we have analyzed the role of these peptides on permeability, restoration of tight junctions expression and inhibition of hyperglycemia/hypoxia‐induced apoptosis, in an experimental in vitro model of outer BRB. Our results have demonstrated that the peptides' treatment have restored the integrity of outer BRB induced by cell exposure to hyperglycemia/hypoxia. Their effect is mediated through the activation of phosphoinositide 3 kinase (PI3K)/Akt and mammalian mitogen activated protein kinase/Erk kinase (MAPK/ERK) signaling pathways. In conclusion, our study further clarifies the mechanism through which PACAP and VIP perform the beneficial effect on retinal damage induced by hyperglycemic/hypoxic insult, responsible of DME progression. J. Cell. Physiol. 232: 1079–1085, 2017. © 2016 Wiley Periodicals, Inc.
Comparative analysis of the male reproductive accessory glands of bats Noctilio albiventris (Noctilionidae) and Rhynchonycteris naso (Emballonuridae)
Authors: Beguelini Mateus R. , Puga Cintia C. I. , Morielle‐Versute Eliana , Taboga Sebastião R.
Published: August 2016

In eutherian mammals, the male reproductive accessory glands (RAGs) comprise the prostate, bulbourethral glands, ampullary glands, and the seminal vesicles. Their composition, anatomy and function vary widely between species. This study aimed to characterize histologically and compare the RAGs of bats. The RAGs of Noctilio albiventris (Noctilionidae) and Rhynchonycteris naso (Emballonuridae) were studied using anatomical and histological methods, and were reconstructed three dimensionally. The RAGs of N. albiventris and R. naso are composed of a compact glandular complex that surrounds the urethra and a pair of bulbourethral glands, which are extra‐abdominally located in the inguinal region. In both species, the glandular complex is composed of two well‐defined prostatic regions (ventral and dorsal). The ventral region showed an atypical epithelium (holocrine), where no obvious cellular limits were observed, and PAS‐positive secretion. The dorsal region had a pseudostratified cuboidal epithelium, with basal and secretory cells, and PAS‐negative secretion. Noctilio albiventris also had urethral glands (Littre glands) surrounding the urethra, however, R. naso had only muscles. Both species had bulbourethral glands, with simple columnar epithelium and PAS‐positive secretion. In conclusion, the RAGs of N. albiventris and R. naso comprised a pair of bulbourethral glands and an intra‐abdominal complex, composed of a prostate with two different regions (ventral and dorsal), while the ampullary glands and seminal vesicles were missing in both species. This morphology was more closely related between N. albiventris and R. naso, and to species of the family Phyllostomidae than to families Molossidae and Vespertilionidae. J. Morphol. 277:1459–1468, 2016. © 2016 Wiley Periodicals, Inc.
Development and validation of a new serum standard for the measurement of anti‐HEV antibodies in animals
Authors: Zhang Yulin , Wang Lin , Zeng Hang , Gong Wanyun , Wang Ling , Zhuang Hui
Published: August 2016

Although hepatitis E virus (HEV) infection is a zoonosis, there is, currently, no standardized assay for quantitatively measuring anti‐HEV antibody levels in HEV animal reservoirs. In this study, anti‐HEV antibody positive serum from a rabbit (RS26) was calibrated by dose‐response parallel line assay using the World Health Organization (WHO) reference standard for anti‐HEV antibodies. After evaluating the stability of the RS26 serum, a quantification assay of anti‐HEV antibodies using RS26 as a standard was developed and evaluated for both reproducibility and suitability to field studies. The anti‐HEV antibody level of RS26 was calculated to be 39.54 IU/ml. A series of standard working serum for anti‐HEV antibodies consisted of five serum dilutions (3.950 IU/ml, 1.975 IU/ml, 0.986 IU/ml, 0.494 IU/ml, and 0.247 IU/ml). The quantitative assay using RS26 showed good range and reproducibility, effectively measuring the dynamics of anti‐HEV antibody concentrations in pigs and rabbits. In conclusion, we have developed a a stable and reproducible serum standard for the quantitation of anti‐HEV antibodies. J. Med. Virol. 89:497–501, 2017. © 2016 Wiley Periodicals, Inc.
A comprehensive analysis of trends in extreme precipitation over southeastern coast of Brazil
Authors: Zilli Marcia T. , Carvalho Leila M. V. , Liebmann Brant , Silva Dias Maria A.
Published: August 2016

Southeast Brazil (SE Brazil) is the most densely populated region in Brazil. Previous studies have shown evidence of positive trends in average precipitation and extreme events in a few locations, suggesting the increase in rainfall‐related hazards with potential impacts to urbanized areas of SE Brazil. This study provides a comprehensive analysis of the spatial variability of trends in extreme precipitation over SE Brazil focusing on regional and local scales. We examine two daily rainfall datasets with more than 70 years of data: individual stations and gridded observed precipitation data. Our results indicate that the frequency of both rainy days and extreme daily precipitation events have increased in Sao Paulo state. Conversely, precipitation has become more concentrated in fewer events in Rio de Janeiro and Espirito Santo states where both data sets indicate positive trends in the intensity of extreme daily rainfall. The increases in frequency and intensity of extreme events have both contributed to positive trends in total seasonal and average daily precipitation over Sao Paulo. Additionally, the individual stations indicate negative trends in the number of light rainy days over large urbanized areas in the state of Sao Paulo. The spatial patterns of trends indicate that they are influenced by the proximity of large urban centres and topographic features, and also suggest variations and changes in the major climatic systems affecting precipitation regimes over SE.
Synthesis and Properties of GO‐Doped Porous Hydrogel Nanocomposites with Semi‐Interpenetrating Network Structure
Authors: Hong Haizhi , Zhu Zhaoqi , Sun Hanxue , Mu Peng , Liang Weidong , Li An
Published: August 2016

Superabsorbent hydrogel nanocomposites (SHN) with semi‐interpenetrating polymer network (semi‐IPN) are synthesized by the polymerization of acrylamide monomer in a polyethylene glycol aqueous solution in the presence of the octadecylamine (ODA)‐modified graphene oxide (GO‐ODA) nanosheets. The hydrogel composites are characterized by Fourier transform infrared spectroscopy, thermal gravity analysis, and scanning electron microscopy. The water absorbency of the resulting SHN in distilled water and saline solutions are measured. The results show that doping GO‐ODA nanosheets into hydrogel semi‐IPN would enhance both their salt resistance and water retention. Using a simple freezing‐dry method, porous SHN with macroscopically interconnected pores is prepared, which exhibits excellent separation ability for removal of trace water from oils. Based on their better water absorbency, salt resistance, and excellent oil/water separation ability, the resulting SHN has great potentials in a wide range of applications, for example, oil dehydration, absorption, and separation.

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The best medicine? The influence of physical activity and inactivity on Parkinson's disease
Authors: LaHue Sara C. , Comella Cynthia L. , Tanner Caroline M.
Published: August 2016

The incidence of Parkinson's disease (PD) is expected to increase as our population ages and will likely strain the projected capacity of our health care system. Despite being the most common movement disorder, there have been few noninvasive therapeutic advances for people with PD since the first levodopa clinical trial in 1961. The study of PD pathogenesis, combined with an appreciation for the biochemical mechanisms by which physical activity and exercise may impact physiology, has resulted in emerging hypotheses for new modifiable risk factors for PD. Physical activity and exercise as a means of preventing PD, or maintaining the functionality of people with PD, are a promising area of investigation. Conversely, physical inactivity is implicated in many disease states, some of which are also correlated with the development of PD, such as metabolic syndrome. The primary relationship between these diseases is likely rooted in heightened inflammation and oxidative stress at the cellular level. Physical activity and exercise as a means of attenuating inflammation have led to increased interest in related potential therapeutic targets for PD. Ultimately, these findings may translate into low‐cost, universally available therapies for PD disease modification or prevention. © 2016 International Parkinson and Movement Disorder Society
Determining mean fractional anisotropy using DDCOSY: preliminary results in biological tissues
Authors: Zong Fangrong , Ancelet Lindsay R. , Hermans Ian F. , Galvosas Petrik
Published: August 2016

Complex materials are ubiquitous in science, engineering and nature. One important parameter for characterising their morphology is the degree of anisotropy. Magnetic resonance imaging offers non‐invasive methods for quantitative measurements of the materials anisotropy, most commonly via diffusion tensor imaging and the subsequent extraction of the spatially resolved fractional anisotropy (FA) value. Here, we propose an alternative way of determining the FA as a sample average for cases where spatially resolved methods are not needed or not applicable. It is based on a particular diffusion–diffusion correlation spectroscopy protocol, allowing for the extraction of the mean (i.e. sample averaged) FA value. We demonstrate that mean FA values obtained from three anisotropic biological tissues are consistent with those extracted using diffusion tensor imaging. Moreover, we show that differences of mean FA values in healthy and tumour‐bearing mouse brains allow to distinguish these tissue types. We anticipate that the proposed method will be beneficial in the wider context of medical and material science. Copyright © 2016 John Wiley & Sons, Ltd.
NTRK3 kinase fusions in Spitz tumours
Authors: Yeh Iwei , Tee Meng Kian , Botton Thomas , Shain A Hunter , Sparatta Alyssa J , Gagnon Alexander , Vemula Swapna S , Garrido Maria C , Nakamaru Kenji , Isoyama Takeshi , McCalmont Timothy H , LeBoit Philip E , Bastian Boris C
Published: August 2016

Oncogenic fusions in TRK family receptor tyrosine kinases have been identified in several cancers and can serve as therapeutic targets. We identified ETV6–NTRK3, MYO5A–NTRK3 and MYH9–NTRK3 fusions in Spitz tumours, and demonstrated that NTRK3 fusions constitutively activate the mitogen‐activated protein kinase, phosphoinositide 3‐kinase and phospholipase Cγ1 pathways in melanocytes. This signalling was inhibited by DS‐6051a, a small‐molecule inhibitor of NTRK1/2/3 and ROS1. NTRK3 fusions expand the range of oncogenic kinase fusions in melanocytic neoplasms and offer targets for a small subset of melanomas for which no targeted options currently exist. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Underlying chronic inflammation alters the profile and mechanisms of acute neutrophil recruitment
Authors: Ma Bin , Whiteford James R , Nourshargh Sussan , Woodfin Abigail
Published: August 2016

Chronically inflamed tissues show altered characteristics that include persistent populations of inflammatory leukocytes and remodelling of the vascular network. As the majority of studies on leukocyte recruitment have been carried out in normal healthy tissues, the impact of underlying chronic inflammation on ongoing leukocyte recruitment is largely unknown. Here, we investigate the profile and mechanisms of acute inflammatory responses in chronically inflamed and angiogenic tissues, and consider the implications for chronic inflammatory disorders. We have developed a novel model of chronic ischaemia of the mouse cremaster muscle that is characterized by a persistent population of monocyte‐derived cells (MDCs), and capillary angiogenesis. These tissues also show elevated acute neutrophil recruitment in response to locally administered inflammatory stimuli. We determined that Gr1low MDCs, which are widely considered to have anti‐inflammatory and reparative functions, amplified acute inflammatory reactions via the generation of additional proinflammatory signals, changing both the profile and magnitude of the tissue response. Similar vascular and inflammatory responses, including activation of MDCs by transient ischaemia–reperfusion, were observed in mouse hindlimbs subjected to chronic ischaemia. This response demonstrates the relevance of the findings to peripheral arterial disease, in which patients experience transient exercise‐induced ischaemia known as claudication.These findings demonstrate that chronically inflamed tissues show an altered profile and altered mechanisms of acute inflammatory responses, and identify tissue‐resident MDCs as potential therapeutic targets. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Preparation, characterization, thermal, and electrical properties of chlorinated ethylene propylene diene monomer/hydroxyapatite nanocomposites
Authors: Nihmath A. , Ramesan M.T.
Published: August 2016

Nanocomposites composed of chlorinated ethylene propylene diene monomer rubber (Cl‐EPDM) with various contents of hydroxyapatite nanoparticles (HA) were prepared in an open two‐roll mixing mill. The effect of nanoparticle concentration on structural, morphological, thermal, and electrical properties were examined by different characterization technique such as Fourier transform infrared spectroscopy (FTIR), UV, X‐ray diffraction (XRD), Scanning Electron Microscopy (SEM), Differential Scanning Calorimetry (DSC), thermogravimetric analysis (TGA), and impedance analyzer. The shift in the IR and UV absorption frequencies of nanohybrid relative to that of chlorinated EPDM indicated the successful encapsulation of crystalline hydroxyapatite particles in the modified elastomer chain. The X‐ray diffraction pattern of the fabricated composite revealed the more ordered arrangement of nanoparticles within the elastomer chains and the amorphous nature of polymer decreases with raise in filler loading. The examination of nanocomposite morphology by SEM showed that the inorganic particles were well dispersed in the organic phases. TGA analysis showed the enhanced thermal stability of the composites with increase in the loading of nanoparticles. Shift in the glass transition temperature to a higher value in DSC thermograms of new hybrid indicated the increased orderness of the Cl‐EPDM/HA nanocomposite. The AC electrical conductivity was influenced significantly by the frequency of applied field and the concentration of nanofiller. Dielectric properties strongly distort at lower frequencies but became independent as frequency increased above 103Hz. POLYM. COMPOS., 39:2093–2100, 2018. © 2016 Society of Plastics Engineers
Thermal‐oxidative aging effects on the properties of long glass fiber reinforced polyamide 10T composites
Authors: Song Haishuo , Zhou Dengfeng , Guo Jianbing
Published: August 2016

The results of thermal‐oxidative aging effects on the properties of long glass fiber reinforced polyamide 10T (LGF/PA10T) composites were investigated. The composite samples were aged at 240°C in a heat‐blast oven. The aging times were 10, 20, 30, 40, and 50 days. The thermal‐oxidative aging resulted in decline of crystallization behavior, dynamic and static mechanical properties of the LGF/PA10T composites. These observations can be attributed to the decomposition of the molecular chain of PA10T resin, carbonization of the matrix and interfacial debonding between the glass fibers and matrix, as illustrated by scanning electron microscopy and FTIR spectra. At the initial stage of aging, the storage modulus and glass transition temperature first increased and then reduced, which indicated that there was slight crosslinking between the molecular chains. After aging for 50 days, the retention rates of tensile strength, flexural strength, and notch impact strength of the composite samples were 4.9, 6.3, and 9.4% lower, respectively, than that of the unaged samples; thus, it can be concluded that molecular degradation dominated and caused deterioration of interfacial adhesive strength between the fiber and the resin during the whole aging process. Therefore, the LGF/PA10T resin cannot serve for a long‐time at 240°C. POLYM. COMPOS., 39:2117–2125, 2018. © 2016 Society of Plastics Engineers
Understanding and predicting protein misfolding and aggregation: Insights from proteomics
Authors: Pallarès Irantzu , Ventura Salvador
Published: August 2016

Protein misfolding and aggregation are being found to be associated with an increasing number of human diseases and premature aging, either because they promote a loss of protein function or, more frequently, because the aggregated species gain a toxic activity. Despite potentially harmful, aggregation seems to be a generic property of polypeptide chains and aggregation‐prone protein sequences seem to be ubiquitous, which, counterintuitively, suggests that they serve evolutionary conserved functions. The in vitro study of individual aggregation reactions of a large number of proteins has provided important insights on the structural and sequential determinants of this process. However, it is clear that understanding the role played by protein aggregation and its regulation in health and disease at the cellular, developmental, and evolutionary levels require more global approaches. The use of model organisms and their proteomic analysis hold the power to provide answers to such issues. In the present review, we address how, initially, computational large‐scale analysis and, more recently, experimental proteomics are helping us to rationalize how, why and when proteins aggregate, as well as to decipher the strategies organisms have developed to control proteins aggregation propensities.
Micro‐scale and rapid expression screening of highly expressed and/or stable membrane protein variants in Saccharomyces cerevisiae
Authors: Shiroishi Mitsunori , Moriya Mai , Ueda Tadashi
Published: August 2016

Purification of milligram quantities of target proteins is required for structural and biophysical studies. However, mammalian membrane proteins, many of which are important therapeutic targets, are too unstable to be expressed in heterologous hosts and to be solubilized by detergents. One of the most promising ways to overcome these limitations is to stabilize the membrane proteins by generating variants via introduction of truncated flexible regions, fusion partners, and site‐directed mutagenesis. Therefore, an effective screening strategy is a key to obtaining successful protein stabilization. Herein, we report the micro‐scale and high‐throughput screening of stabilized membrane protein variants using Saccharomyces cerevisiae as a host. All steps of the screening, including cultivation and disruption of cells, solubilization of the target protein, and the pretreatment for fluorescence‐detected size exclusion chromatography (FSEC), could be performed in a 96‐well microplate format. We demonstrated that the dispersion among wells was small, enabling detection of a small but important improvement in the protein stability. We also demonstrated that the thermally stable mutants of a human G protein‐coupled receptor could be distinguished based on an increase of the peak height in the FSEC profile, which was well correlated with increased ligand binding activity of the protein. This strategy represents a significant platform for handling numerous mutants, similar to alanine scanning.
Simplifying and enhancing the use of PyMOL with horizontal scripts
Authors: Mooers Blaine H.M.
Published: August 2016

Scripts are used in PyMOL to exert precise control over the appearance of the output and to ease remaking similar images at a later time. We developed horizontal scripts to ease script development. A horizontal script makes a complete scene in PyMOL like a traditional vertical script. The commands in a horizontal script are separated by semicolons. These scripts are edited interactively on the command line with no need for an external text editor. This simpler workflow accelerates script development. In using PyMOL, the illustration of a molecular scene requires an 18‐element matrix of view port settings. The default format spans several lines and is laborious to manually reformat for one line. This default format prevents the fast assembly of horizontal scripts that can reproduce a molecular scene. We solved this problem by writing a function that displays the settings on one line in a compact format suitable for horizontal scripts. We also demonstrate the mapping of aliases to horizontal scripts. Many aliases can be defined in a single script file, which can be useful for applying costume molecular representations to any structure. We also redefined horizontal scripts as Python functions to enable the use of the help function to print documentation about an alias to the command history window. We discuss how these methods of using horizontal scripts both simplify and enhance the use of PyMOL in research and education.