bluuebunny/crossref_metadata_2025 huggingface dataset:
Group-SMA Algorithm Based Joint Estimation of Train Parameter and State
Authors: Zheng Wei , Han Juan , Kong Weijie , Wang Lixiang
Published: March 2015

The braking rate and train arresting operation is important in the train braking performance. It is difficult to obtain the states of the train on time because of the measurement noise and a long calculation time. A type of Group Stochastic M-algorithm (GSMA) based on Rao-Blackwellization Particle Filter (RBPF) algorithm and Stochastic M-algorithm (SMA) is proposed in this paper. Compared with RBPF, GSMA based estimation precisions for the train braking rate and the control accelerations were improved by 78% and 62%, respectively. The calculation time of the GSMA was decreased by 70% compared with SMA.
Standardization of Road Danger Signs in the European Union
Authors: Castelluccio Francesco , Catalano Mario , Fichera Davide , Migliore Marco , Amoroso Salvatore
Published: March 2015

The aim of this research is to find a solution for the standardization of road signs in the EU zone by a comparative analysis of different national sign systems to establish a common set from a single country. This work is based on the idea that road sign standardization might increase the safety level of transnational journeys and foster the relationships among the various members of the EU Community. This paper presents the outcome of the first step of the research, which focuses on the harmonization of danger signs. In more detail, a multicriteria approach is applied to rank 19 EU Member States on the basis of three main aspects: the installation cost of new signs, new sign learning issues and the effectiveness of sign systems. The study allows for the installation cost by quantifying the degree of similarity among road sign systems and the roadway network extension, on which new signs should be placed.
Marketing Research on Passenger Satisfaction With Public Transport Service in the City of Belgrade
Authors: Radnović Branislav , Marić Radenko Miloš , Radnović Vladana , Ilić Milena , Lukač Dragan
Published: March 2015

The aim of this paper is to determine, based on conducted marketing research, the level of passenger satisfaction with public transport services for the purpose of making better marketing decisions in the example of the City of Belgrade. The main task is to test the hypothesis on the existence of significant influence of factors, such as quality service, attitude and behaviour of employees (e.g. driver), adequate informing, quality of vehicles, line routes and timetable, on passenger satisfaction. Correlation coefficient and regression analysis were used for interpreting the obtained results and examining the formulated hypothesis. Empirical research has shown that there is a significant correlation between the aforementioned factors and passenger satisfaction with public transport services. The obtained results provided recommendations and guidelines for improving and increasing the quality of public transport services. The research results also provide the basis for future research that could examine the relationship between passenger satisfaction with services and sub-groups within the analyzed factors.
A Framework for Economic Evaluation of Highway Development Projects Based on Network-Level Life Cycle Cost Analysis
Authors: Ziari Hassan , Behbahani Hamid , Amini Amir Ali
Published: March 2015

For economic evaluation of a highway development project, multiple criteria must be considered on a timeframe longer than the project implementation interval and a geographical area larger than the project zone. In this study, a framework is proposed based on the Network-Level Life Cycle Cost Analysis (NL-LCCA) to assess the effect of highway development projects on mobility, safety, economy, environment and other monetizable criteria. In this approach, project impacts are estimated within physical boundaries of highway network over the network life cycle. This framework can be used as a decision-making support for evaluation and ranking of pre-defined development projects, proposing new cost-effective development projects, assessment of cost efficiency of existing highway network and budget allocation optimization.
The HIV care cascade: models, measures and moving forward
Authors: MacCarthy Sarah , Hoffmann Michael , Ferguson Laura , Nunn Amy , Irvin Risha , Bangsberg David , Gruskin Sofia , Dourado Ines
Published: March 2015

Introduction

This article seeks to identify where delays occur along the adult HIV care cascade (“the cascade”), to improve understanding of what constitutes “delay” at each stage of the cascade and how this can be measured across a range of settings and to inform service delivery efforts. Current metrics are reviewed, measures informed by global guidelines are suggested and areas for further clarification are underscored.

Discussion

Questions remain on how best to evaluate late entry into each stage of the cascade. The delayed uptake of HIV testing may be more consistently measured once rapid CD4 testing is administered at the time of HIV testing. For late enrolment, preliminary research has begun to determine how different time intervals for linking to HIV care affect individual health. Regarding treatment, since 2013, the World Health Organization (WHO) and UNAIDS recommend treatment initiation when CD4 <500 cells/mm3; these guidelines provide a useful albeit evolving threshold to define late treatment initiation. Finally, WHO guidelines for high‐, low‐ and middle‐income countries also could be used to standardize measures for achieving viral suppression.

Conclusions

There is no “one size fits all” model as the provision of services may differ based on a range of factors. Nonetheless, measures informed by global guidelines are needed to more consistently evaluate the scope of and factors associated with delays to each stage of the cascade. Doing so will help identify how practitioners can best deliver services and facilitate access to and continued engagement in care.
Isolation of Integrin‐Based Adhesion Complexes
Authors: Jones Matthew C. , Humphries Jonathan D. , Byron Adam , Millon‐Frémillon Angélique , Robertson Joseph , Paul Nikki R. , Ng Daniel H. J. , Askari Janet A. , Humphries Martin J.
Published: March 2015

The integration of cells with their extracellular environment is facilitated by cell surface adhesion receptors, such as integrins, which play important roles in both normal development and the onset of pathologies. Engagement of integrins with their ligands in the extracellular matrix, or counter‐receptors on other cells, initiates the intracellular assembly of a wide variety of proteins into adhesion complexes such as focal contacts, focal adhesions, and fibrillar adhesions. The proteins recruited to these complexes mediate bidirectional signaling across the plasma membrane, and, as such, help to coordinate and/or modulate the multitude of physical and chemical signals to which the cell is subjected. The protocols in this unit describe two approaches for the isolation or enrichment of proteins contained within integrin‐associated adhesion complexes, together with their local plasma membrane/cytosolic environments, from cells in culture. In the first protocol, integrin‐associated adhesion structures are affinity isolated using microbeads coated with extracellular ligands or antibodies. The second protocol describes the isolation of ventral membrane preparations that are enriched for adhesion complex structures. The protocols permit the determination of adhesion complex components via subsequent downstream analysis by western blotting or mass spectrometry. © 2015 by John Wiley & Sons, Inc.
Evidence of the formation of noctilucent clouds due to propagation of an isolated gravity wave caused by a tropospheric occluded front
Authors: Dalin P. , Pogoreltsev A. , Pertsev N. , Perminov V. , Shevchuk N. , Dubietis A. , Zalcik M. , Kulikov S. , Zadorozhny A. , Kudabayeva D. , Solodovnik A. , Salakhutdinov G. , Grigoryeva I.
Published: February 2015

We consider a unique case of a propagating internal gravity wave that has generated in situ a compact and thin layer of noctilucent clouds (NLC) at 82.7–85.2 km with a characteristic horizontal scale of 65–70 km, as observed in the Moscow region on the night of 18–19 July 2013. This particular transient isolated gravity wave together with the whole NLC layer suddenly appeared in the clear twilight sky and lasted about 1 h traveling eastward, which differs significantly from previously observed cases of gravity waves propagating through preexisting NLC layers. Our model studies demonstrate that the wave had a tropospheric source connected to the passage of an occluded front. The wave was likely generated due to strong horizontal wind shears at about 5 km altitude.
On the latitudinal distribution of mesospheric temperatures during sudden stratospheric warming events
Authors: Singh Ravindra P. , Pallamraju Duggirala
Published: February 2015

Mesospheric rotational temperatures from O2(0‐1) and OH(6‐2) band nightglow emissions that originate from 94 and 87 km altitudes, respectively, were obtained from a low‐latitude location, Mount Abu (24.6°N, 72.8°E), in India using a high spectral resolution grating spectrograph, which showed significant enhancements during the major sudden stratospheric warming (SSW) event of January 2013. To investigate the relationship of these enhancements in the context of SSW occurrences, a detailed study was carried out for 11 SSW events that occurred during 2004–2013 using SABER (Sounding of the Atmosphere using Broadband Emission Radiometry) data. In addition to SABER, Optical Spectrograph and Infrared Imaging System and Solar Occultation For Ice Experiment mesospheric temperatures were also used which showed similar latitudinal behavior as obtained by SABER. The longitudinal mean mesospheric temperatures at different latitudes of Northern and Southern Hemispheres have been derived. It is found that during SSW events the well‐known mesospheric cooling over the Northern Hemispheric high latitudes turns to heating over midlatitudes and then reverts to cooling closer to equatorial regions. This trend continues into the Southern Hemisphere as well. These variations in the mesospheric temperatures at different latitudes have been characterized based on northern hemispheric stratospheric temperature enhancements at high latitudes during SSW periods. In comparison with the COSPAR International Reference Atmosphere‐86‐derived temperatures, the SABER temperatures show an increase/decrease in Southern/Northern Hemisphere. Such a characterization in mesospheric temperatures with respect to latitudes reveals a hitherto unknown intriguing nature of the latitudinal coupling in the mesosphere that gets set up during the SSW events.
On the local Hurst exponent of geomagnetic field fluctuations: Spatial distribution for different geomagnetic activity levels
Authors: Michelis Paola De , Consolini Giuseppe
Published: March 2015

This study attempts to characterize the spatial distribution of the scaling features of the short time scale magnetic field fluctuations obtained from 45 ground‐based geomagnetic observatories distributed in the Northern Hemisphere. We investigate the changes of the scaling properties of the geomagnetic field fluctuations by evaluating the local Hurst exponent and reconstruct maps of this index as a function of the geomagnetic activity level. These maps permit us to localize the different latitudinal structures responsible for disturbances and related to the ionospheric current systems. We find that the geomagnetic field fluctuations associated with the different ionospheric current systems have different scaling features, which can be evidenced by the local Hurst exponent. We also find that in general, the local Hurst exponent for quiet magnetospheric periods is higher than that for more active periods suggesting that the dynamical processes that are activated during disturbed times are responsible for changes in the nature of the geomagnetic field fluctuations.
Magnetosphere‐ionosphere mapping at Jupiter: Quantifying the effects of using different internal field models
Authors: Vogt Marissa F. , Bunce Emma J. , Kivelson Margaret G. , Khurana Krishan K. , Walker Raymond J. , Radioti Aikaterini , Bonfond Bertrand , Grodent Denis
Published: February 2015

The lack of global field models accurate beyond the inner magnetosphere (<30 RJ) makes it difficult to relate Jupiter's polar auroral features to magnetospheric source regions. We recently developed a model that maps Jupiter's equatorial magnetosphere to the ionosphere using a flux equivalence calculation that requires equal flux at the equatorial and ionospheric ends of flux tubes. This approach is more accurate than tracing field lines in a global field model but only if it is based on an accurate model of Jupiter's internal field. At present there are three widely used internal field models—Voyager Io Pioneer 4 (VIP4), the Grodent Anomaly Model (GAM), and VIP Anomaly Longitude (VIPAL). The purpose of this study is to quantify how the choice of an internal field model affects the mapping of various auroral features using the flux equivalence calculation. We find that different internal field models can shift the ionospheric mapping of points in the equatorial plane by several degrees and shift the magnetospheric mapping to the equator by ~30 RJ radially and by less than 1 h in local time. These shifts are consistent with differences in how well each model maps the Ganymede footprint, underscoring the need for more accurate Jovian internal field models. We discuss differences in the mapping of specific auroral features and the size and location of the open/closed field line boundary. Understanding these differences is important for the continued analysis of Hubble Space Telescope images and in planning for Juno's arrival at Jupiter in 2016.
A statistical study into the spatial distribution and dawn‐dusk asymmetry of dayside magnetosheath ion temperatures as a function of upstream solar wind conditions
Authors: Dimmock A. P. , Nykyri K. , Karimabadi H. , Osmane A. , Pulkkinen T. I.
Published: March 2015

The magnetosheath contains the shocked solar wind and behaves as a natural filter to the solar wind plasma before it reaches the magnetosphere. The redistribution of kinetic energy at the bow shock results in significant thermalization of the solar wind plasma, resulting in a magnetosheath temperature profile which is highly nonhomogeneous and nonisotropic and differs between the dawn and dusk flanks. The present study attempts to study the spatial distribution of magnetosheath ion temperature as a function of upstream solar wind conditions. We pay particular attention to the dawn/dusk asymmetry in which we attempt to quantify using experimental data collected over a 7 year period. We also compare these data to simulated data from both the Block‐Adaptive‐Tree‐Solarwind‐Roe‐Upwind‐Scheme (BATS‐R‐US) MHD code and a kinetic hybrid model. We present evidence that the dawn flank is consistently hotter than the dusk flank for a variety of upstream conditions. Our statistical data also suggest a dependency on solar wind speed such that the level of asymmetry increases with faster speeds. We conclude that the dawn‐favored asymmetry of the magnetosheath seed population is insufficient to explain the dawn asymmetry (30–40%) of cold component ions in the cold, dense plasma sheet, and therefore, other mechanisms are likely required.
Argo data assimilation and its effect on climate state estimation and forecasting in the western North Pacific using a coupled model
Authors: Nishikawa Shiro , Ishikawa Yoichi , Masuda Shuhei , Hiyoshi Yoshihisa , Sasaki Yuji , Igarashi Hiromichi
Published: March 2015

In this study, we investigated the effects of ocean subsurface data (Argo data) on climate state estimation and forecasting, focusing on the reproduction of North Pacific subtropical mode water (STMW) using a four‐dimensional variational data assimilation system with a coupled model. We produced two reanalysis plus forecast data sets for the ocean and atmosphere in 2010 using a 3 month assimilation period: the first including Argo data (Argo case) and the second did not include Argo data (control case). In the control case, the Kuroshio, Kuroshio Extension front, and recirculation gyres along the front were not adequately reproduced. Consequently, there were large biases in temperature and salinity in the western North Pacific. The assimilation of Argo data effectively corrected these biases and significantly improved reproduction of the Kuroshio fronts and recirculation gyres, resulting in a more realistic reproduction of the winter mixed layer and STMW. The correction of these biases is critical to the 1–3 year predictions of the STMW core properties, and the assimilation of Argo data enables prediction of these properties for more than a year. We showed that assimilation of Argo data affects the surface atmospheric temperature above the STMW formation region.
Airborne measurements of organosulfates over the continental U.S.
Authors: Liao Jin , Froyd Karl D. , Murphy Daniel M. , Keutsch Frank N. , Yu Ge , Wennberg Paul O. , St. Clair Jason M. , Crounse John D. , Wisthaler Armin , Mikoviny Tomas , Jimenez Jose L. , Campuzano‐Jost Pedro , Day Douglas A. , Hu Weiwei , Ryerson Thomas B. , Pollack Ilana B. , Peischl Jeff , Anderson Bruce E. , Ziemba Luke D. , Blake Donald R. , Meinardi Simone , Diskin Glenn
Published: February 2015

Organosulfates are important secondary organic aerosol (SOA) components and good tracers for aerosol heterogeneous reactions. However, the knowledge of their spatial distribution, formation conditions, and environmental impact is limited. In this study, we report two organosulfates, an isoprene‐derived isoprene epoxydiols (IEPOX) (2,3‐epoxy‐2‐methyl‐1,4‐butanediol) sulfate and a glycolic acid (GA) sulfate, measured using the NOAA Particle Analysis Laser Mass Spectrometer (PALMS) on board the NASA DC8 aircraft over the continental U.S. during the Deep Convective Clouds and Chemistry Experiment (DC3) and the Studies of Emissions and Atmospheric Composition, Clouds, and Climate Coupling by Regional Surveys (SEAC4RS). During these campaigns, IEPOX sulfate was estimated to account for 1.4% of submicron aerosol mass (or 2.2% of organic aerosol mass) on average near the ground in the southeast U.S., with lower concentrations in the western U.S. (0.2–0.4%) and at high altitudes (<0.2%). Compared to IEPOX sulfate, GA sulfate was more uniformly distributed, accounting for about 0.5% aerosol mass on average, and may be more abundant globally. A number of other organosulfates were detected; none were as abundant as these two. Ambient measurements confirmed that IEPOX sulfate is formed from isoprene oxidation and is a tracer for isoprene SOA formation. The organic precursors of GA sulfate may include glycolic acid and likely have both biogenic and anthropogenic sources. Higher aerosol acidity as measured by PALMS and relative humidity tend to promote IEPOX sulfate formation, and aerosol acidity largely drives in situ GA sulfate formation at high altitudes. This study suggests that the formation of aerosol organosulfates depends not only on the appropriate organic precursors but also on emissions of anthropogenic sulfur dioxide (SO2), which contributes to aerosol acidity.
WRF simulations of two extreme snowfall events associated with contrasting extratropical cyclones over the western and central Himalaya
Authors: Norris J. , Carvalho L. M. V. , Jones C. , Cannon F.
Published: March 2015

Two extreme snowfall events associated with extratropical cyclones, one interacting with the western and one with the central Himalaya, are simulated with the Weather Research and Forecasting (WRF) model over 8 days. One event in January 1999 was driven by a longwave trough over west Asia, with the cyclone becoming terrain‐locked in the western Himalayan notch. Another event in March 2006 was driven by a trough further south and east, facilitating the passage of two successive cyclones along the entire Himalayan ridge, drawing moisture from warm tropical waters. These flow patterns are typical for extreme winter precipitation in the western and central Himalaya, respectively, but were amplified in these two cases. In the WRF simulations, snowfall is confined to the western Himalaya in the January simulation, while a near‐continuous band of accumulated snowfall along the Himalayan ridge forms in the March simulation. Precipitation rate throughout both simulations is largely determined by cross‐barrier moisture flux, which is generally greatest wherever the cyclonic winds converge on the mountains at each time. However, the March 2006 simulation evolves in an environment with greater convective instability upwind of and moisture transport toward the mountains than in the January 1999 event. Hence, greater precipitation rates and more solid snowbands are generated in the March than in the January simulation. However, due to the terrain‐locking of the cyclone in the January event, individual locations receive more persistent snowfall, so that the greatest 8 day accumulations are similar between the two events, although these accumulations are more widespread in the March event.
Modeling stepped leaders using a time‐dependent multidipole model and high‐speed video data
Authors: Karunarathne Sumedhe , Marshall Thomas C. , Stolzenburg Maribeth , Karunarathna Nadeeka , Orville Richard E
Published: February 2015

A full negative stepped leader and portions of four negative stepped leaders preceding negative cloud‐to‐ground lightning return strokes were modeled; each model was constrained to match electric field change measurements recorded at three or four sites located within 30 km of the leader. The time evolution and 2‐D locations of stepped leaders were obtained from data collected with a high‐speed video camera operated at 50,000 frames/s. The Lu et al. (Charge transfer during intracloud lightning from a time‐dependent multidipole model, Journal of Geophysical Research, 2011) time‐dependent multidipole model was used with some modifications. The model used a time step equal to one video frame, 20μs. At each time step, negative charges were deposited at stepped leader tips based on measured light intensity, and an equivalent positive charge was deposited at one of the locations of the initial breakdown pulses that preceded the stepped leaders. The method has the unique advantage of obtaining locations of CG stepped leaders including its branches all the way to the ground. Three main quantities were obtained from the model: total charge transfer of −1.50 to −7.51 C, average line charge density of −0.113 to −0.413 mC/m (mean =− 0.196 mC/m), and average current of −0.084 to −0.456 kA (mean =− 0.31 kA). From the video data, the estimated 2‐D speeds were 2.43–4.95×105 m/s (mean 3.34 × 105 m/s), and the cumulative lengths of the all branches were 3.5–9.2 times the vertical distance traveled by the visible stepped leader.
Characterization of black carbon‐containing particles from soot particle aerosol mass spectrometer measurements on the R/V Atlantis during CalNex 2010
Authors: Massoli Paola , Onasch Timothy B. , Cappa Christopher D. , Nuamaan Ibraheem , Hakala Jani , Hayden Katherine , Li Shao‐Meng , Sueper Donna T. , Bates Timothy S. , Quinn Patricia K. , Jayne John T. , Worsnop Douglas R.
Published: February 2015

We present mass spectrometry measurements of black carbon‐containing particles made on board the R/V Atlantis during the CalNex (California Research at the Nexus of Air Quality and Climate Change) 2010 study using an Aerodyne Research Inc. soot particle aerosol mass spectrometer (SP‐AMS). The R/V Atlantis was deployed to characterize air masses moving offshore the California coast and to assess emissions from sources in urban ports. This work presents a first detailed analysis of the size‐resolved chemical composition of refractory black carbon (rBC) and of the associated coating species (NR‐PMBC). A colocated standard high‐resolution aerosol mass spectrometer (HR‐AMS) measured the total nonrefractory submicron aerosol (NR‐PM1). Our results indicate that, on average, 35% of the measured NR‐PM1 mass (87% of the primary and 28% of the secondary NR‐PM1, as obtained from the mass‐weighted average of the NR‐PMBC species) was associated with rBC. The peak in the average size distribution of the rBC‐containing particles measured by the SP‐AMS in vacuum aerodynamic diameter (dva) varied from ~100 nm to ~450 nm dva, with most of the rBC mass below 200 dva. The NR‐PMBC below 200 nm dva was primarily organic, whereas inorganics were generally found on larger rBC‐containing particles. Positive matrix factorization analyses of both SP‐AMS and HR‐AMS data identified organic aerosol factors that were correlated in time but had different fragmentation patterns due to the different instruments vaporization techniques. Finally, we provide an overview of the volatility properties of NR‐PMBC and report the presence of refractory oxygen species in some of the air masses encountered.
Coastal sea level from inland CryoSat‐2 interferometric SAR altimetry
Authors: Abulaitijiang Adili , Andersen Ole Baltazar , Stenseng Lars
Published: February 2015

The European Space Agency's CryoSat‐2 satellite can operate in a novel synthetic aperture radar interferometric (SARIn) mode where its nominal footprint (swath) is observed by two antennas and the phase difference between the signals is used to determination the exact location of the scatterer through an off‐nadir correction. The potential of SARIn for sea level determination is investigated over the fjords of Eastern Greenland. In principle the satellite should only track sea level within its nominal footprint of 7 km across track, but we observe that scattering targets (fjords) within twice its nominal footprint are frequently observed but mislocated in CryoSat‐2 due to phase wrapping. We devised a way to relocate the observations and correct the range accordingly. When CryoSat‐2 is flying inland we consequently observed that the satellite occasionally provide valid sea level in fjords up to 13 km away in the across‐track direction.
Diffraction‐Unlimited Fluorescence Microscopy of Living Biological Samples Using pcSOFI
Authors: Duwé Sam , Moeyaert Benjamien , Dedecker Peter
Published: March 2015

The 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

Purification 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

Rapid 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

Providing 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

In 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

In 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

Video 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

This 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

Cobalt 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

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

The 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.
Metal‐Mediated Protein Modification
Authors: Whittaker James W.
Published: February 2015

Posttranslational modification of proteins is important for the analysis of protein structure, for expanding protein functionality, and for creating new protein‐based materials. Many of these protein processing reactions are mediated by metal complexes, underscoring the close connections between inorganic and biological chemistry.
SoxAXCytochromes
Authors: Kappler Ulrike , Maher Megan J
Published: February 2015

SoxAX 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

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

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

Adenine 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.