bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrostatics Explains the Position‐Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes
Authors: Abi‐Ghanem Josephine , Rabin Clémence , Porrini Massimiliano , Dausse Eric , Toulmé Jean‐Jacques , Gabelica Valérie 
Published: August 2017

AbstractIn the RNA realm, non‐Watson–Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop–loop interaction is modulated by non‐Watson–Crick pairs. Mass spectrometry, surface plasmon resonance, and UV‐melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson–Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop–loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications.
Supramolecular Architecture of Substituted Tetraphenyl‐carbo‐benzenes from the Energetic Viewpoint
Authors: Shishkina Svitlana V. , Dyakonenko Viktoriya V. , Shishkin Oleg V. , Maraval Valérie , Chauvin Remi 
Published: August 2017

AbstractThe use of DFT‐calculated energy‐vector diagrams (EVDs) featuring the topology of pairwise intermolecular interaction energies is applied to crystals of carbo‐benzenes. A homogeneous set of six ideally centrosymmetric tetraphenyl‐carbo‐benzenes is selected, with various substituents R in para positions: R=4‐anisyl, 1‐ethyl‐2‐phenyl‐1H‐indol‐3‐yl, 2‐chloro‐2‐(1‐ethyl‐2‐phenyl‐1H‐indol‐3‐yl)ethenyl, tetradecyl, and 9,9‐dihexyl‐9H‐fluoren‐2‐yl, 2‐(9,9‐dihexyl‐9H‐fluoren‐2‐yl)ethynyl. The basic structural motifs (BSMs) of the crystals vary from layers to columns, depending on the size and shape of the substituents R. The BSM cohesion is shown to rely on π‐stacking, CH‐π and dispersive interactions. Solvate molecules are shown to have a negligible role in the formation of the BSM, whereas they loosen the interaction between neighbouring BSMs.
A Real‐Time Cytotoxicity Assay as an Alternative to the Standard Chromium‐51 Release Assay for Measurement of Human NK and T Cell Cytotoxic Activity
Authors: Fassy Julien , Tsalkitzi Kyriaki , Goncalves‐Maia Maria , Braud Véronique M. 
Published: August 2017

AbstractThis unit describes the monitoring and quantification of cellular cytotoxicity using a non‐radioactive and real‐time cytotoxic assay. The extent of target‐cell lysis is monitored over time by imaging and quantifying live fluorescent target cells using a cell‐imaging multimode reader. This assay is performed in a 96 well plate in optimized culture conditions at 37°C in the presence of 5% CO2. The basic protocol describes natural killer cell‐mediated cytotoxic assay that can be adapted to include antibodies blocking inhibitory NK receptors or triggering antibody‐dependent cell‐mediated cytotoxicity (ADCC). The assay is also suitable for antigen specific T‐cell cytotoxic assays. Until now, the standard chromium 51 (51Cr)‐release assay has remained the sole sensitive assay but its major drawbacks include cost and hazard of handling radioactivity. The real‐time cytotoxic assay is therefore an effective alternative providing a robust and sensitive assay that accurately monitors lysis of target cells over time. © 2017 by John Wiley & Sons, Inc.
Universal Precautions: Necessary Safety Procedures When Handling Human Blood, Body Fluids, and Specimens
Authors: Bierer Barbara E. 
Published: August 2017

AbstractUniversal precautions are observed whenever handling human blood, body fluids, or specimens as a means of preventing exposure to blood‐borne pathogens. This appendix outlines safety procedures to follow whenever undertaking research activities that involve human blood, body fluids, and specimens. © 2017 by John Wiley & Sons, Inc.
Mass‐Tag Labeling Using Acyl‐PEG Exchange for the Determination of Endogenous Protein S‐Fatty Acylation
Authors: Percher Avital , Thinon Emmanuelle , Hang Howard 
Published: August 2017

AbstractThe covalent coupling of fatty acids to proteins provides an important mechanism of regulation in cells. In eukaryotes, cysteine fatty acylation (S‐fatty acylation) has been shown to be critical for protein function in a variety of cellular pathways as well as microbial pathogenesis. While methods developed over the past decade have improved the detection and profiling of S‐fatty acylation, these are hampered in their ability to characterize endogenous protein S‐fatty acylation levels under physiological conditions. Furthermore, understanding the contribution of specific sites and levels of S‐fatty acylation remains a major challenge. To evaluate S‐fatty acylation of endogenous proteins as well as to determine the number of S‐fatty acylation events, we developed the acyl‐PEG exchange (APE) that utilizes cysteine‐specific chemistry to exchange S‐fatty acylation sites with mass‐tags of defined size, which can be readily observed by western blotting. APE provides a readily accessible approach to investigate endogenous S‐fatty acylation from any sample source, with high sensitivity and broad applicability that complements the current toolbox of methods for thioester‐based post‐translational modifications. © 2017 by John Wiley & Sons, Inc.
Voronoi‐Tessellated Graphite Produced by Low‐Temperature Catalytic Graphitization from Renewable Resources
Authors: Zhao Leyi , Zhao Xiuyun , Burke Luke T. , Bennett J. Craig , Dunlap Richard A. , Obrovac Mark N. 
Published: August 2017

AbstractA highly crystalline graphite powder was prepared from the low temperature (800–1000 °C) graphitization of renewable hard carbon precursors using a magnesium catalyst. The resulting graphite particles are composed of Voronoi‐tessellated regions comprising irregular sheets; each Voronoi‐tessellated region having a small “seed” particle located near their centroid on the surface. This suggests nucleated outward growth of graphitic carbon, which has not been previously observed. Each seed particle consists of a spheroidal graphite shell on the inside of which hexagonal graphite platelets are perpendicularly affixed. This results in a unique high surface area graphite with a high degree of graphitization that is made with renewable feedstocks at temperatures far below that conventionally used for artificial graphites.
Distributed‐element modelling for spiral resonators used in wireless power transfer
Authors: Najjarzadegan M. , Ghotbi I. , Bassirian P. , Jafarabadi Ashtiani S. , Shoaei O. , Shahabadi M. 
Published: August 2017

SummaryIn this paper, a circuit model for the printed circular spiral resonators based on the piece electrical equivalent circuit is presented. Lumped circuit elements such as inductors, resistors, and mutual inductances are calculated using the conventional formulae for circular loops, whereas the mutual capacitances are calculated by a numerical algorithm. These capacitances are renormalized by scaling factors derived from a simulation‐based library of the self‐resonant frequency of the spiral resonators. It is shown that involving minuscule effects such as mutual capacitances of nonadjacent turns causes a more accurate estimation of the current distribution and high‐frequency characteristics of the resonator. Finally, a closed‐form formula for estimating the capacitor values is extracted by curve fitting leading to a decrease in analysis time. The proposed model predicts the input impedance, quality factor, and current distribution along the resonator in agreement with the results generated by full‐wave simulation and experimental results.
Peptide Technologies in the Development of Chemical Tools for Chromatin‐Associated Machinery
Authors: Barnash Kimberly D. , Lamb Kelsey N. , James Lindsey I. , Frye Stephen V. 
Published: August 2017

ABSTRACT

Preclinical Research

Discerning a mechanistic understanding of the cause‐and‐effect relationships between chromatin post‐translational modifications (PTMs) and DNA accessibility for replication, transcription, and repair is an elusive goal being pursued using molecular and cellular biology, biochemistry, and more recently chemical inhibition. Chemical intervention of the chromatin‐associated complexes that regulate PTM maintenance and chromatin structure faces numerous challenges due to the broad surface‐groove interactions between many of these proteins and histones; yet, the increasing interest in understanding chromatin‐modifying complexes suggests tractable lead compounds will be critical for elucidating the mechanisms of chromatin dysregulation in disease states and validating the druggability of these domains. Peptides and peptidomimetics afford several advantages to efficient inhibitor development including a rational starting point, modular assembly, and retention of secondary structure. Numerous peptide technologies have been employed in the chromatin field to characterize substrate interactions, evaluate ligand selectivity, and optimize potent peptidomimetic inhibitors. We describe the progress and advantages of these efforts, and provide a perspective on their implications for future chemical probe and drug discovery efforts. Drug Dev Res 78 : 300–312, 2017. © 2017 Wiley Periodicals, Inc.
Cross‐species comparison of behavioral neurodevelopmental milestones in the common marmoset monkey and human child
Authors: Ausderau Karla K. , Dammann Caitlin , McManus Kathy , Schneider Mary , Emborg Marina E. , Schultz‐Darken Nancy 
Published: August 2017

AbstractThe common marmoset (Callithrix jacchus) is an increasingly popular non‐human primate species for developing transgenic and genomic edited models of neurological disorders. These models present an opportunity to assess from birth the impact of genetic mutations and to identify candidate predictive biomarkers of early disease onset. In order to apply findings from marmosets to humans, a cross‐species comparison of typical development is essential. Aiming to identify similarities, differences, and gaps in knowledge of neurodevelopment, we evaluated peer‐reviewed literature focused on the first 6 months of life of marmosets and compared to humans. Five major developmental constructs, including reflexes and reactions, motor, feeding, self‐help, and social, were compared. Numerous similarities were identified in the developmental sequences with differences often influenced by the purpose of the behavior, specifically for marmoset survival. The lack of detailed knowledge of marmoset development was exposed as related to the vast resources for humans.
Nanomaterials as stationary phases and supports in liquid chromatography
Authors: Beeram Sandya R. , Rodriguez Elliott , Doddavenkatanna Suresh , Li Zhao , Pekarek Allegra , Peev Darin , Goerl Kathryn , Trovato Gianfranco , Hofmann Tino , Hage David S. 
Published: August 2017

AbstractThe development of various nanomaterials over the last few decades has led to many applications for these materials in liquid chromatography (LC). This review will look at the types of nanomaterials that have been incorporated into LC systems and the applications that have been explored for such systems. A number of carbon‐based nanomaterials and inorganic nanomaterials have been considered for use in LC, ranging from carbon nanotubes, fullerenes and nanodiamonds to metal nanoparticles and nanostructures based on silica, alumina, zirconia and titanium dioxide. Many ways have been described for incorporating these nanomaterials into LC systems. These methods have included covalent immobilization, adsorption, entrapment, and the synthesis or direct development of nanomaterials as part of a chromatographic support. Nanomaterials have been used in many types of LC. These applications have included the reversed‐phase, normal‐phase, ion‐exchange, and affinity modes of LC, as well as related methods such as chiral separations, ion‐pair chromatography and hydrophilic interaction liquid chromatography. Both small and large analytes (e.g., dyes, drugs, amino acids, peptides and proteins) have been used to evaluate possible applications for these nanomaterial‐based methods. The use of nanomaterials in columns, capillaries and planar chromatography has been considered as part of these efforts. Potential advantages of nanomaterials in these applications have included their good chemical and physical stabilities, the variety of interactions many nanomaterials can have with analytes, and their unique retention properties in some separation formats.
Preparation and characterization of a Cu (II)‐IDA poly HEMA monolith syringe for proteomic applications
Authors: Khaparde Ashish , M. A. Vijayalakshmi , Tetala Kishore K. R. 
Published: August 2017

AbstractHerein, we report the preparation of a metal‐chelate immobilized hydrophilic poly hydroxyethylmethacrylate‐based monolith of 100 μL volume in a plastic syringe. The monolith is elastic in nature, contains well interconnected pores with a permeability (k) of 1.3 × 10−12 m2. Immobilization of iminodiacetic acid (IDA) is performed via schiff base reaction. Adsortion of IgG on this copper‐IDA monolith is of langmuir isotherm with a maximum adsorption capacity of ∼25 mg IgG per g monolith. IgG adsorption capacity of this affinity monolith remained unaffected with increase of flow rate. This proposed metal‐chelate monolith in syringe format has the potential for application in proteomics.
Embodiment Mediates the Relationship between Avoidant Attachment and Eating Disorder Psychopathology
Authors: Monteleone Alessio Maria , Castellini Giovanni , Ricca Valdo , Volpe Umberto , De Riso Francesco , Nigro Massimiliano , Zamponi Francesco , Mancini Milena , Stanghellini Giovanni , Monteleone Palmiero , Treasure Janet , Maj Mario 
Published: August 2017

AbstractObjectiveThe overvaluation of body shape and weight of persons with eating disorders (EDs) is putatively explained by a disturbance in the way they experience their own body (embodiment). Moreover, attachment disorders seem to promote the use of body as source for self‐definition. Therefore, we assessed the role of embodiment in the connection between attachment styles and ED psychopathology.MethodOne‐hundred and thirteen ED patients and 117 healthy subjects completed the Identity and Eating Disorders (IDEA) Questionnaire, the Eating Disorder Inventory‐2 (EDI‐2) and the Experiences in Close Relationships Scale.ResultsEating disorder patients displayed IDEA, EDI‐2 and Experiences in Close Relationships scores significantly higher than controls. IDEA total and subtotal scores mediated entirely the influence of avoidant attachment on EDI‐2 interoceptive awareness and impulsivity.DiscussionThese findings demonstrate a relationship between insecure attachment and disorders of identity and embodiment and point to embodiment as a possible mediator between avoidant attachment and specific ED psychopathological traits. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.
The influence of climate and microclimate (aspect) on soil creep efficiency: Cinder cone morphology and evolution along the eastern Mediterranean Golan Heights
Authors: Ben‐Asher Matan , Haviv Itai , Roering Joshua J. , Crouvi Onn 
Published: August 2017

AbstractAlthough hillslope evolution has been subject to much investigation for more than a century, the effect of climate on the morphology of soil‐mantled hillslopes remains poorly constrained. In this study, we perform numerical simulations of volcanic cinder cones in the Golan Heights (eastern Mediterranean) to estimate soil transport efficiency across a significant north–south gradient in mean annual precipitation (1100 to 500 mm). We use the initial cinder cone morphology (constrained by stratigraphy), the modern hillslope form (surveyed with sub‐meter accuracy) and the eruption age (based on 40Ar–39Ar chronology) to predict the best‐fit value of the soil transport coefficient (‘diffusivity’) based on a nonlinear transport model. Our results indicate that the best‐fit diffusivity (K) varies from 1 to 6 m2 ka−1 among the five cinder cones in our field area. Diffusivity (K) values vary systematically with precipitation and hillslope aspect; specifically, K is higher on south‐facing (drier) hillslopes and decreases with mean annual precipitation. We interpret this climate dependency to reflect vegetation‐driven variations in apparent soil cohesion, which increases with root network density, and attenuation of rain splash and overland flow erosion, which increases with vegetative ground cover. To assess how vegetative root mass and ground cover vary with precipitation and aspect, we quantified the spatial distribution of NDVI (normalized difference vegetation index) from ASTER satellite images and observed spatial variations that correlate with our calibrated values of K. Analysis of previously studied cinder cones in the USA can be used to extend our framework to arid domains. This endeavor suggests a humped relationship between K and precipitation with maximum diffusivity at mean annual precipitation of 400–600 mm. Copyright © 2017 John Wiley & Sons, Ltd.
Examining Students' Ability to Critique Arguments and Exploring the Implications for Assessment and Instruction
Authors: Song Yi , Deane Paul , Fowles Mary 
Published: August 2017

AbstractThis study assessed 1,706 eighth‐grade students' reasoning abilities through a critique task in an integrated argumentative reading and writing test. Results indicate that the majority of students did not detect fallacious arguments or clearly explain problems in the arguments. They encountered various challenges in critiquing an argument: (a) being off‐task, (b) failing to identify fallacious arguments, (c) having difficulty explaining specific problems in reasoning, and (d) not connecting their criticisms with particular parts of the text being critiqued. Task design and instructional implications are discussed.
Variational multiscale approximation of the one‐dimensional forced Burgers equation: The role of orthogonal subgrid scales in turbulence modeling
Authors: Bayona Camilo , Baiges Joan , Codina Ramon 
Published: August 2017

SummaryA numerical approximation for the one‐dimensional Burgers equation is proposed by means of the orthogonal subgrid scales–variational multiscale (OSGS‐VMS) method. We evaluate the role of the variational subscales in describing the Burgers “turbulence” phenomena. Particularly, we seek to clarify the interaction between the subscales and the resolved scales when the former are defined to be orthogonal to the finite‐dimensional space. Direct numerical simulation is used to evaluate the resulting OSGS‐VMS energy spectra. The comparison against a large eddy simulation model is presented for numerical discretizations in which the grid is not capable of solving the small scales. An accurate approximation to the phenomena of turbulence is obtained with the addition of the purely dissipative numerical terms given by the OSGS‐VMS method without any modification of the continuous problem.
Procedure to select test organisms for environmental risk assessment of genetically modified crops in aquatic systems
Authors: Hilbeck Angelika , Bundschuh Rebecca , Bundschuh Mirco , Hofmann Frieder , Oehen Bernadette , Otto Mathias , Schulz Ralf , Trtikova Miluse 
Published: July 2017

Abstract

For a long time, the environmental risk assessment (ERA) of genetically modified (GM) crops focused mainly on terrestrial ecosystems. This changed when it was scientifically established that aquatic ecosystems are exposed to GM crop residues that may negatively affect aquatic species. To assist the risk assessment process, we present a tool to identify ecologically relevant species usable in tiered testing prior to authorization or for biological monitoring in the field. The tool is derived from a selection procedure for terrestrial ecosystems with substantial but necessary changes to adequately consider the differences in the type of ecosystems. By using available information from the Water Framework Directive (2000/60/EC), the procedure can draw upon existing biological data on aquatic systems. The proposed procedure for aquatic ecosystems was tested for the first time during an expert workshop in 2013, using the cultivation of Bacillus thuringiensis (Bt) maize as the GM crop and 1 stream type as the receiving environment in the model system. During this workshop, species executing important ecological functions in aquatic environments were identified in a stepwise procedure according to predefined ecological criteria. By doing so, we demonstrated that the procedure is practicable with regard to its goal: From the initial long list of 141 potentially exposed aquatic species, 7 species and 1 genus were identified as the most suitable candidates for nontarget testing programs. Integr Environ Assess Manag 2017;13:974–979. © 2017 SETAC

Key Points
A species selection procedure is described to identify potential test species that are likely exposed in the field and may be at risk to suffer from the cultivation of genetically modified (GM) crops. Thereby this procedure could support the environmental risk assessment of GM crops. Potential improvements for the selection procedure are discussed.
Risk of appendiceal endometriosis among women with deep‐infiltrating endometriosis
Authors: Moulder Janelle K. , Siedhoff Matthew T. , Melvin Kathryn L. , Jarvis Elizabeth G. , Hobbs Kumari A. , Garrett Joanne 
Published: July 2017

AbstractObjectiveTo determine whether deep‐infiltrating endometriosis (DE) carries an increased risk of appendiceal endometriosis (AppE) as compared with superficial endometriosis or no endometriosis.MethodsIn a retrospective study, data were obtained by chart review of an internal database for women who underwent coincidental appendectomy during benign gynecologic surgery between July 2009 and February 2014 at a tertiary referral center in the USA. Univariate, bivariate, and regression analyses were performed. The primary exposure was surgically documented endometriosis (DE, superficial, or no endometriosis). The primary outcome was AppE.ResultsEndometriosis was diagnosed for 151 (38.2%) of 395 women; 82 (54.3%) had DE. The prevalence of AppE was 13.2% (52/395) overall; 8 (11.6%) of 69 women with superficial endometriosis and 32 (39.0%) of 82 with DE were affected. Frequency of AppE was increased among women with DE, abnormal appendix appearance, and surgical indication (all P<0.001). Women with DE had a 5.9‐fold (95% confidence interval [CI] 2.9–11.9) higher risk of AppE compared with women without endometriosis, controlling for appendiceal appearance and surgical indication, and a 2.7‐fold (95% CI 1.2–6.2) higher risk of AppE compared with those with superficial endometriosis.ConclusionWomen with DE have increased risk of AppE. Coincidental appendectomy should form part of complete endometriosis excision for these patients.