bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lightning activity in the Mediterranean: quantification of cyclones contribution and relation to their intensity
Authors: Galanaki Elissavet , Flaounas Emmanouil , Kotroni Vassiliki , Lagouvardos Konstantinos , Argiriou Athanassios 
Published: August 2016

AbstractA 10‐year data set of intense Mediterranean cyclones was used for a twofold objective: first to quantify the cyclone's contribution to lightning occurrence in the region and second to investigate potential connection of lightning with cyclones intensity. For this reason, we used cyclone tracks, lightning observations and reanalysis from the European Centre for Medium Range Weather Forecasts, for the 10‐year period of 2005–2014. Results showed that intense cyclones provoke <10% of lightning activity over the Mediterranean Sea, however, in certain areas, cyclone contributions might reach 20–30%.The intense cyclones, which are associated with lightning activity close to their centre, constitute about one third (36%) of the total number of tracked cyclones. Therefore two cyclone groups are identified: those associated with and those without lightning. The first group presents in average 35% more ice and 15% more liquid cloud water content within the upper and lower atmospheric levels, respectively, while is related to approximately three times greater values of convective available potential energy in average. Further analysis shows that the intensities of the cyclones in the two groups present no significant differences, suggesting that deep convection may not be a major mechanism for the occurrence of intense Mediterranean cyclones. Finally, we show that cyclones associated with lightning present the highest lightning activity about 6 h prior to the cyclones maximum intensity.
Genome‐Wide Assessment of the Binding Effects of Artificial Transcriptional Activators by High‐Throughput Sequencing
Authors: Chandran Anandhakumar , Syed Junetha , Li Yue , Sato Shinsuke , Bando Toshikazu , Sugiyama Hiroshi 
Published: August 2016

AbstractOne of the major goals in DNA‐based personalized medicine is the development of sequence‐specific small molecules to target the genome. SAHA‐PIPs belong to such class of small molecule. In the context of the complex eukaryotic genome, the differential biological effects of SAHA‐PIPs are unclear. This question can be addressed by identifying the binding regions across the genome; however, it is a challenge to enrich small‐molecule‐bound DNA without chemical crosslinking. Here, we developed a method that employs high‐throughput sequencing to map the binding area of small molecules throughout the chromatinized human genome. Analysis of the sequenced data confirmed the presence of specific binding sites for SAHA‐PIPs from the enriched sequence reads. Mapping the binding sites and enriched regions on the human genome clarifies the reason for the distinct biological effects of SAHA‐PIP. This approach will be useful for identifying the function of other small molecules on a large scale.
Minimalist Antibodies and Mimetics: An Update and Recent Applications
Authors: Bruce Virginia J. , Ta Angeline N. , McNaughton Brian R. 
Published: August 2016

AbstractThe immune system utilizes antibodies to recognize foreign or disease‐relevant receptors, initiating an immune response to destroy unwelcomed guests. Because researchers can evolve antibodies to bind virtually any target, it is perhaps unsurprising that these reagents, and their small‐molecule conjugates, are used extensively in clinical and basic research environments. However, virtues of antibodies are countered by significant challenges. Foremost among these is the need for expression in mammalian cells (largely due to often necessary post‐translational modifications). In response to these challenges, researchers have developed an array of minimalist antibodies and mimetics, which are smaller, more stable, simpler to express in Escherichia coli, and amendable to laboratory evolution and protein engineering. Here we describe these scaffolds and discuss recent applications of minimalist antibodies and mimetics.
SMT‐based context‐bounded model checking for CUDA programs
Authors: Pereira Phillipe , Albuquerque Higo , da Silva Isabela , Marques Hendrio , Monteiro Felipe , Ferreira Ricardo , Cordeiro Lucas 
Published: August 2016

SummaryWe present ESBMC‐GPU tool, an extension to the Efficient SMT‐Based Context‐Bounded Model Checker (ESBMC), which is aimed at verifying Graphics Processing Unit (GPU) programs written for the Compute Unified Device Architecture (CUDA) platform. ESBMC‐GPU uses an operational model, that is, an abstract representation of the standard CUDA libraries, which conservatively approximates their semantics, in order to verify CUDA‐based programs. It then explicitly explores the possible interleavings (up to the given context bound), while treats each interleaving itself symbolically. Additionally, ESBMC‐GPU employs the monotonic partial order reduction and the two‐thread analysis to prune the state space exploration. Experimental results show that ESBMC‐GPU can successfully verify 82% of all benchmarks, while keeping lower rates of false results. Going further than previous attempts, ESBMC‐GPU is able to detect more properties violations than other existing GPU verifiers due to its ability to verify errors of the program execution flow and to detect array out‐of‐bounds and data race violations. Copyright © 2016 John Wiley & Sons, Ltd.
Methods for the Detection of Autophagy in Mammalian Cells
Authors: Zhang Ziyan , Singh Rajat , Aschner Michael 
Published: August 2016

AbstractMacroautophagy (hereafter referred to as autophagy) is a degradation pathway that delivers cytoplasmic materials to lysosomes via double‐membraned vesicles designated autophagosomes. Cytoplasmic constituents are sequestered into autophagosomes, which subsequently fuse with lysosomes, where the cargo is degraded. Autophagy is a crucial mechanism involved in many aspects of cell function, including cellular metabolism and energy balance; alterations in autophagy have been linked to various human pathological processes. Thus, methods that accurately measure autophagic activity are necessary. In this unit, we introduce several approaches to analyze autophagy in mammalian cells, including immunoblotting analysis of LC3 and p62, detection of autophagosome formation by fluorescence microscopy, and monitoring autophagosome maturation by tandem mRFP‐GFP fluorescence microscopy. Overall, we recommend a combined use of multiple methods to accurately assess the autophagic activity in any given biological setting. © 2016 by John Wiley & Sons, Inc.
Neural plasticity following lesions of the primate occipital lobe: The marmoset as an animal model for studies of blindsight
Authors: Hagan Maureen A. , Rosa Marcello G. P. , Lui Leo L. 
Published: August 2016

ABSTRACTFor nearly a century it has been observed that some residual visually guided behavior can persist after damage to the primary visual cortex (V1) in primates. The age at which damage to V1 occurs leads to different outcomes, with V1 lesions in infancy allowing better preservation of visual faculties in comparison with those incurred in adulthood. While adult V1 lesions may still allow retention of some limited visual abilities, these are subconscious—a characteristic that has led to this form of residual vision being referred to as blindsight. The neural basis of blindsight has been of great interest to the neuroscience community, with particular focus on understanding the contributions of the different subcortical pathways and cortical areas that may underlie this phenomenon. More recently, research has started to address which forms of neural plasticity occur following V1 lesions at different ages, including work using marmoset monkeys. The relatively rapid postnatal development of this species, allied to the lissencephalic brains and well‐characterized visual cortex provide significant technical advantages, which allow controlled experiments exploring visual function in the absence of V1. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 314–327, 2017
Comparison of trout hepatocytes and liver S9 fractions as in vitro models for predicting hepatic clearance in fish
Authors: Fay Kellie A. , Fitzsimmons Patrick N. , Hoffman Alex D. , Nichols John W. 
Published: August 2016

Abstract

Isolated hepatocytes and liver S9 fractions have been used to collect in vitro biotransformation data for fish as a means of improving modeled estimates of chemical bioaccumulation. To date, however, there have been few direct comparisons of these 2 methods. In the present study, cryopreserved trout hepatocytes were used to measure in vitro intrinsic clearance rates for 6 polycyclic aromatic hydrocarbons (PAHs). These rates were extrapolated to estimates of in vivo intrinsic clearance and used as inputs to a well stirred liver model to predict hepatic clearance. Predicted rates of hepatic clearance were then evaluated by comparison with measured rates determined previously using isolated perfused livers. Hepatic clearance rates predicted using hepatocytes were in good agreement with measured values (&lt;2.1-fold difference for 5 of 6 compounds) under 2 competing binding assumptions. These findings, which may be attributed in part to high rates of PAH metabolism, are similar to those obtained previously using data from liver S9 fractions. For 1 compound (benzo[a]pyrene), the in vivo intrinsic clearance rate calculated using S9 data was 10-fold higher than that determined using hepatocytes, possibly due to a diffusion limitation on cellular uptake. Generally, however, there was good agreement between calculated in vivo intrinsic clearance rates obtained using either in vitro test system. These results suggest that both systems can be used to improve bioaccumulation assessments for fish, particularly when vitro rates of activity are relatively high, although additional work is needed to determine if the chemical domain of applicability for each system differs. Environ Toxicol Chem 2017;36:463–471. Published 2016 SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
Activating Metal Sites for Biological Electron Transfer
Authors: Solomon Edward I. , Hadt Ryan G. , Snyder Benjamin E. R. 
Published: August 2016

AbstractThis review focuses on the unique spectroscopic features of the blue copper active sites. These reflect a novel electronic structure that activates the site for rapid long‐range electron transfer in its biological function. The role of the protein in determining the geometric and electronic structure of this site is defined, as is its contribution to function. This has been referred to as the entatic/rack‐induced state. These concepts are then extended to cytochrome c, which is also determined to be in an entatic state.
Comparative performance of airyscan and structured illumination superresolution microscopy in the study of the surface texture and 3D shape of pollen
Authors: Sivaguru Mayandi , Urban Michael A. , Fried Glenn , Wesseln Cassandra J. , Mander Luke , Punyasena Surangi W. 
Published: August 2016

AbstractThe visualization of taxonomically diagnostic features of individual pollen grains can be a challenge for many ecologically and phylogenetically important pollen types. The resolution of traditional optical microscopy is limited by the diffraction of light (250 nm), while high resolution tools such as electron microscopy are limited by laborious preparation and imaging workflows. Airyscan confocal superresolution and structured illumination superresolution (SR‐SIM) microscopy are powerful new tools for the study of nanoscale pollen morphology and three‐dimensional structure that can overcome these basic limitations. This study demonstrates their utility in capturing morphological details below the diffraction limit of light. Using three distinct pollen morphotypes (Croton hirtus, Dactylis glomerata, and Helianthus sp.) and contrast‐enhancing fluorescent staining, we were able to assess the effectiveness of the Airyscan and SR‐SIM. We further demonstrate that these new superresolution methods can be easily applied to the study of fossil pollen material.
The Association of Combat Exposure With Postdeployment Behavioral Health Problems Among U.S. Army Enlisted Women Returning From Afghanistan or Iraq
Authors: Adams Rachel Sayko , Nikitin Ruslan V. , Wooten Nikki R. , Williams Thomas V. , Larson Mary Jo 
Published: August 2016

AbstractAn association between combat exposure and postdeployment behavioral health problems has been demonstrated among U.S. military service members returning from Afghanistan or Iraq in predominantly male samples, yet few studies have focused on the experiences of women. Using data from the longitudinal, observational Substance Use and Psychological Injury Combat (SUPIC) Study, we explored the self‐report of 4 combat exposure items and postdeployment behavioral health screening results for 42,397 Army enlisted women who had returned from Afghanistan or Iraq from fiscal years 2008 through 2011. We ran multivariate logistic regression models to examine how a constructed composite combat exposure score (0, 1, 2, 3+) was associated with screening positive postdeployment for posttraumatic stress disorder (PTSD), depression, and at‐risk drinking among active duty (AD) and National Guard/Reserve (NG/R) women. AD and NG/R women commonly reported being wounded, injured, assaulted, or hurt (17.3% and 29.0%, respectively). In all 6 multivariate models, Army women with any report of combat exposure had increased odds of the behavioral health problem (i.e., PTSD, depression, or at‐risk drinking). The magnitude of the association between combat exposure and PTSD was most striking, indicating increased odds of PTSD as combat exposure score increased. AD and NG/R women with a combat exposure score of 3+ had increased odds of PTSD, 20.7, 95% confidence interval (CI) [17.0, 25.1] and 27.8, 95% CI [21.0, 36.9], respectively. Women who report combat exposure may benefit from early prevention and confidential intervention to promote postdeployment health and reduce long‐term behavioral health problems.
Synthesis of High Molecular Weight Polyetherethersulfone‐Allyl Copolymers of Controlled Glass Transition
Authors: Faye Adrien , Furtos Alexandra , Brisson Josée 
Published: August 2016

Polyetherethersulfones with double bonds inserted along the main polymer chain are synthesized by polycondensation. The glass transition is modulated by increasing the size of aromatic etherethersulfone rigid blocks and decreasing the ratio of flexible allyl segments which contain a double bond. Resulting copolymers have a Mn of up to 60 000 g mol−1, moderate polydispersity indices (Đ or Ip) of 1.70 to 2.11, and are shown, by the presence of a single glass transition temperature in differential scanning calorimetry and by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry, to be random. The glass transition of copolymers follows the Gordon–Taylor relationship. The thermal resistance of copolymers increases when decreasing the amount of the flexible segment and increasing the length of the rigid block. Chemical aging of films is investigated by immersion in bleach, which is commonly used to clean membranes. Films show high resistance to bleach, therefore making this approach relevant to membrane fabrication.
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Synthetic Mimics of Antimicrobial Peptides (SMAMPs) in Layer‐by‐Layer Architectures: Possibilities and Limitations
Authors: Dorner Franziska , Malek‐Luz Alicia , Saar Julia S. , Bonaus Sebastian , Al‐Ahmad Ali , Lienkamp Karen 
Published: August 2016

Polymer‐based synthetic mimics of antimicrobial peptides (SMAMPs) show promising antimicrobial activity in solution and as surface‐attached networks. In this paper, their potential as active ingredients in layer‐by‐layer (LbL) assemblies is evaluated. These consist of the weak, anionic polyelectrolyte poly(acrylic acid), and either the hydrophobic butyl SMAMP or the hydrophilic diamine SMAMP (both of which are cationic, weak polyelectrolytes). In situ surface plasmon resonance spectroscopy is used to optimize the LbL assembly conditions. An “overshooting” is observed when depositing the SMAMP layer. Zeta potential measurements show that the layer charge inversion is reduced at each build‐up step due to layer interpenetration. Thus, the positive charge of LbL assemblies with SMAMPs as the top layer is low; a significant part is consumed to maintain layer stability. This leads to reduced antimicrobial activity. Fine‐tuning of the assembly and post‐treatment conditions leads to SMAMP‐PAA LbL systems with optimized antimicrobial activity and stability.
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Diffusion‐weighted DESS protocol optimization for simultaneous mapping of the mean diffusivity, proton density and relaxation times at 3 Tesla
Authors: Gras Vincent , Farrher Ezequiel , Grinberg Farida , Shah N. Jon 
Published: August 2016

PurposeTo design a general framework for the optimization of an MRI protocol based on the the diffusion‐weighted dual‐echo steady‐state (DW‐DESS) sequence, enabling quantitative and simultaneous mapping of proton density (PD), relaxation times
and
and diffusion coefficient D.MethodsA parameterization of the DW‐DESS sequence minimizing the Cramér‐Rao lower bound of each parameter estimate was proposed and tested in a phantom experiment. An extension of the protocol was implemented for brain imaging to return the rotationally invariant mean diffusivity (MD).ResultsIn an NiCl2‐doped agar gel phantom wherein
ms, the parameter estimation errors were below 3% for PD and
and below 7% for
and D while the measured signal‐to‐noise ratio always exceeded 20. In the human brain, the in vivo parametric maps obtained were overall in reasonable agreement with gold standard measurements, despite a broadening of the distributions due to physiological motion.ConclusionWithin the optimization framework presented here, DW‐DESS images can be quantitatively interpreted to yield four intrinsic parameters of the tissue. Currently, the method is limited by the sensitivity of the DW‐DESS sequence in terms of physiological motion. Magn Reson Med 78:130–141, 2017. © 2016 International Society for Magnetic Resonance in Medicine
Funken im Labor: kleine Brüder der Blitze
Authors: Vollmer Michael , Möllmann Klaus‐Peter 
Published: August 2016

AbstractBlitze haben die Menschen schon jeher fasziniert [1], und die wissenschaftliche Blitzforschung ist seit langem ein eigenes Spezialgebiet. Ihre räumliche Ausbreitung kann man mit Hochgeschwindigkeits‐Videos sehr gut beobachten, wenn man einen Blitz gerade erwischt. Im Labor lassen sich die kleineren Brüdern der Blitze, die Funken, zwar kontrolliert erzeugen, ihre Beobachtung ist aber wegen der schnelleren zeitlichen Entwicklung schwierig.Dieser Artikel wurde aus technischen Problemen doppelt veröffentlicht 10.1002/piuz.201690047.
Folding recombinant spider‐silk in H2O: Effect of osmolytes on the solution conformation of a 15‐repeat spider‐silk mimetic
Authors: McLachlan Glendon D. , Gandjian Babak , Alhumaidan Hind 
Published: August 2016

AbstractThe folding of a recombinant spider silk protein‐polymer in the presence of the tri‐methylamine osmolytes TMANO and Betaine in 80% H2O is reported. Circular dichroism measurements (CD) reveal an increase in α‐helical secondary structure with increasing osmolyte concentrations, as determined by an increase in ellipticity at 222 nm. Consistent with this observation, the signal for random coil sampling, observed at 205 nm, is greatly reduced with increasing trimethylamine. Fluorescence spectra of a single tyrosine positioned within the conserved 33‐amino acid repeat primary sequence (of the spider‐silk mimetic) complements the conformational changes observed by CD. Importantly, there is a correlation between the number of Alkyl‐groups (CH3‐) on the amine of the osmolyte and enhanced helicity of the 15‐repeat silk‐mimetic for the osmolytes tested, ie TMANO, Betaine, Sarcosine and Glycine. These preliminary results are applicable to storing and processing recombinant silk sequences in H2O, an important mile‐stone for widespread use of recombinant silk polymers.
Transport through graphene nanoribbons: Suppression of transverse quantization by symmetry breaking
Authors: Libisch Florian , Kliman Andrej , Rotter Stefan , Burgdörfer Joachim 
Published: August 2016

AbstractWe investigate transport through graphene nanoribbons in the presence of disorder scattering. We show that size quantization patterns are only present when pseudospin symmetry is preserved. Symmetry breaking disorder strongly suppresses signatures of transverse quantization due to the inherent entanglement of pseudospin and transverse quantum numbers in graphene. To quantitatively distinguish the influence of symmetry breaking and symmetry conserving disorder on transport, we consider weak localization: we observe a transition from weak antilocalization to weak localization as symmetry‐breaking disorder is introduced. We discuss implications for experimental observations of size quantization signatures.
The selected matrix influences the matrix‐assisted laser desorption/ionization time‐of‐flight mass spectral patterns of partially deuterated glycosaminoglycan disaccharides
Authors: Nimptsch Ariane , Schiller Jürgen 
Published: August 2016

RationaleIf carbohydrates are investigated by nuclear magnetic resonance (NMR) spectroscopy, they are normally dissolved in deuterated solvents, such as D2O. The incorporation of deuterium leads to a high complexity of subsequently recorded mass spectra and reduced sensitivity because different deuterated ions become detectable. Here, we demonstrate that the applied matrix‐assisted laser desorption/ionization (MALDI) matrix solution has a considerable impact on the observed isotopic distribution.MethodsUnsaturated disaccharides of chondroitin (CS) and dermatan sulfate (DS) were prepared by enzymatic digestion of the polysaccharides in D2O and analyzed by MALDI time‐of‐flight mass spectrometry (TOF MS) using 2,5‐dihydroxybenzoic acid (DHB) and 9‐aminoacridine (9‐AA) according to previously published protocols.ResultsThe extent of deuteration of a given compound can be easily determined by using the mass shift between the non‐deuterated and deuterated ions. However, such a determination is more difficult when considering sugars due to their high content of exchangeable groups. Therefore, both the solvent and the matrix have a considerable impact on the MS patterns. Additionally, there are significant differences if the spectra are recorded at different laser fluences.ConclusionsGreat caution should be taken when the deuterium content of disaccharides is determined by MALDI MS. Aside from the use of non‐protic solvents, DHB is the matrix of choice, whereas 9‐AA shows a considerable influence on the observed isotope pattern in dependence on the applied laser fluence. Copyright © 2016 John Wiley & Sons, Ltd.