bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diffraction‐Unlimited Fluorescence Microscopy of Living Biological Samples Using pcSOFI
Authors: Duwé Sam , Moeyaert Benjamien , Dedecker Peter 
Published: March 2015

AbstractThe complex microscopic nature of many live biological processes is often obscured by the diffraction limit of light, requiring diffraction‐unlimited fluorescence microscopy to resolve them. Because of the vast range of different processes that can be studied, sub‐diffraction imaging should work efficiently under many different conditions. Photochromic stochastic optical fluctuation imaging (pcSOFI) is a recent addition to the field of diffraction‐unlimited fluorescence microscopy. This robust and versatile method employs a statistical analysis of random fluctuations in the emission of single labels, in this case reversibly switchable fluorescent proteins (RSFPs), to retrieve super‐resolution information. Added to the resolution enhancement, pcSOFI also offers contrast enhancement and background reduction in a practical and convenient way. Here, we describe the necessary steps to obtain diffraction‐unlimited images, including multicolor and three‐dimensional imaging, and highlight the advantages of pcSOFI together with the circumstances under which pcSOFI can be favorably applied. © 2015 by John Wiley & Sons, Inc.
Preparation and Separation of DNA‐Wrapped Carbon Nanotubes
Authors: Ao Geyou , Zheng Ming 
Published: March 2015

AbstractPurification of single‐chirality single‐wall carbon nanotubes (SWCNTs) from their synthetic mixture is a prerequisite for many applications. DNA‐controlled carbon nanotube (CNT) purification has evolved over a decade along with other separation techniques utilizing different types of dispersing agents such as surfactants and polymers. The size of single‐stranded DNA (ssDNA) libraries affords practically unlimited ways of coating SWCNTs. Recent developments in separating surfactant‐dispersed SWCNTs by polymer aqueous two‐phase (ATP) extraction has enabled rapid and efficient SWCNT separation on a larger volume scale. Applying the ATP separation method to DNA‐SWCNT hybrids opens a new route for effective sorting of nanotubes into each and every single‐chirality species. Here, we report protocols for purifying as many as 15 single‐chirality nanotube species from a synthetic mixture based on the separation of DNA‐SWCNTs by the aqueous two‐phase (ATP) method. © 2015 by John Wiley & Sons, Inc.
SNIPER Peptide‐Mediated Degradation of Endogenous Proteins
Authors: Fan Xuelai , Wang Yu Tian 
Published: March 2015

AbstractRapid and reversible methods for altering the function of endogenous proteins are not only indispensable tools for probing complex biological systems, but may potentially drive the development of new therapeutics for the treatment of human diseases. Genetic approaches have provided insights into protein function, but are limited in speed, reversibility and spatiotemporal control. To overcome these limitations, we have developed a peptide‐based method (SNIPER: Selective Native Protein Eradication) to degrade any given endogenous protein at the post‐translational level by harnessing chaperone‐mediated autophagy, a major intracellular protein degradation pathway. This unit presents a typical strategy in the design and validation of a protein‐knockdown peptide. © 2015 by John Wiley & Sons, Inc.
Mouse Anesthesia and Analgesia
Authors: Adams Sean , Pacharinsak Cholawat 
Published: March 2015

AbstractProviding anesthesia and analgesia for mouse subjects is a common and critical practice in the laboratory setting. These practices are necessary for performing invasive procedures, achieving prolonged immobility for sensitive imaging modalities (magnetic resonance imaging for instance), and providing intra‐ and post‐procedural pain relief. In addition to facilitating the procedures performed by the investigator, the provision of anesthesia and analgesia is crucial for the preservation of animal welfare and for humane treatment of animals used in research. Furthermore, anesthesia and analgesia are important components of animal use protocols reviewed by Institutional Animal Care and Use Committees, requiring careful consideration and planning for the particular animal model. In this article, we provide technical outlines for the investigator covering the provision of anesthesia by two routes (injectable and inhalant), guidelines for monitoring anesthesia, current techniques for recognition of pain, and considerations for administering preventative analgesia. © 2015 by John Wiley & Sons, Inc.
Computer Models for Digital Imaging
Authors: Jenny Patrick , Šormaz Miloš , Mourad Safer 
Published: March 2015

AbstractIn this chapter, mathematical and computational light scattering models relevant for halftone reproduction and other simulation studies in digital imaging are discussed. While in principle Maxwell's electromagnetic equations provide a very accurate and general description of light propagation, their numerical solution in highly heterogeneous domains is computationally too expensive for the kind of practical applications considered in this book. Therefore, the focus here will be on the computationally much more efficient transport theory. Besides discussing its limitations, the most general solution approach, that is, the Monte Carlo method, is explained and compared with more simple models, which involve further approximations.
Single‐Sensor Imaging Devices: An Overview
Authors: Battiato Sebastiano 
Published: March 2015

AbstractIn the last decade, multimedia devices (camcorders,PDAs, mobile phones) have been dramatically diffused. Moreover, the increasing of their computational performances combined with a higher storage capability permits them to elaborate large amount of data. In order to reduce their cost and complexity, manufacturers place a color filter array (CFA) on top of a single image sensor, which is basically a monochromatic device, to capture color information of the true visual scene. Cameras make use of an electronic sensor to acquire the spatial variations in light intensity and then use image processing algorithms to reconstruct a color picture from the data provided by the sensor (i.e., shape, weight, style, etc.). The chapter analyses the various aspects of the imaging pipeline from theCFAdata to final true‐color image/video just before encoding. A typical imaging pipeline is composed of two functional modules (preacquisition and postacquisition), where the data coming from the sensor in theCFAformat are properly processed. The termpreacquisitionis referred to the stage in which the current input data coming from the sensor are analyzed just to collect statistics useful to set parameters (e.g., white balancing, exposure) for correct acquisition. Typical imaging pipelines implemented in single‐sensor cameras are usually designed to find a trade‐off between suboptimal solutions (devoted to solve imaging acquisition issues) and technological problems (e.g., color balancing and thermal noise) in a context of limited hardware resources. State‐of‐the‐art techniques to process multichannel pictures, obtained through nonlinear color interpolation fromCFAdata, are very advanced.A rough understanding of the overall ingredients of a typical imaging pipeline is also important to consider the performance of any imaging devices, from low to high level, as the result of several components that run together to compose a complex system. The final image/video quality is the result of a certain number of design choices that involve, in almost all cases, all aspects of the hardware and software technology.
TV Display Technology and Video Processing
Authors: Bellers E.B. , de Haan G. 
Published: March 2015

AbstractVideo processing demands are strongly influenced by the display device. The revolution in television displays from the Cathode Ray Tubes (CRTs) to modern flat panel displays, like the Plasma Display Panel (PDP) and Liquid Crystal Display (LCD), has accelerated the innovation in video processing.The larger screen sizes and increased brightness, but also the increased diversity in content quality, along with the transition to High Definition television (HDTV) and beyond, has profoundly increased our picture quality expectations.New challenges had to be overcome with video processing, as the new display technologies have some very good, but often also some unfavorable properties. Therefore, new video processing algorithms were necessary to provide adequate solutions. It is fair to say that the display revolution along with the advances in video sources has made video processing an interesting field for many researchers during the last few decades.This chapter briefly reviews the characteristics of the Human Visual System that impact the system design, followed by a review of a number of modern display technologies. Some of the characteristics that negatively affect our perception will be discussed. It will appear that none of the modern displays is ideal for rendering video, and video processing technologies which alleviate the impact from these flaws will be presented.
Bismuth: Inorganic Chemistry
Authors: Whitmire Kenton H. 
Published: February 2015

AbstractThis review presents findings from 420 references. Bismuth has a diverse chemistry from the properties of the element to those of its important solid‐state compounds and its varied coordination complexes. Bismuth is the heaviest stable element whose chemistry is dominated by the +3 oxidation state, but −3, +1, +2, and +5 oxidation numbers are also accessible. In contrast to the lighter pnictogens, very few inorganic bismuth(V) compounds have been reported. The best characterized of these is BiF5, which is a strongly oxidizing Lewis acid that readily forms the BiF6−ion in the presence of a variety of F− ion donors. In this review, the chemistry of bismuth is organized by compound classification. Included are sections on the properties of the element, its intermetallic compounds and important solid‐state materials such as the bismuth oxides, chalcogenides, and pnictides. Recent work has been directed toward production of elemental bismuth and key solid‐state compounds in nanoparticle form. The solid‐state materials have important applications including high TC superconductors, ferroelectric, and piezoelectric materials, oxide ion conductors, catalysts, thermoelectric materials, etc. In its reduced compounds with alkali and alkaline earth metals, bismuth forms a number of homometallic and heterometallic anionic Zintl ions showing Bi–Bi bonding and a strong tendency toward cluster formation. Cationic clusters in reduced halide species have been observed. Bi–Bi single and double bonds are known. Molecular compounds are discussed and organized by the donor elements coordinated to bismuth, including sections on amines and amides, alkoxides, carboxylates, thiolates, and halides. The halides along with Bi(NO3)3 · 5H2O are amongst the most common starting materials for synthesizing other bismuth complexes. The alkoxide and carboxylate complexes are subject to facile hydrolysis leading to a wide variety of oxo‐alkoxide and oxo‐carboxylate complexes. Particularly stable configurations for these oxo clusters are Bi9and Bi38. These latter two cluster sizes stabilized by salicylate ligands are good model compounds for the bismuth subcarboxylate compounds, which have found widespread medicinal usage. High coordination numbers ranging from two to nine are common and the Bi3+ion is well‐known for its high Lewis acidity. Despite its identity as a heavy metal, its compounds are generally nontoxic to humans and enjoy a wide application as antibacterial and antifungal agents. Aspects of the biological chemistry of bismuth compounds are surveyed. A rich chemistry of bismuth coordinated to organometallic transition metal fragments is well developed. Many Fe, Co, Ru, Os, and Re metal carbonyl complexes have been reported as well as cyclopentadienyl metal derivatives. Unusual structure and bonding patterns have been observed in these compounds that include representatives from Groups 6 through 11 as well as one organometallic lanthanide complex.
Cobalt:B12Enzymes and Coenzymes
Authors: Kräutler Bernhard 
Published: February 2015

AbstractCobalt has its important biological role as metal center of vitamin B12and of its cofactor variants. The natural B12derivatives are remarkably complex cobalt‐corrins and belong to the larger class of the tetrapyrrolic natural products. The cofactor forms of vitamin B12, theantipernicious anemia factor, are required for human and animal health. With the exception of the (higher) plants, most forms of life appear to depend on vitamin B12and its natural derivatives. The corrinoids play a particularly basic role in carbon metabolism in archaea and bacteria, which are the only natural sources of the B12derivatives. These microorganisms have developed extraordinary means for the biosynthesis of the B12derivatives and for its regulation, in order to cope with the structural and functional complexity of the cobalt‐corrinoids. The other B12‐dependent forms of life have evolved intricate strategies for the economic and efficient uptake and transport of the corrinoids. The known cofactor functions of the cobalt‐corrinoids are due to their extraordinary organometallic chemistry, coupled with their redox chemistry under physiological conditions: adenosylcorrinoids, methylcorrinoids, and reduced corrinoids are the cofactors in various important and unique organometallic enzymes, whose intricate structural and mechanistic properties have been the focus of extensive research activities. The essential role of the corrinoids in organometallic paths of carbon fixation and further carbon metabolism in anerobic microorganisms has attracted particular attention. Indeed, the main chemical reactivity of the corrinoids and their essential biological roles may reflect their possible contributions to the early stages of life on earth. Vitamin B12and its derivatives thus hold an important position in the life sciences and are at the center of interdisciplinary interests from medicine, biology, chemistry, and physics.
Iron: Non‐Heme Proteins with Diiron‐Carboxylate Active Sites
Authors: Kurtz Donald M. , Boice Emily , Caranto Jonathan D. , Frederick Rosanne E. , Masitas Cesar A. , Miner Kyle D. 
Published: February 2015

Abstract

Non‐heme diiron‐carboxylate (
NHDC
) active sites are found in several classes of monooxygenases, oxidases, and dioxygen transport or sensing proteins, as well as a few metallohydrolases. The unique and defining structural feature of
NHDC
sites consists of two non‐heme irons bridged by at least one carboxylate‐containing amino acid residue. A second characteristic feature is a bridging solvent ligand, either oxo or hydroxo in at least the diferric state.
NHDC
sites also feature terminal ligands derived from histidine and carboxylate residues. The hemerythrin superfamily functions have expanded from reversible dioxygen binding to include sensing of iron, dioxygen, or redox status. Substantial progress has been made in characterization of flavo‐diiron enzymes, including its nitric oxide reductase mechanism. A diiron urease is a recent addition to the metallohydrolase family. The variety of characterized

NHDC O
2

‐activating enzymes has increased substantially since the previous compilation in this encyclopedia. Novel monooxygenation mechanisms have been identified.
Zintl Compounds
Authors: Janka Oliver , Kauzlarich Susan M. 
Published: February 2015

AbstractThe term “Zintl phase” refers to a class of compounds and is used to recognize contributions to the field of solid‐state inorganic chemistry by Eduard Zintl. Zintl phases were initially defined as a subgroup of intermetallic phases where the anions or anionic network could be considered formally to be valence satisfied. These compounds are made up of electropositive elements from groups 1and 2 that, in a formal sense, donate their electrons to the electronegative elements from groups 13, 14, and 15, which use them to form the correct number of bonds such that each element has a filled shell. The initial definition has been expanded from the initial binary phases to include ternary phases and further enlarged to include transition metals and rare earth elements in some cases. The compounds that make up this class are described along with the corresponding Zintl anions arising from solution chemistry. Recent results in the field, such as the use of Zintl phases for novel materials, are also described.
SoxAXCytochromes
Authors: Kappler Ulrike , Maher Megan J 
Published: February 2015

AbstractSoxAX cytochromes catalyze the formation of a disulfide bond between a reduced inorganic sulfur substrate and a conserved cysteine residue present on the SoxYZ carrier protein. The reaction liberates two electrons that are transferred to an external electron acceptor, usually a smallc‐type cytochrome. SoxAX cytochromes are essential components of the bacterial sulfur oxidation (Sox) pathway that is found in both chemo‐ and phototrophic bacteria, and currently there are three known structurally distinct types of SoxAX cytochromes that may represent adaptations of this enzyme to specific metabolic functions. Crystal structures are available for two of the three types of SoxAX proteins and revealed that one of the two active site hemes has a His/Cys‐persulfide ligand environment. This specific ligand field gives rise to extremely negative redox potentials, and in addition to several heme groups SoxAX cytochromes may contain a Cu redox center. Evidence from electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) spectroscopy indicates a high flexibility of the SoxAX active site heme environment and suggests that the reaction mechanism may involve a ligand exchange reaction.
Benzoyl‐
CoA
Epoxidase of Azoarcus evansii
Authors: Weinert Tobias , Rather‐Adler Liv J , Bill Eckhard , Fuchs Georg , Ermler Ulrich 
Published: February 2015

Abstract

Mineralization of aromatic compounds—present in large amounts in the biosphere—is a challenging chemical process. Nature developed several sophisticated degradation strategies, one of them being the benzoate‐degrading CoA‐linked Box pathway that is present in 5% of all sequenced bacterial genomes. The central dearomatization and cleavage reaction is accomplished by the BoxABC multicomponent system; BoxA is a reductase, BoxB an epoxidase using a single O
2
molecule, and BoxC a stimulator for the BoxB reaction and a hydrolase for subsequent ring cleavage. BoxB is a member of the important diiron carboxylate protein family characterized by a catalytic diiron center embedded in a central four‐helix bundle. Benzoyl‐CoA is located inside a 20 Å long channel of BoxB. The position of its phenyl ring relative to the diiron center is accurately defined in the X‐ray structure and allowed valuable insight into O
2
binding and activation, epoxidation, and the stereoselectivity of the reaction. Kinetic‐ and electron paramagnetic resonance (EPR)‐spectroscopic investigations provided information about the reaction dynamics and reaction intermediates. On the basis of the total data available, a detailed enzymatic mechanism is proposed.
Zinc‐Dependent Metalloprotease‐1 (Zmp1)
Authors: Ferraris Davide M , Rizzi Menico 
Published: February 2015

Abstract

M13
endopeptidases are single‐pass, transmembrane zinc‐metallopeptidases responsible for the regulation of the biological activity of many hormones and peptides in humans and are involved in many important processes such as blood pressure regulation (neprilysin or NEP), cardiovascular development (
endothelin converting enzyme‐1
or
ECE‐1
), and prevention of hemolytic reaction (
KELL
) and phosphate homeostasis (
PHEX
). Zmp1 is a soluble enzyme member of the
M13
endopetidases family, which plays a key role in
Mycobacterium tuberculosis
pathogenicity through a still to be elucidated mechanism that likely initiates on enzyme secretion.
Adenine Deaminase
Authors: Kamat Siddhesh S , Raushel Frank M 
Published: February 2015

AbstractAdenine deaminase(ADE) is a member of the amidohydrolase superfamily of enzymes and this enzyme catalyzes the deamination of adenine to hypoxanthine. Biologically, this enzyme functions as a member of the purine salvage and catabolism pathways.ADE, expressed and purified from various bacterial sources, exhibits multiple levels of oxygenation modifications that lead to inactivation of catalytic activity. A special iron‐free expression protocol is needed to obtain an active form ofADE. The X‐ray structure ofADEexhibits a protein‐fold that is somewhat different from other members of the amidohydrolase superfamily, although it maintains the central (β/α)8‐barrel fold that is a characteristic feature of this superfamily. The active site contains a binuclear metal center with the metal ligands composed of four histidines, an aspartate, a glutamate, and another glutamate that bridges the two metals. The active form ofADEcan utilize iron, manganese, or zinc with comparable catalytic efficiencies. Through a series of kinetic, biochemical, spectroscopic, and structural studies, the mechanism of deamination has been elucidated. The di‐iron form ofADEshows a unique and aberrant catalase activity. In the presence of hydrogen peroxide the di‐iron enzyme catalyzes the formation of reactive oxygen species that modify active site residues thereby resulting in enzyme inactivation.
Knee Instability and Basic and Advanced Function Decline in Knee Osteoarthritis
Authors: Sharma Leena , Chmiel Joan S. , Almagor Orit , Moisio Kirsten , Chang Alison H. , Belisle Laura , Zhang Yunhui , Hayes Karen W. 
Published: March 2015

ObjectiveManifestations of instability in knee osteoarthritis (OA) include low overall knee confidence, low confidence that the knees will not buckle, buckling, and excessive motion during gait. Confidence and buckling may particularly influence activity choices, contributing to events leading to disability. Buckling is more likely to affect advanced than basic functional tasks. In this prospective longitudinal study, we tested the hypothesis that overall knee confidence, buckling confidence, buckling, and frontal plane motion during gait are associated with advanced 2‐year function outcomes in persons with knee OA.MethodsPersons with knee OA were queried about overall knee confidence (higher score = worse confidence), buckling confidence, and knee buckling, and underwent quantitative gait analysis to quantify varus–valgus excursion and angular velocity. Physical function was assessed using the Late‐Life Function and Disability Instrument Basic and Advanced Lower Extremity Domain scores. Logistic regression was used to evaluate the relationship between baseline instability measures and baseline‐to‐2‐year function outcome, adjusting for potential confounders.ResultsThe sample was comprised of 212 persons (mean age 64.6 years, 76.9% women). Buckling was significantly associated with poor advanced function outcome (adjusted odds ratio [OR] 2.08, 95% confidence interval [95% CI] 1.03–4.20) but not basic function outcome. Overall knee confidence was significantly associated with advanced outcome (adjusted OR 1.65, 95% CI 1.01–2.70), while associations between buckling confidence and both outcomes approached significance. Neither varus–valgus excursion nor angular velocity during gait was associated with either outcome.ConclusionKnee buckling and low knee confidence were each associated with poor 2‐year advanced function outcomes. Current treatment does not address these modifiable factors; interventions to address them may improve outcome in knee OA.