bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why Pressure Scales Cause So Much Confusion
Authors: Buonaquisti Anthony D 
Published: March 2018

Abstract
Pressure scales can be extremely confusing to new operators. This is not surprising. To my mind, there are three primary areas of confusion.
Firstly, the pressure of gas inside an instrument changes over many orders of magnitude during pumpdown. The change is about 9 orders of magnitude for a traditional Scanning Electron Microscope and about 13 orders of magnitude for an ultra-high vacuum instrument such as a Scanning Auger Microprobe.
To give an idea about the scale of change involved in vacuum, consider that the change in going from ambient pressure to that inside a typical ultra high vacuum system is like comparing one meter with the mean radius of the planet Pluto's orbit. The fact is that we don't often get to play with things on that scale. As a consequence, many of us have to keep reminding ourselves that 1 X 10-3 is one thousand times the value of 1 X 10-6 - not twice the value.
Breaking Old Rules
Authors: Carmichael Stephen W 
Published: March 2018

Abstract
It has been dogma for more than a hundred years that the light microscope cannot resolve structures that are much closer together than the length of the wavelength of light. This limit is on the order of a few hundred nanometers. This rule was “broken” by using the electron beam as the illumination source. The shorter wavelength of the electron beam gave correspondingly better resolution, down in the nanometer range. The rule was “broken” again when non-optical scanning probe microscopes (such as the scanning tunneling and atomic force microscopes) were developed. This technology gave us resolution in the sub-nanometer range, imaging individual atoms and molecules. However, scanning probe microscopes scan the surface of the specimen, excluding what's underneath from our view.
Exploring the Detection Limits of Chemical Microscopy
Authors: Milne C , Morris C , MacDonald HS 
Published: March 2018

Abstract
Chemical microscopy techniques were once a major source of information for scientists who wanted to detect the presence of metals in samples. Many microscopists used such techniques, which, when properly applied and appropriate checks for interferences made, could conclusively prove the presence of small quantities of specific metals.
The fact that the identification could be conclusive for trace amounts following relatively simple and cheap processes, and that visual evidence resulted, made these techniques quite robust, Chamot and Mason's lest “Handbook of Chemical Microscopy” is held to be a definitive resource for these techniques1. With the development of absorpilon and emission based spectral analytical techniques, the application of chemical microscopy techniques dwindled, perhaps because the skills needed by analysts using spectral techniques were to be more rapidly acquired than those involving microscopy,
Some Reflections On How Much Information la There On A Piece Of Film, On How Film Compares With CCD Cameras And What Features A Scanner Would Meed To Digitize TEM Negatives
Authors: Eades Alwyn 
Published: March 2018

Abstract
The world of electron microscopy is in a period of transition from acquiring images on film to acquiring images digitally, using CCD cameras, for example. It would be useful to knew how much information there is on a piece of film, in order to know how film compares with digital methods and to be able to make good judgements on the optimum moment to change from one technology to the other.
This is an attempt to use simple arguments to estimate just how much information there is in an image exposed on film in the transmission electron microscope, the main reason for addressing this issue Is that, while many people are affected by it there seems to be little agreement on the answer.
Uranium Is The Issue
Authors: Soeldner Al 
Published: March 2018

Abstract
Uranium compounds, especially uranyl acetate, have been widely and routinely used as transmission electron microscopy centrist stains for biological materials since 1958. Those of us who do TEM of biologicals use small quantities of uranyl acetate, nitrate, formate, sulfate and perhaps other uranium compounds almost daily and therefore keep inventories of these salts and their solutions.
In the 1980's growing concerns about medical and research wastes entering regional dump sites prompted state radiation officials in Oregon to begin tightening the regulations for monitoring and controlling all radioactive substances including the uranium compounds commonly used in processing biological specimens for TEM.
The Champagne Artifact in Negative Staining TEM
Authors: Bozzola John J 
Published: March 2018

Abstract
Negative staining is a simple yet extremely useful procedure for examining nanometer-sized specimens such as intact microorganisms (viruses and some bacteria), subcellular components, and even nonbidogical particulates. It is a well established procedure, with extensive literature in many disciplines (Hayat and Miller, 1990). Although numerous variations exist, the basic procedure involves placing the specimen and stain onto a grid containing a substrate - usually plastic with or without a carbon backing. The stains consist of salts of heavy metals such as tungsten, uranium, or molybdenum which surround and often penetrate the specimen. Afier drying into an amorphous, glass-like background, the stains provide contrast based upon differential thickness.
The Nematode Caenorhabditis elegans A Model Animal “Made for Microscopy”
Authors: Hall David H 
Published: March 2018

Abstract
The small unassuming nematode, Caenorhabditis elegans is only one millimeter long and lives in the soil munching on bacteria. While many nematode (roundworm) species are parasites with medical or agricultural importance, C. elegans seems to harm no one. Yet, this animal has attained a status in medical science that compares to more complex organisms such as the mouse or fruit fly in its utility for scientific discovery. It has been the subject of thousands of studies dealing with topics as diverse as nutrition, aging, and nervous system development. About 5000 scientists are now pursuing this single species in hundreds of laboratories worldwide. In 2002, the Nobel Prize in Medicine was awarded to three of the pioneers in establishing C. elegans as a “model organism“: Sydney Brenner, John Sulston, and H. Robert Horvitz. Why study worms?
Sydney Brenner first turned his attention to C. elegans in the 1960's. Working at the Medical Research Council in England, he was looking for a small animal with inexpensive tastes that could be easily cultured in the laboratory.
Lightning and the Electron Microscope
Authors: Rivaud Lydia 
Published: March 2018

Abstract
The chain of events that led to the invention of the electron microscope is an interesting story by itself. This chain has a common theme, namely electrons, and its first link is a natural phenomenon: lightning.
A flash of lightning generates a stream of electrons with a potential energy difference of 100 to 200 megavolts between clouds acting as electrodes, Benjamin Franklin envisioned this as a source of energy and tried to snatch electricity from the skies, but this proved to be too dangerous.
At the beginning of the century, lightning was a problem for electrical utilities because it produced surges that disrupted the steady flow of electricity along high tension lines. For this reason, in 1929 a high tension laboratory was founded in Germany with the sole aim of finding a way to test electrical transmission lines so as to make them capable of withstanding the lightning surges.
Modern Microscopy on The Light Side: An Instrumental Approach to Small Particle Identification
Authors: Gavrilovic John 
Published: March 2018

Abstract
Developments in space exploration, microelectronics, and other high-tech industries have promoted cleanroom technology and increased the need to identify particles sometimes too small to handle with the polarizing light microscope. Light microscopy has traditionally been the most commonly used technique for small particle identification and many microscopists are very proficient in identifying particles using a polarizing light microscope as the principal investigative tool. The polarizing light microscope, in the hands of a good microscopist, is an extremely efficient instrument for particles down to a few micrometers in size. However, in the size range below 5 pm, an instrumental approach to small particle identification is essential. The development of electron microbeam instruments in the early '60s and 70s introduced a new dimension to small particle identification. In these instruments, particles of 1 urn and smaller can be chemically identified when chemical characterization of particles is combined with cathodoluminesence and a relatively simple optical characterization in the instrument itself.
Photon Tunneling Microscopy
Authors: Guerra John M 
Published: March 2018

Abstract
The Photon Tunneling Microscope is used to provide high resolution (subnanometer vertical), quantifiable, real-time, 3-D (with continuously variable viewpoint) imaging and profilometry of homogenous dielectric samples, whether transparent or absorbing. A partial list of these includes: thin films (micraroughness. damage evaluation, step height) optical storage media (pit depth and shape measurement), magnetic media (microroughness, wear tracks), polymers (surface characterization), optical surfaces (microroughness, damage, polishing evaluation), diamond-turned optical surfaces (tool and machine characteristics from surface topography), binary optic surfaces, porous silicon structure, photographic grain analysis, replicas of metal surfaces, microlithography evaluation, and manufacturing web evaluation (film base, magnetic media base).
Prebiotic attenuation of olanzapine-induced weight gain in rats: analysis of central and peripheral biomarkers and gut microbiota
Authors: Kao Amy Chia-Ching , Spitzer Sonia , Anthony Daniel C. , Lennox Belinda , Burnet Philip W. J. 
Published: March 2018

AbstractOlanzapine is an effective antipsychotic drug but since it causes significant weight gain, it is not well tolerated by psychosis patients. The prebiotic, B-GOS®, attenuates metabolic dysfunction in obese subjects, and in rodents, alters central NMDA receptors and may affect serotonin receptors that are relevant in psychosis. We have determined whether B-GOS®influenced olanzapine-associated weight gain and central NMDA and serotonin receptors. Circulating acetate, IL-1β, IL-8 and TNFα, liver acetyl-CoA carboxylase (ACC), white adipose tissue (WAT) acetate receptor GPR43, and specific faecal bacteria genera were also measured to provide mechanistic information. Adult female Sprague-Dawley rats were administered a B-GOS®(0.5 g/kg/day) solution or water for 21 days, and received a single, daily, intraperitoneal injection of olanzapine or saline on days 8–21. The intake of B-GOS®significantly attenuated olanzapine-induced weight gain without altering frontal cortex 5-HT2AR blockade. Cortical GluN1 levels were elevated by olanzapine in the presence of B-GOS®. Plasma acetate concentrations increased following B-GOS®or olanzapine administration alone, but reduced when prebiotic and drug were administered in combination. This pattern was paralleled by hepatic ACC mRNA expression. The abundance of WAT GPR43 mRNA was reduced by olanzapine, only in the absence of B-GOS®. Co-administration of B-GOS®and olanzapine also elevated plasma TNFα, which is reported to influence lipid metabolism. Finally, B-GOS®elevated faecalBifidobacteriumspp. and reduced some bacteria in the Firmicutes phylum, whilst olanzapine treatment either alone or with B-GOS®, was without effect. These data suggest that inclusion of B-GOS®as an adjunct to olanzapine treatment in schizophrenia may prevent weight gain and have benefits on cognitive function in psychosis. The role of acetate in these effects requires further investigation.
Understanding and tailoring ligand interactions in the self-assembly of branched colloidal nanocrystals into planar superlattices
Authors: Castelli Andrea , de Graaf Joost , Marras Sergio , Brescia Rosaria , Goldoni Luca , Manna Liberato , Arciniegas Milena P. 
Published: March 2018

AbstractColloidal nanocrystals can self-assemble into highly ordered superlattices. Recent studies have focused on changing their morphology by tuning the nanocrystal interactions via ligand-based surface modification for simple particle shapes. Here we demonstrate that this principle is transferable to and even enriched in the case of a class of branched nanocrystals made of a CdSe core and eight CdS pods, so-called octapods. Through careful experimental analysis, we show that the octapods have a heterogeneous ligand distribution, resembling a cone wrapping the individual pods. This induces location-specific interactions that, combined with variation of the pod aspect ratio and ligands, lead to a wide range of planar superlattices assembled at an air–liquid interface. We capture these findings using a simple simulation model, which reveals the necessity of including ligand-based interactions to achieve these superlattices. Our work evidences the sensitivity that ligands offer for the self-assembly of branched nanocrystals, thus opening new routes for metamaterial creation.
Suppression of low-frequency charge noise in superconducting resonators by surface spin desorption
Authors: de Graaf S. E. , Faoro L. , Burnett J. , Adamyan A. A. , Tzalenchuk A. Ya. , Kubatkin S. E. , Lindström T. , Danilov A. V. 
Published: March 2018

AbstractNoise and decoherence due to spurious two-level systems located at material interfaces are long-standing issues for solid-state quantum devices. Efforts to mitigate the effects of two-level systems have been hampered by a lack of knowledge about their chemical and physical nature. Here, by combining dielectric loss, frequency noise and on-chip electron spin resonance measurements in superconducting resonators, we demonstrate that desorption of surface spins is accompanied by an almost tenfold reduction in the charge-induced frequency noise in the resonators. These measurements provide experimental evidence that simultaneously reveals the chemical signatures of adsorbed magnetic moments and highlights their role in generating charge noise in solid-state quantum devices.
Inhibitory gain modulation of defense behaviors by zona incerta
Authors: Chou Xiao-lin , Wang Xiyue , Zhang Zheng-gang , Shen Li , Zingg Brian , Huang Junxiang , Zhong Wen , Mesik Lukas , Zhang Li I. , Tao Huizhong Whit 
Published: March 2018

AbstractZona incerta (ZI) is a functionally mysterious subthalamic nucleus containing mostly inhibitory neurons. Here, we discover that GABAergic neurons in the rostral sector of ZI (ZIr) directly innervate excitatory but not inhibitory neurons in the dorsolateral and ventrolateral compartments of periaqueductal gray (PAG), which can drive flight and freezing behaviors respectively. Optogenetic activation of ZIr neurons or their projections to PAG reduces both sound-induced innate flight response and conditioned freezing response, while optogenetic suppression of these neurons enhances these defensive behaviors, likely through a mechanism of gain modulation. ZIr activity progressively increases during extinction of conditioned freezing response, and suppressing ZIr activity impairs the expression of fear extinction. Furthermore, ZIr is innervated by the medial prefrontal cortex (mPFC), and silencing mPFC prevents the increase of ZIr activity during extinction and the expression of fear extinction. Together, our results suggest that ZIr is engaged in modulating defense behaviors.
The prevalence of chaotic dynamics in games with many players
Authors: Sanders James B. T. , Farmer J. Doyne , Galla Tobias 
Published: March 2018

AbstractWe study adaptive learning in a typical p-player game. The payoffs of the games are randomly generated and then held fixed. The strategies of the players evolve through time as the players learn. The trajectories in the strategy space display a range of qualitatively different behaviours, with attractors that include unique fixed points, multiple fixed points, limit cycles and chaos. In the limit where the game is complicated, in the sense that the players can take many possible actions, we use a generating-functional approach to establish the parameter range in which learning dynamics converge to a stable fixed point. The size of this region goes to zero as the number of players goes to infinity, suggesting that complex non-equilibrium behaviour, exemplified by chaos, is the norm for complicated games with many players.
Solutions for maximum coupling in multiferroic magnetoelectric composites by material design
Authors: Jayachandran K. P. , Guedes J. M. , Rodrigues H. C. 
Published: March 2018

AbstractElectrical control of magnetization offers an extra degree of freedom in materials possessing both electric and magnetic dipole moments. A stochastic optimization combined with homogenization is applied for the solution for maximum magnetoelectric (ME) coupling coefficient α of a laminar ME composite with the thickness and orientation of ferroelectric phase as design variables. Simulated annealing with a generalized Monte Carlo scheme is used for optimization problem. Optimal microstructure with single and poly-crystalline configurations that enhances the overall α is identified. It is found that juxtaposing a preferentially oriented ferroelectric material with a ferromagnetic ferrite into a composite would result in manifold increase in magnetoelectric coupling. The interface shear strains are found to be richly contributing to the ME coupling. The preferential orientation of the ferroelectric phase in the optimal ME composite laminate is demonstrated using the optimal pole figure analyses.
Modeling Environmentally-Induced Motor Neuron Degeneration in Zebrafish
Authors: Morrice Jessica R. , Gregory-Evans Cheryl Y. , Shaw Christopher A. 
Published: March 2018

AbstractZebrafish have been used to investigate motor neuron degeneration, including as a model system to examine the pathogenesis of amyotrophic lateral sclerosis (ALS). The use of zebrafish for this purpose has some advantages over otherin vivomodel systems. In the current paper, we show that bisphenol A (BPA) exposure in zebrafish embryos results in motor neuron degeneration with affected motor function, reduced motor axon length and branching, reduced neuromuscular junction integrity, motor neuron cell death and the presence of activated microglia. In zebrafish, motor axon length is the conventional method for estimating motor neuron degeneration, yet this measurement has not been confirmed as a valid surrogate marker. We also show that reduced motor axon length as measured from the sagittal plane is correlated with increased motor neuron cell death. Our preliminary timeline studies suggest that axonopathy precedes motor cell death. This outcome may have implications for early phase treatments of motor neuron degeneration.
Effect of CCL5 expression in the recruitment of immune cells in triple negative breast cancer
Authors: Araujo Jhajaira M. , Gomez Andrea C. , Aguilar Alfredo , Salgado Roberto , Balko Justin M. , Bravo Leny , Doimi Franco , Bretel Denisse , Morante Zaida , Flores Claudio , Gomez Henry L. , Pinto Joseph A. 
Published: March 2018

AbstractTriple negative breast cancer (TNBC) is the most aggressive form of breast cancer with limited options of targeted therapy. Recent findings suggest that the clinical course of TNBC may be modified by the presence of tumor-infiltrating lymphocytes (TILs) and chemokine’s expression, such as CCL5. Diverse studies have shown that CCL5 suppresses anti-tumor immunity and it has been related to poor outcome in different types of cancer while in other studies, this gene has been related with a better outcome. We sought to determine the association of CCL5 with the recruitment of TILs and other immune cells. With this aim we evaluated a retrospective cohort of 72 TNBC patients as well as publicly available datasets. TILs were correlated with residual tumor size after neoadjuvant chemotherapy (NAC) and CCL5 expression. In univariate analysis, TILs and CCL5 were both associated to the distant recurrence free survival; however, in a multivariate analysis, TILs was the only significant marker (HR = 0.336; 95%IC: 0.150–0.753; P = 0.008). CIBERSORT analysis suggested that a high CCL5 expression was associated with recruitment of CD8 T cells, CD4 activated T cells, NK activated cells and macrophages M1. The CD8A gene (encoding for CD8) was associated with an improved outcome in several public breast cancer datasets.
Climate change effect on wheat phenology depends on cultivar change
Authors: Rezaei Ehsan Eyshi , Siebert Stefan , Hüging Hubert , Ewert Frank 
Published: March 2018

AbstractChanging crop phenology is considered an important bio-indicator of climate change, with the recent warming trend causing an advancement in crop phenology. Little is known about the contributions of changes in sowing dates and cultivars to long-term trends in crop phenology, particularly for winter crops such as winter wheat. Here, we analyze a long-term (1952–2013) dataset of phenological observations across western Germany and observations from a two-year field experiment to directly compare the phenologies of winter wheat cultivars released between 1950 and 2006. We found a 14–18% decline in the temperature sum required from emergence to flowering for the modern cultivars of winter wheat compared with the cultivars grown in the 1950s and 1960s. The trends in the flowering day obtained from a phenology model parameterized with the field observations showed that changes in the mean temperature and cultivar properties contributed similarly to the trends in the flowering day, whereas the effects of changes in the sowing day were negligible. We conclude that the single-cultivar concept commonly used in climate change impact assessments results in an overestimation of winter wheat sensitivity to increasing temperature, which suggests that studies on climate change effects should consider changes in cultivars.
Expression of Carbonic Anhydrase III, a Nucleus Pulposus Phenotypic Marker, is Hypoxia-responsive and Confers Protection from Oxidative Stress-induced Cell Death
Authors: Silagi Elizabeth S. , Batista Philip , Shapiro Irving M. , Risbud Makarand V. 
Published: March 2018

AbstractThe integrity of the avascular nucleus pulposus (NP) phenotype plays a crucial role in the maintenance of intervertebral disc health. While advances have been made to define the molecular phenotype of healthy NP cells, the functional relevance of several of these markers remains unknown. In this study, we test the hypothesis that expression of Carbonic Anhydrase III (CAIII), a marker of the notochordal NP, is hypoxia-responsive and functions as a potent antioxidant without a significant contribution to pH homeostasis. NP, but not annulus fibrosus or end-plate cells, robustly expressed CAIII protein in skeletally mature animals. Although CAIII expression was hypoxia-inducible, we did not observe binding of HIF-1α to select hypoxia-responsive-elements on Car3 promoter using genomic chromatin-immunoprecipitation. Similarly, analysis of discs from NP-specific HIF-1α null mice suggested that CAIII expression was independent of HIF-1α. Noteworthy, silencing CAIII in NP cells had no effect on extracellular acidification rate, CO2 oxidation rate, or intracellular pH, but rather sensitized cells to oxidative stress-induced death mediated through caspase-3. Our data clearly suggests that CAIII serves as an important antioxidant critical in protecting NP cells against oxidative stress-induced injury.