bluuebunny/crossref_metadata_2025 huggingface dataset:
PROTEIN SECONDARY STRUCTURE PREDICTION USING NMR CHEMICAL SHIFT DATA
Authors: ZHAO YUZHONG , ALIPANAHI BABAK , LI SHUAI CHENG , LI MING
Published: June 2010

Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q3 accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at .
ONE-DIMENSIONAL HYDRODYNAMIC MODEL SIMULATING WATER STAGE IN OPEN CHANNELS (WS-1)
Authors: NASSAR M. A.
Published: June 2010

One-dimensional (1D) numerical model was developed to simulate water stage in open channels in order to suggest solutions for practical problems in the Nile River and its branches. The continuity and momentum equations describe the unsteady flow were solved using the finite difference technique. The developed model is verified using two types of data. The first type, simulating steady flow, is a field data collected at Elbogdady reach. It is a reach located 712.80 km upstream of Roda's staff gauge on the Nile River. The second type, simulating unsteady flow, is a result of the 1D SOBEK model. It is simulating the flow field at El-Mahrousa canal. It is one of El-Kanobia canal branches at 11.47 km left side, which is fed from El-Mahmoudia canal. Simplifications were made to simulate the flow patterns around the hydraulic structures using the developed hydrodynamic model. Actually, the water levels in many branch canals under continuous flow after implementation of Irrigation Improvement Project (IIP) need to be checked. The model could be applied to estimate the water stage under different abstraction values where some reaches of the Nile River and its branch suffering. In addition, it can be used to assess the impact of water allocation. Good agreement was observed between the model results and the field observations.
COMPUTATIONAL TECHNIQUES FOR MODELING NON-NEWTONIAN FLOW IN POROUS MEDIA
Authors: SOCHI TAHA
Published: June 2010

Modeling the flow of non-Newtonian fluids in porous media is a challenging subject. Several approaches have been proposed to tackle this problem. These include continuum models, numerical methods, and pore-scale network modeling. The latter proved to be more successful and realistic than the rest. The reason is that it captures the essential features of the flow and porous media using modest computational resources and viable modeling strategies. In this article we present pore-scale network modeling techniques for simulating non-Newtonian flow in porous media. These techniques are partially validated by theoretical analysis and comparison to experimental data.
THREE-STEP TAYLOR GALERKIN METHOD FOR SINGULARLY PERTURBED GENERALIZED HODGKIN–HUXLEY EQUATION
Authors: SANGWAN VIVEK , KUMAR B. V. RATHISH , MURTHY S. V. S. S. N. V. G. K. , NIGAM MOHIT
Published: June 2010

A numerical study is carried out for the singularly perturbed generalized Hodgkin–Huxley equation. The equation is nonlinear which mimics the ionic processes at a real nerve membrane. A small parameter called singular perturbation parameter is introduced in the highest order derivative term. Keeping other parameters fixed, as this singular perturbation parameter approaches to zero, a boundary layer occurs in the solution. Three-step Taylor Galerkin finite element method is employed on a piecewise uniform Shishkin mesh to solve the equation. To procure more accurate temporal differencing, the method employs forward-time Taylor series expansion including time derivatives of third order which are evaluated from the governing singularly perturbed generalized Hodgkin–Huxley equation. This yields a generalized time-discretized equation which is successively discretized in space by means of the standard Bubnov–Galerkin finite element method. The method is third-order accurate in time. The code based on the purposed scheme has been validated against the cases for which the exact solution is available. It is also observed that for the Singularly Perturbed Generalized Hodgkin–Huxley equation, the boundary layer in the solution manifests not only by varying the singular perturbation parameter but also by varying the other parameters appearing in the model.
Disruption of playa–lacustrine depositional systems at the Permo-Triassic boundary: evidence from Vyazniki and Gorokhovets on the Russian Platform
Authors: Newell Andrew J. , Sennikov Andrey G. , Benton Michael J. , Molostovskaya Iya I. , Golubev Valeriy K. , Minikh Alla V. , Minikh Maxim G.
Published: June 2010

Permo-Triassic sections at Vyazniki and Gorokhovets provide evidence on terrestrial events at, or close to, the Permo-Triassic boundary, the time of the largest ever mass extinction. The sedimentary succession records the overrun of a muddy playa–lacustrine depositional system by major channel belts transporting sand-grade sediments. Biostratigraphy of sections at Vyazniki and Gorokhovets (Zhukov Ravine) shows that this event occurred either at the very end of the Permian or 8 m above in the sections. The timing and nature of this event, which records increased sediment flux from the Ural Mountains, is closely comparable with that from the Southern Uralian Foreland Basin. The Vyazniki and Gorokhovets sections are 800 km from the mountain front and in a separate depositional basin, which strengthens the case that increased sediment flux from the Urals at the Permo-Triassic boundary is related to devegetation of upland catchments (increasing sediment yield) and a switch toward low-frequency but high-magnitude discharge events (increasing sediment delivery). The interbedding of fluvial and aeolian deposits provides further evidence for climatic instability and extremes in the Early Triassic.

Supplementary material:

Detailed reports on the ostracodes and fossil fish remains from the Zhukov Ravine sections are available at
http://www.geolsoc.org.uk/SUP18402
.
Multiple post-Caledonian exhumation episodes across NW Scotland revealed by apatite fission-track analysis
Authors: Holford Simon P. , Green Paul F. , Hillis Richard R. , Underhill John R. , Stoker Martyn S. , Duddy Ian R.
Published: June 2010

The post-Caledonian exhumation history of NW Scotland is a controversial issue, with some studies advocating largely continual emergence whereas others suggest dominantly early Palaeogene plume-driven exhumation. Apatite fission-track analysis (AFTA) data for samples of Precambrian basement and Permian–Cretaceous sediments from onshore and offshore reveal multiple phases of post-Caledonian cooling: Triassic (beginning 245–225 Ma), Cretaceous (140–130 Ma; 110–90 Ma) and Cenozoic (65–60 Ma; 40–25 Ma; 15–10 Ma), all of which are interpreted at least in part as recording exhumation. Basement and sedimentary cover rocks display similar thermal histories, emphasizing the regional nature of these episodes and implying that sedimentary outliers represent the remnants of previously more extensive sequences. Significant thicknesses of Jurassic rocks may once have covered NW Scotland. Palaeocene palaeothermal effects are most pronounced in the vicinity of igneous centres, probably reflecting combined effects of heating by elevated heat flow, deeper burial and hydrothermal activity. Most of the region underwent kilometre-scale Neogene exhumation. Contrary to the common assumption of monotonic cooling and denudation histories, integration of geological evidence with AFTA data defines an episodic thermal history involving repeated cycles of burial and exhumation. We suggest that onshore passive margins and continental interiors may also best be characterized by similar histories.
Vlogging
Authors: Gao Wen , Tian Yonghong , Huang Tiejun , Yang Qiang
Published: June 2010

In recent years, blogging has become an exploding passion among Internet communities. By combining the grassroots blogging with the richness of expression available in video, videoblogs (vlogs for short) will be a powerful new media adjunct to our existing televised news sources. Vlogs have gained much attention worldwide, especially with Google's acquisition of YouTube. This article presents a comprehensive survey of videoblogging (vlogging for short) as a new technological trend. We first summarize the technological challenges for vlogging as four key issues that need to be answered. Along with their respective possibilities, we give a review of the currently available techniques and tools supporting vlogging, and envision emerging technological directions for future vlogging. Several multimedia technologies are introduced to empower vlogging technology with better scalability, interactivity, searchability, and accessability, and to potentially reduce the legal, economic, and moral risks of vlogging applications. We also make an in-depth investigation of various vlog mining topics from a research perspective and present several incentive applications such as user-targeted video advertising and collective intelligence gaming. We believe that vlogging and its applications will bring new opportunities and drives to the research in related fields.
A Comparison Study on Implementing Optical Flow and Digital Communications on FPGAs and GPUs
Authors: Bodily John , Nelson Brent , Wei Zhaoyi , Lee Dah-Jye , Chase Jeff
Published: June 2010

FPGA devices have often found use as higher-performance alternatives to programmable processors for implementing computations. Applications successfully implemented on FPGAs typically contain high levels of parallelism and often use simple statically scheduled control and modest arithmetic. Recently introduced computing devices such as coarse-grain reconfigurable arrays, multi-core processors, and graphical processing units promise to significantly change the computational landscape and take advantage of many of the same application characteristics that fit well on FPGAs. One real-time computing task, optical flow, is difficult to apply in robotic vision applications because of its high computational and data rate requirements, and so is a good candidate for implementation on FPGAs and other custom computing architectures. This article reports on a series of experiments mapping a collection of different algorithms onto both an FPGA and a GPU. For two different optical flow algorithms the GPU had better performance, while for a set of digital comm MIMO computations, they had similar performance. In all cases the FPGA implementations required 10x the development time. Finally, a discussion of the two technology’s characteristics is given to show they achieve high performance in different ways.
Titan-R
Authors: Papadopoulos Konstantinos , Papaefstathiou Ioannis
Published: June 2010

Data compression techniques can alleviate bandwidth problems in even multigigabit networks and are especially useful when combined with encryption. This article demonstrates a reconfigurable hardware compressor/decompressor core, the Titan-R, which can compress/decompress data streams at 8.5 Gb/sec, making it the fastest reconfigurable such device ever proposed; the presented full-duplex implementation allows for fully symmetric compression and decompression rates at 8.5 Gbps each. Its compression algorithm is a variation of the most widely used and efficient such scheme, the Lempel-Ziv (LZ) algorithm that uses part of the previous input stream as the dictionary. In order to support this high network throughput, the Titan-R utilizes a very fine-grained pipeline and takes advantage of the high bandwidth provided by the distributed on-chip RAMs of state-of-the-art FPGAs.
SARFUM
Authors: Badrignans Benoît , Champagne David , Elbaz Reouven , Gebotys Catherine , Torres Lionel
Published: June 2010

Remote update of hardware platforms or embedded systems is a convenient service enabled by Field Programmable Gate Array (FPGA)-based systems. This service is often essential in applications like space-based FPGA systems or set-top boxes. However, having the source of the update be remote from the FPGA system opens the door to a set of attacks that may challenge the confidentiality and integrity of the FPGA configuration, the bitstream. Existing schemes propose to encrypt and authenticate the bitstream to thwart these attacks. However, we show that they do not prevent the replay of old bitstream versions, and thus give adversaries an opportunity for downgrading the system. In this article, we propose a new architecture called
sarfum
that, in addition to ensuring bitstream confidentiality and integrity, precludes the replay of old bitstreams.
sarfum
also includes a protocol for the system designer to remotely monitor the running configuration of the FPGA. Following our presentation and analysis of the security protocols, we propose an example of implementation with the CCM (Counter with CBC-MAC) authenticated encryption standard. We also evaluate the impact of our architecture on the configuration time for different FPGA devices.
Improving the Robustness of Ring Oscillator TRNGs
Authors: Yoo Sang-Kyung , Karakoyunlu Deniz , Birand Berk , Sunar Berk
Published: June 2010

A ring oscillator-based true-random number generator design (Rings design) was introduced in Sunar et al. [2007]. The design was rigorously analyzed under a simple mathematical model and its performance characteristics were established. In this article we focus on the practical aspects of the Rings design on a reconfigurable logic platform and determine their implications on the earlier analysis framework. We make recommendations for avoiding pitfalls in real-life implementations by considering ring interaction, transistor-level effects, narrow signal rejection, transmission line attenuation, and sampler bias. Furthermore, we present experimental results showing that changing operating conditions such as the power supply voltage or the operating temperature may affect the output quality when the signal is subsampled. Hence, an attacker may shift the operating point via a simple noninvasive influence and easily bias the TRNG output. Finally, we propose modifications to the design which significantly improve its robustness against attacks, alleviate implementation-related problems, and simultaneously improve its area, throughput, and power performance.
Energy-driven distribution of signal processing applications across wireless sensor networks
Authors: Shen Chung-Ching , Plishker William L. , Ko Dong-Ik , Bhattacharyya Shuvra S. , Goldsman Neil
Published: June 2010

Wireless sensor network (WSN) applications have been studied extensively in recent years. Such applications involve resource-limited embedded sensor nodes that have small size and low power requirements. Based on the need for extended network lifetimes in WSNs in terms of energy use, the energy efficiency of computation and communication operations in the sensor nodes becomes critical. Digital Signal Processing (DSP) applications typically require intensive data processing operations and as a result are difficult to implement directly in resource-limited WSNs. In this article, we present a novel design methodology for modeling and implementing computationally intensive DSP applications applied to wireless sensor networks. This methodology explores efficient modeling techniques for DSP applications, including data sensing and processing; derives formulations of Energy-Driven Partitioning (EDP) for distributing such applications across wireless sensor networks; and develops efficient heuristic algorithms for finding partitioning results that maximize the network lifetime. To address such an energy-driven partitioning problem, this article provides a new way of aggregating data and reducing communication traffic among nodes based on application analysis. By considering low data token delivery points and the distribution of computation in the application, our approach finds energy-efficient trade-offs between data communication and computation.
Dynamic multiroot, multiquery processing based on data sharing in sensor networks
Authors: Zhang Zhiguo , Kshemkalyani Ajay D. , Shatz Sol M.
Published: June 2010

Applications that exploit the capabilities of sensor networks have triggered significant research on query processing in sensor systems. Energy constraints make optimizing query processing particularly important. This article addresses multiroot, multiquery optimization for region queries. The work focuses on application-layer issues exploiting query semantics. The article formulates three algorithms: a naïve algorithm, without data sharing, and a static and heuristic data-sharing algorithm. The heuristic algorithm allows sharing of partially aggregated results of preconfigured geographic regions and exploits the location attribute of sensor nodes as a grouping criterion. Simulation studies indicate the potential for significant energy savings with the proposed algorithms.
Identifying the role of proprioception in upper-limb prosthesis control
Authors: Blank Amy , Okamura Allison M. , Kuchenbecker Katherine J.
Published: June 2010

Proprioception plays a crucial role in enabling humans to move purposively and interact with their physical surroundings. Current technology in upper-limb prostheses, while beginning to incorporate some haptic feedback, does not provide amputees with proprioceptive information about the state of the limb. Thus, the wearer must visually monitor the limb, which is often inconvenient or even impossible for some tasks. This work seeks to quantify the potential benefits of incorporating proprioceptive motion feedback into upper-limb prosthesis designs. We apply a noninvasive method for controlling the availability of proprioceptive motion feedback in unimpaired individuals in a human subject study to compare the benefits of visual and proprioceptive motion feedback in targeted motion tasks. Combined results of the current study and our previous study using a different task indicate that the addition of proprioceptive motion feedback improves targeting accuracy under nonsighted conditions and, for some tasks, under sighted conditions as well. This work motivates the development of methods for providing artificial proprioceptive feedback to a prosthesis wearer.
“Writing with music”
Authors: Andersen Tue Haste , Zhai Shumin
Published: June 2010

We investigate the use of auditory feedback in pen-gesture interfaces in a series of informal and formal experiments. Initial iterative exploration showed that gaining performance advantage with auditory feedback was possible using absolute cues and state feedback after the gesture was produced and recognized. However, gaining learning or performance advantage from auditory feedback tightly coupled with the pen-gesture articulation and recognition process was more difficult. To establish a systematic baseline, Experiment 1 formally evaluated gesture production accuracy as a function of auditory and visual feedback. Size of gestures and the aperture of the closed gestures were influenced by the visual or auditory feedback, while other measures such as shape distance and directional difference were not, supporting the theory that feedback is too slow to strongly influence the production of pen stroke gestures. Experiment 2 focused on the subjective aspects of auditory feedback in pen-gesture interfaces. Participants' rating on the dimensions of being wonderful and stimulating was significantly higher with musical auditory feedback. Several lessons regarding pen gestures and auditory feedback are drawn from our exploration: a few simple functions such as indicating the pen-gesture recognition results can be achieved, gaining performance and learning advantage through tightly coupled process-based auditory feedback is difficult, pen-gesture sets and their recognizers can be designed to minimize visual dependence, and people's subjective experience of gesture interaction can be influenced using musical auditory feedback. These lessons may serve as references and stepping stones toward future research and development in pen-gesture interfaces with auditory feedback.
Social sites research through CourseRank
Authors: Bercovitz Benjamin , Kaliszan Filip , Koutrika Georgia , Liou Henry , Parameswaran Aditya , Venetis Petros , Zadeh Zahra Mohammadi , Garcia-Molina Hector
Published: June 2010

Social sites such as FaceBook, Orkut, Flickr, MySpace and many others have become immensely popular. At these sites, users share their resources (e.g., photos, profiles, blogs) and learn from each other. On the other hand, higher education applications help students and administrators track and manage academic information such as grades, course evaluations and enrollments. Despite the importance of both these areas, there is relatively little research on the mechanisms that make them effective. Apart from being both a successful social site and an academic planning site, CourseRank provides a live testbed for studying fundamental questions related to social networking, academic planning, and the fusion of these areas. In this paper, we provide a system overview and our main research efforts through CourseRank.
Arity-generic datatype-generic programming
Authors: Weirich Stephanie , Casinghino Chris
Published: June 2010

Some programs are doubly-generic. For example, map is datatype-generic in that many different data structures support a mapping operation. A generic programming language like Generic Haskell can use a single definition to generate map for each type. However, map is also arity-generic because it belongs to a family of related operations that differ in the number of arguments. For lists, this family includes repeat, map, zipWith, zipWith3, zipWith4, etc. With dependent types or clever programming, one can unify all of these functions together in a single definition.

However, no one has explored the combination of these two forms of genericity. These two axes are not orthogonal because the idea of arity appears in Generic Haskell: datatype-generic versions of repeat, map and zipWith have different arities of kind-indexed types. In this paper, we define arity-generic datatype-generic programs by building a framework for Generic Haskell-style generic programming in the dependently-typed programming language Agda 2.
Challenge benchmarks for verification of real-time programs
Authors: Kalibera Tomas , Parizek Pavel , Haddad Ghaith , Leavens Gary T. , Vitek Jan
Published: June 2010

Real-time systems, and in particular safety-critical systems, are a rich source of challenges for the program verification community as software errors can have catastrophic consequences. Unfortunately, it is nearly impossible to find representative safety-critical programs in the public domain. This has been significant impediment to research in the field, as it is very difficult to validate new ideas or techniques experimentally. This paper presents open challenges for verification of real-time systems in the context of the Real-time Specification for Java. But, our main contribution is a family of programs, called CDx, which we present as an open source benchmark for the verification community.
Online Learning 101: Part I
Authors: Landay Susan
Published: June 2010

The first part of this three-part series focuses on authoring and course development tools and techniques for integrating e-learning. In Part II, Susan Landay explores games and interactivity solutions for e-learning. Part III looks at tools used for web conferencing, as well as learning-management systems.
Online Learning 101: Part III
Authors: Landay Susan
Published: June 2010

In this exclusive three-part series, Susan Landay of Trainers Warehouse has been identifying the best ways for face-to-face trainers to add a component of e-learning to their repertoire, without the assistance of a fancy IT team or tens of thousands of dollars of investment. In Part I, she focused on tools for authoring and course development. In Part II, she looked at software for games and interactive learning. Here in Part III, she finishes with learning-management systems and conferencing applications to conduct live webinars.
Electrochemical Impedance Spectroscopy
Authors: Chang Byoung-Yong , Park Su-Moon
Published: June 2010

This review describes recent advances in electrochemical impedance spectroscopy (EIS) with an emphasis on its novel applications to various electrochemistry-related problems. Section 1 discusses the development of new EIS techniques to reduce measurement time. For this purpose, various forms of multisine EIS techniques were first developed via a noise signal synthesized by mixing ac waves of various frequencies, followed by fast Fourier transform of the signal and the resulting current. Subsequently, an entirely new concept was introduced in which true white noise was used as an excitation source, followed by Fourier transform of both excitation and response signals. Section 2 describes novel applications of the newly developed techniques to time-resolved impedance measurements as well as to impedance imaging. Section 3 is devoted to recent applications of EIS techniques, specifically traditional measurements in various fields with a special emphasis on biosensor detections.
Single-Molecule DNA Analysis
Authors: Efcavitch J. William , Thompson John F.
Published: June 2010

The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.
Microsystems for the Capture of Low-Abundance Cells
Authors: Dharmasiri Udara , Witek Małgorzata A. , Adams Andre A. , Soper Steven A.
Published: June 2010

Efficient selection and enumeration of low-abundance biological cells are highly important in a variety of applications. For example, the clinical utility of circulating tumor cells (CTCs) in peripheral blood is recognized as a viable biomarker for the management of various cancers, in which the clinically relevant number of CTCs per 7.5 ml of blood is two to five. Although there are several methods for isolating rare cells from a variety of heterogeneous samples, such as immunomagnetic-assisted cell sorting and fluorescence-activated cell sorting, they are fraught with challenges. Microsystem-based technologies are providing new opportunities for selecting and isolating rare cells from complex, heterogeneous samples. Such approaches involve reductions in target-cell loss, process automation, and minimization of contamination issues. In this review, we introduce different application areas requiring rare cell analysis, conventional techniques for their selection, and finally microsystem approaches for low-abundance-cell isolation and enumeration.
Adaptive Microsensor Systems
Authors: Gutierrez-Osuna Ricardo , Hierlemann Andreas
Published: June 2010

We provide a broad review of approaches for developing chemosensor systems whose operating parameters can adapt in response to environmental changes or application needs. Adaptation may take place at the instrumentation level (e.g., tunable sensors) and at the data-analysis level (e.g., adaptive classifiers). We discuss several strategies that provide tunability at the device level: modulation of internal sensing parameters, such as frequencies and operation voltages; variation of external parameters, such as exposure times and catalysts; and development of compact microanalysis systems with multiple tuning options. At the data-analysis level, we consider adaptive filters for change, interference, and drift rejection; pattern classifiers that can adapt to changes in the statistical properties of training data; and active-sensing techniques that can tune sensing parameters in real time. We conclude with a discussion of future opportunities for adaptive sensing in wireless distributed sensor systems.
Evaluation of DNA/Ligand Interactions by Electrospray Ionization Mass Spectrometry
Authors: Brodbelt Jennifer S.
Published: June 2010

Electrospray ionization mass spectrometry (ESI-MS) has enabled the detection and characterization of DNA/ligand complexes, including evaluation of both relative binding affinities and selectivities of DNA-interactive ligands. The noncovalent complexes that are transferred from the solution to the gas phase retain the signature of the native species, thus allowing the use of MS to screen DNA/ligand complexes, reveal the stoichiometries of the complexes, and provide insight into the nature of the interactions. Ligands that bind to DNA via metal-mediated modes and those that bind to unusual DNA structures, such as quadruplexes, are amenable to ESI. Chemical probe methods applied to DNA/ligand complexes with ESI-MS detection afford information about ligand-binding sites and conformational changes of DNA that occur upon ligand binding.
In Situ Optical Studies of Solid-Oxide Fuel Cells
Authors: Pomfret Michael B. , Owrutsky Jeffrey C. , Walker Robert A.
Published: June 2010

Thermal imaging and vibrational spectroscopy have become important tools for examining the physical and chemical changes that occur in real time in solid-oxide fuel cells (SOFCs). Imaging techniques can resolve temperature differences as fine as 0.1°C across a SOFC electrode at temperatures higher than 600°C. Vibrational spectroscopy can identify molecular species and changes in material phases in operating SOFCs. This review discusses the benefits and challenges associated with directly observing processes that are important to SOFC performance and durability. In situ optical methods can provide direct insight into reaction mechanisms that can be inferred only indirectly from electrochemical measurements such as voltammetry and electrochemical impedance spectroscopy and from kinetic models and postmortem, ex situ examinations of SOFC components. Particular attention is devoted to recent advances that, hopefully, will spur the development of new generations of efficient, versatile energy-producing devices.
Rotationally Induced Hydrodynamics: Fundamentals and Applications to High-Speed Bioassays
Authors: Wang Gufeng , Driskell Jeremy D. , Hill April A. , Dufek Eric J. , Lipert Robert J. , Porter Marc D.
Published: June 2010

Bioassays are indispensable tools in areas ranging from fundamental life science research to clinical practice. Improving assay speed and levels of detection will have a profound impact in all of these areas. We recently developed a rapid, sensitive format for immunosorbent assays that expedites antigen mass transport by rotating the capture substrate. This review outlines the theoretical foundation of rotationally induced hydrodynamics and its application in heterogeneous assays. We describe a general solution that solves the rates of immunoreactions on rotating capture substrates, taking into account both diffusion and the rate of reaction between antibody and antigen. The general solution applies to a wide range of rotation rates, including mass transport–limited to reaction rate–limited assays, and is validated experimentally. We discuss several applications that demonstrate how immunoassays can be tailored to increase speed as well as lower the limit of detection of viral particles, pathogens, toxins, and proteins.
Scanning Electrochemical Microscopy in Neuroscience
Authors: Schulte Albert , Nebel Michaela , Schuhmann Wolfgang
Published: June 2010

This article reviews recent work involving the application of scanning electrochemical microscopy (SECM) to the study of individual cultured living cells, with an emphasis on topographical and functional imaging of neuronal and secretory cells of the nervous and endocrine system. The basic principles of biological SECM and associated negative amperometric-feedback and generator/collector-mode SECM imaging are discussed, and successful use of the methodology for screening soft and fragile membranous objects is outlined. The drawbacks of the constant-height mode of probe movement and the benefits of the constant-distance mode of SECM operation are described. Finally, representative examples of constant-height and constant-distance mode SECM on a variety of live cells are highlighted to demonstrate the current status of single-cell SECM in general and of SECM in neuroscience in particular.
Ambient Ionization Mass Spectrometry
Authors: Huang Min-Zong , Yuan Cheng-Hui , Cheng Sy-Chyi , Cho Yi-Tzu , Shiea Jentaie
Published: June 2010

Mass spectrometric ionization methods that operate under ambient conditions and require minimal or no sample pretreatment have attracted much attention in such fields as biomedicine, food safety, antiterrorism, pharmaceuticals, and environmental pollution. These technologies usually involve separate ionization and sample-introduction events, allowing independent control over each set of conditions. Ionization is typically performed under ambient conditions through use of existing electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) techniques. Rapid analyses of gas, liquid, and solid samples are possible with the adoption of various sample-introduction methods. This review sorts different ambient ionization techniques into two main subcategories, primarily on the basis of the ionization processes, that are further differentiated in terms of the approach used for sampling.
Electrochemical Aspects of Electrospray and Laser Desorption/Ionization for Mass Spectrometry
Authors: Abonnenc Mélanie , Qiao Liang , Liu BaoHong , Girault Hubert H.
Published: June 2010

Soft-ionization methods, namely electrospray ionization and laser desorption/ionization, are widely used to transfer large molecules as intact gas-phase ions either from a solution or from a solid substrate. During both processes, in-source electrochemical and photoelectrochemical reactions occur. These electrode reactions, which take place at interfaces, play important roles in influencing the ionization products, but they have received little attention. We show that having good control over both types of electrochemical reactions can lead to new analytical applications. Examples include online tagging by grafting of mass tags and in-source photooxidation of peptides.
Involvement of TAGE-RAGE System in the Pathogenesis of Diabetic Retinopathy
Authors: Takeuchi Masayoshi , Takino Jun-ichi , Yamagishi Sho-ichi
Published: June 2010

Diabetic complications are a leading cause of acquired blindness, end-stage renal failure, and accelerated atherosclerosis, which are associated with the disabilities and high mortality rates seen in diabetic patients. Continuous hyperglycemia is involved in the pathogenesis of diabetic micro- and macrovascular complicationsviavarious metabolic pathways, and numerous hyperglycemia-induced metabolic and hemodynamic conditions exist, including increased generation of various types of advanced glycation end-products (AGEs). Recently, we demonstrated that glyceraldehyde-derived AGEs, the predominant structure of toxic AGEs (TAGE), play an important role in the pathogenesis of angiopathy in diabetic patients. Moreover, recent evidence suggests that the interaction of TAGE with the receptor for AGEs (RAGE) elicits oxidative stress generation in numerous types of cells, all of which may contribute to the pathological changes observed in diabetic complications. In this paper, we discuss the pathophysiological role of the TAGE-RAGE system in the development and progression of diabetic retinopathy.
Surface Functionality Features of Nanosized Silica Obtained by Electron Beam Evaporation at Ambient Pressure
Authors: Bardakhanov S. P. , Vasiljeva I. V. , Kuksanov N. K. , Mjakin S. V.
Published: June 2010

A series of nanosized silica powders with different specific surface values are synthesized by electron beam evaporation in air at ambient pressure. The obtained silica samples are featured with relatively low apparent density and high content of oxygen and hydroxyl groups on the surface making these materials promising for specific applications.
Mechanism of Cytosolic Phospholipase Activation in Ghrelin Protection of Salivary Gland Acinar Cells against Ethanol Cytotoxicity
Authors: Slomiany Bronislaw L. , Slomiany Amalia
Published: June 2010

Ghrelin, a peptide hormone, newly identified in oral mucosal tissues, has emerged recently as an important mediator of the processes of mucosal defense. Here, we report on the mechanism of ghrelin protection against ethanol cytotoxicity in rat sublingual salivary gland cells. The protective effect of ghrelin was associated with the increase in NO and PGE2, and upregulation in cytosolic phospholipase () activity and arachidonic acid (AA) release. The loss in countering effect of ghrelin occurred with cNOS inhibitor, L-NAME, as well as indomethacin and COX-1 inhibitor, SC-560, while COX-2 inhibitor, NS-398, and iNOS inhibitor, 1400W, had no effect. The effect of L-NAME was reflected in the inhibition of ghrelin-induced cell capacity for NO production, activation and PGE2 generation, whereas indomethacin caused only the inhibition in PGE2. Moreover, the ghrelin-induced up-regulation in AA release was reflected in the phosphorylation and S-nitrosylation. Inhibition in ghrelin-induced S-nitrosylation was attained with L-NAME, whereas the ERK inhibitor, PD98059, caused the blockage in protein phosphorylation as well as S-nitrosylation. Thus, ghrelin protection of salivary gland cells against ethanol involves cNOS-derived NO induction of activation through S-nitrosylation for the increase in AA release at the site of COX-1 action for PGE2 synthesis.
Modelling and Quasilinear Control of Compressor Surge and Rotating Stall Vibrations
Authors: Vepa Ranjan
Published: June 2010

An unsteady nonlinear and extended version of the Moore‐Greitzer model is developed to facilitate the synthesis of a quasilinear stall vibration controller. The controller is synthesised in two steps. The first step defines the equilibrium point and ensures that the desired equilibrium point is stable. In the second step, the margin of stability at the equilibrium point is tuned or increased by an appropriate feedback of change in the mass flow rate about the steady mass flow rate at the compressor exit. The relatively simple and systematic non‐linear modelling and linear controller synthesis approach adopted in this paper clearly highlights the main features on the controller that is capable of inhibiting compressor surge and rotating stall vibrations. Moreover, the method can be adopted for any axial compressor provided its steady‐state compressor and throttle maps are known.
Approach Merotopological Spaces and their Completion
Authors: Khare Mona , Tiwari Surabhi
Published: June 2010

This paper introduces the concept of an approach merotopological space and studies its category‐theoretic properties. Various topological categories are shown to be embedded into the category whose objects are approach merotopological spaces. The order structure of the family of all approach merotopologies on a nonempty set is discussed. Employing the theory of bunches, bunch completion of an approach merotopological space is constructed. The present study is a unified look at the completion of metric spaces, approach spaces, nearness spaces, merotopological spaces, and approach merotopological spaces.
The Solution of Mitchell′s Problem for the Elastic Infinite Cone with a Spherical Crack
Authors: Popov G. Ya. , Vaysfel′d N. D.
Published: June 2010

The new problem about the stress concentration around a spherical crack inside of an elastic cone is solved for the point tensile force enclosed to a cone′s edge. The constructed discontinuous solutions of the equilibrium equations have allowed to express the displacements and stress in a cone through their jumps and the jumps of their normal derivatives across the crack′s surface. The application of the integral transformation method under the generalized scheme has reduced the problem solving to the solving of the integrodifferential equation system with regard to the displacements′ jumps. This system was solved approximately by the orthogonal polynomial method. The use of this method has allowed to take into consideration the order of the solution′s singularities at the ends of an integral interval. The correlation between the crack′s geometrical parameters, its distance from an edge, and the SIF values is established after the numerical analysis. The limit of the proposed method applicability is specified.
Anti-TNF-α Therapies in Systemic Lupus Erythematosus
Authors: Zhu Lang-Jing , Yang Xiao , Yu Xue-Qing
Published: June 2010

Tumor necrosis factor (TNF)- is not just a proinflammatory cytokine. It has also been proposed to be an immunoregulatory molecule that can alter the balance of T regulatory cells. Anti-TNF- therapies have been provided clinical benefit to many patients and introduced for treating moderate to severe rheumatoid arthritis, Crohn's disease, and other chronic inflammatory disorders. However, their use also is accompanied by new or aggravated forms of autoimmunity, such as formation of autoantibodies, including antinuclear antibodies (ANAs), antidouble-stranded DNA (dsDNA) antibodies, and anticardiolipin antibodies (ACL). Systemic lupus erythematosus (SLE) is a disease with autoimmune disturbance and inflammatory damage. The role of TNF- in human SLE is controversial. Here we review the role of TNF- in the pathophysiological processes of SLE and the likely effects of blocking TNF- in treatment of SLE.
Imprinting and Promoter Usage of Insulin‐Like Growth Factor II in Twin Discordant Placenta
Authors: Luo Yan-Min , Fang Qun , Shi Hui-Juan , Huang Lin-Huan , Liang Run-Cai , Zhuang Guang-Lun
Published: June 2010

Case reports from infant twins suggest that abnormal genomic imprinting may be one of the important causes of twin discordance, but it is unknown whether abnormal genomic imprinting occurs in the placenta. Therefore, we sought to determine the relationship between the imprinting of insulin‐like growth factor II (IGF‐II) in placenta and twin discordance. We analyzed the imprinting and promoter usage of IGF‐II in placenta of normal twins (T0 group), weight discordance (T1 group), and phenotype discordance (T2 group). We found the incidence of loss of imprinting (LOI) for IGF‐II was higher in the T2 group than that in the T0 and T1 groups, while there was no difference between T0 and T1 groups. The transcripts of promoter 3 were lower in the T2 group than in the T0 and T1 groups, and lower in the twin placenta with LOI than in those with normal imprinting. Our findings indicate that the promoter 3 specific LOI of the IGF‐II gene may be closely related with phenotype discordance, not weight discordance.
Lagochilascaris minor: Susceptibility and Resistance to Experimental Infection in Mice Is Independent of H-2aHaplotype and Correlates with the Immune Response in Immunized Animals
Authors: Spadafora-Ferreira Mônica , Fernandes Luciana Caetano , Hoffman Pfrimer Irmtraut Araci , Pichiteli Cássia Regina , Vilarinho Tambourgi Denise , Lino-Junior Ruy de Souza , Carvalhaes Mara Silvia
Published: June 2010

Recently, we demonstrated that C57BL/6 mice are more susceptible to experimental lagochilascariosis than BALB/c mice. To investigate the pattern of infection and the role of the genetic background on susceptibility to infection, we studied experimental lagochilascariosis in H-2aidentical B10.A and A/J mice. Infected B10.A mice had a lower survival ratio and more severe lesions in the lungs than did A/J mice. Splenocytes of A/J mice immunized with the crude extract of the parasite showed increased proliferation and produced a higher level of interleukin 10 and interferon-γin the presence of CE or concanavalin A when compared to B10.A mice. This suggests that resistance of A/J mice may be due to less severe lesions in lungs and other organs and a better immune response to parasite antigens. This paper provides evidence that major histocompatibility complex haplotype does not influence the survival to experimental infection withL. minor.
Interactions of Trivalent Lanthanide Cations with a New Hexadentate Di‐Schiff Base: New Lanthanide(III) Complexes from (NE,N′E)‐2,2′‐(ethane‐1,2‐diylbis(oxy))bis(N‐(pyridin‐2‐ylmethylene)ethanamine)
Authors: Tsiouri Mantha , Skorda Konstantina , Papadimitriou Christos , Li Yang , Woollins J. Derek , Plakatouras John C.
Published: June 2010

The novel lanthanide(III) complexes 3MeOH (Ln = La 1, Pr 2) and 2MeOH (Ln = Gd 3, Yb 4), where L = (NE,N′E)‐2,2′‐(ethane‐1,2‐diylbis(oxy))bis(N‐(pyridin‐2‐ylmethylene)ethanamine), have been obtained by direct reaction of the Schiff base ligand and the corresponding hydrated lanthanide(III) nitrates in methanol. All complexes were characterized spectroscopically and thermogravimetrically. Complex 4 was also characterized with crystallographic studies: orthorhombic P212121, a = 10.6683(14), b = 13.4752(15), c = 19.3320(26) Å. In the molecular structure of 4, Yb(III) is surrounded by all donor atoms of the Schiff base (four nitrogen and two oxygen atoms) and four oxygen atoms belonging to two bidentate chelating nitrato ligands.
Ten-Year (1999–2009) Epidemiological and Virological Surveillance of Influenza in South Italy (Apulia)
Authors: Campa Annamaria , Quattrocchi Manuela , Guido Marcello , Gabutti Giovanni , Germinario Cinzia , De Donno Antonella , Group The Influenza Collaborative
Published: June 2010

Clinical and epidemiological surveillance of influenza and other Acute Respiratory Infections (ARI) are currently a major objective of Public Health.
The aim was to describe the epidemiology of influenza using the Italian surveillance system. Vaccination Coverage (VC) rates were calculated during 1999-2009 influenza seasons. Molecular studies of influenza virus isolated, from patients with ILI, living in Apulia, are described.
1269 nasal-pharyngeal swabs were taken from patients with ILI and ARI in order to isolate and identify viruses using PCR.
Influenza isolates are typed as being types A and B and influenza A isolates are A/H1 and A/H3.
The progression of the ILI cases registered in Apulia was similar to the data recorded on a national level.
The VC data recorded in Apulia showed a progressive increase in the vaccine doses administered to subjects over 65 years old.
The virological surveillance showed a major circulation of the type A/H3N2 influenza virus during the peak incidence of the illness in seasons 1999-2000, 2002-2003, 2004-2005 and 2008-2009. During the same period, the lowest incidence was registered when the type A/H1N1 and B viruses were in circulation. In contrast, during the other seasons the lowest incidence was reported with A/H3N2 and B viruses.