bluuebunny/crossref_metadata_2025 huggingface dataset:
Neanderthal genomics and the evolution of modern humans: Figure 1.
Authors: Noonan James P.
Published: May 2010

Humans possess unique physical and cognitive characteristics relative to other primates. Comparative analyses of the human and chimpanzee genomes are beginning to reveal sequence changes on the human lineage that may have contributed to the evolution of human traits. However, these studies cannot identify the genetic differences that distinguish modern humans from archaic human species. Here, I will discuss efforts to obtain genomic sequence from Neanderthal, the closest known relative of modern humans. Recent studies in this nascent field have focused on developing methods to recover nuclear DNA from Neanderthal remains. The success of these early studies has inspired a Neanderthal genome project, which promises to produce a reference Neanderthal genome sequence in the near future. Technical issues, such as the level of Neanderthal sequence coverage that can realistically be obtained from a single specimen and the presence of modern human contaminating sequences, reduce the detection of authentic human–Neanderthal sequence differences but may be remedied by methodological improvements. More critical for the utility of a Neanderthal genome sequence is the evolutionary relationship of humans and Neanderthals. Current evidence suggests that the modern human and Neanderthal lineages diverged before the emergence of contemporary humans. A fraction of biologically relevant human–chimpanzee sequence differences are thus likely to have arisen and become fixed exclusively on the modern human lineage. A reconstructed Neanderthal genome sequence could be integrated into human–primate genome comparisons to help reveal the evolutionary genetic events that produced modern humans.
β-Galactosidase Activity Staining of Frozen Adult Drosophila Retinas
Authors: Wolff Tanya
Published: May 2010

INTRODUCTION

This protocol provides a method for identification of specific cell types in frozen adult Drosophila retina using β-galactosidase staining.
Preparation and Analysis of PEGylated Poly-L-Lysine DNA Nanoparticles for Gene Delivery
Authors: Davis Pamela B. , Kowalczyk Tomasz H.
Published: May 2010

INTRODUCTION

PEGylated poly-L-lysine DNA nanoparticles are composed of plasmid DNA compacted with poly-L-lysine conjugated with polyethylene glycol (PEG). They are soluble and stable in saline and tissue fluids, transfect nondividing cells, display minimal toxicity, and are effective in vivo and in humans. Moreover, they are easy to prepare in a reliable and reproducible fashion. These properties represent a substantial advance for nonviral gene transfer. This article describes the conjugation of methoxy-PEG-maleimide with the peptide CK30 and the compaction of DNA with the resultant PEGylated polylysine. It also describes the analyses used to check the morphology and colloidal stability of the nanoparticles. These assays should be performed each time the nanoparticles are prepared because, although the compaction procedure is very reproducible, variations in product quality do sometimes occur (e.g., the particles are unstable or have an unacceptable morphology). Variations seem to happen most often when the source of plasmid or method of plasmid production is changed.
Chloramphenicol Acetyltransferase Assay
Authors: Smale Stephen T.
Published: May 2010

INTRODUCTION

When a transient or stable transfection assay is developed for a promoter, a primary objective is to quantify promoter strength. Because transfection efficiency in such assays can be low, promoters are commonly fused to heterologous reporter genes that encode enzymes that can be quantified using highly sensitive assays. The reporter protein’s activity or fluorescence within a transfected cell population is approximately proportional to the steady-state mRNA level. In this protocol, cells transfected with an Escherichia coli transposon chloramphenicol acetyltransferase (CAT) reporter plasmid are lysed by repeated cycles of freezing and thawing and cellular debris is removed by centrifugation. The lysate is incubated with [14C]chloramphenicol and acetyl-coenzyme A; CAT catalyzes the acetylation of chloramphenicol. The acetylated products and the unmodified reactants are separated from the aqueous solution by organic extraction with ethyl acetate. Acetylation is monitored by autoradiography following thin-layer chromatography (TLC) to separate the acetylated from the unacetylated forms. The percent conversion of [14C]chloramphenicol to acetyl-[14C]chloramphenicol can be measured by PhosphorImager analysis of the TLC plate, by excising the radioactive spots from the TLC plate and counting in a scintillation counter, or by densitometry analysis of an autoradiograph. The acetylated 14C-labeled product can also be quantified without TLC by organic extraction and scintillation counting using reagent-grade chemicals.
SEC/Reversed-Phase Separation of E. coli Proteins: Figure 1.
Authors: Apffell Alex
Published: May 2010

INTRODUCTION

Although many chromatographic modes can be coupled for the multidimensional separation of a complex mixture, a very favorable combination is that of size-exclusion chromatography (SEC) and reversed-phase chromatography. The separation mechanisms are largely orthogonal and the mobile phases are compatible. The use of a retentive second dimension allows trapping of specific fractions from the SEC separation and transferring them to the reversed-phase separation. One of the advantages of multidimensional chromatography is that it is scalable in terms of automation. In a completely manual system, fractions eluting from a first dimension can be manually collected and injected into a second separation dimension. In an automated system, fraction transfer can be accomplished through automated valving. The following protocol illustrates this approach, with both a manual method and an external column switching method integrated into an automated high-performance liquid chromatography (HPLC) method. As an illustration, soluble proteins from Escherichia coli are separated.
Preparation of Fixed Xenopus Embryos for Confocal Imaging
Authors: Wallingford John B.
Published: May 2010

INTRODUCTION

Although live imaging of embryonic development is a powerful approach, it is often essential to use immunostaining or in situ hybridization to reveal structures or to localize proteins or gene expression patterns. For these approaches, fixed embryos must be used, and Xenopus offers many advantages. Xenopus is a vertebrate tetrapod closely related to mammals. The large size of their embryos makes them ideal for imaging patterns of gene expression during development. Also, individual Xenopus embryonic cells are larger than those of other vertebrate models, making them suitable for imaging cell morphology and subcellular processes. Xenopus embryos are amenable to simple manipulations of gene function, including knockdown and misexpression, and the large numbers of embryos produced allow even an inexperienced researcher to perform such manipulations on hundreds of embryos per day. Transgenesis is quite effective as well. Finally, because the fate map of Xenopus embryos is stereotypical, simple targeted microinjections can reliably deliver reagents into specific tissues and cell types for gene manipulation or for imaging. To improve image quality for fixed specimens, the pigment of the Xenopus embryo can be removed by bleaching. Also, although Xenopus embryos are opaque because of the large amounts of yolk stored in each cell, they can easily be rendered transparent using a process called clearing. This protocol describes the methods for bleaching and clearing Xenopus embryos, as well as a simple procedure for vibratome sectioning. These approaches are effective for imaging embryos and cells following immunostaining or in situ hybridization.
High-Magnification In Vivo Imaging of Xenopus Embryos for Cell and Developmental Biology
Authors: Kieserman Esther K. , Lee Chanjae , Gray Ryan S. , Park Tae Joo , Wallingford John B.
Published: May 2010

INTRODUCTION

Embryos of the frog Xenopus laevis are an ideal model system for in vivo imaging of dynamic biological processes, from the inner workings of individual cells to the reshaping of tissues during embryogenesis. Their externally developing embryos are more amenable to in vivo analysis than internally developing mammalian embryos, and the large size of the embryos make them particularly suitable for time-lapse analysis of tissue-level morphogenetic events. In addition, individual cells in Xenopus embryos are larger than those in other vertebrate models, making them ideal for imaging cell behavior and subcellular processes (e.g., following the dynamics of fluorescent fusion proteins in living or fixed cells and tissues). Xenopus embryos are amenable to simple manipulations of gene function, including knockdown and misexpression, and the large number of embryos available allows even an inexperienced researcher to perform hundreds of such manipulations per day. Transgenesis is quite effective as well. Finally, because the fate map of Xenopus embryos is stereotypical, simple targeted microinjections can reliably deliver reagents into specific tissues and cell types for gene manipulation or for imaging. Although yolk opacity can hinder deep imaging in intact embryos, almost any cell in the early embryo can be placed into organotypic culture, such that the cells of interest are directly apposed to the cover glass. Furthermore, live imaging techniques can be complemented with immunostaining and in situ hybridization approaches in fixed tissues. This protocol describes methods for labeling and high-magnification time-lapse imaging of cell biological and developmental processes in Xenopus embryos by confocal microscopy.
FAST Technique for Agrobacterium-Mediated Transient Gene Expression in Seedlings of Arabidopsis and Other Plant Species
Authors: Li Jian-Feng , Nebenführ Andreas
Published: May 2010

INTRODUCTION

Genome sequencing has identified a massive number of uncharacterized genes in Arabidopsis thaliana and several other plant species. To decipher these unknown gene functions, several transient expression assays have been developed as rapid and convenient alternatives to the lengthy creation of transgenic plants. As one of these transient assays, Agrobacterium-mediated transformation harnesses the natural capability of Agrobacterium to transfer foreign DNA into plant cells with intact cell walls. However, pioneering applications of Agrobacterium-based transient transformation to Arabidopsis have led to rather limited success with great variability. In this protocol, we describe a Fast Agrobacterium-mediated Seedling Transformation (FAST) technique for transient gene expression analysis in Arabidopsis and other dicot or monocot species. This technique makes use of the cocultivation of young plant seedlings with Agrobacterium in the presence of the surfactant Silwet L-77. The young seedlings can be grown easily and were found to be more susceptible to Agrobacterium transformation compared with adult plants. The surfactant facilitates transformation of plant cells, thus replacing wounding or a device-dependent vacuum step during plant transformation. This protocol provides a quick, efficient, and economical assay for gene function in intact plants with minimal manual handling and without the need for a dedicated device.
Yeast Two-Hybrid System for Studying Protein-Protein Interactions--Stage 1: Construction and Characterization of a Bait Protein
Authors: Serebriiskii Ilya
Published: May 2010

INTRODUCTION

An important element in the characterization of the function of a protein is the identification of other proteins with which it interacts. A powerful genetic strategy for this purpose, termed the yeast two-hybrid system, uses transcriptional reporters in yeast to indirectly reflect the interaction between two proteins. The term two-hybrid derives from the two classes of chimeric, or “hybrid,” proteins used in each screen. The first, commonly referred to as the “bait,” is a fusion of a protein of interest “x” with a DNA-binding domain (DBD-x). The second, sometimes called the “prey,” is a fusion of a cDNA library “y” to a transcriptional activation domain (AD-y). Together, DBD-x and AD-y provide the basis of the detection system. The two-hybrid approach has gained wide popularity because of the relative ease and speed with which it can be used to identify novel protein-protein interactions and to analyze known interactions. In stage 1 of the method, detailed in this protocol, characterization of a novel bait is described, with attention to controls that increase the chance of the bait functioning in a two-hybrid screen.
Yeast Two-Hybrid System for Studying Protein-Protein Interactions--Stage 2: Transforming and Characterizing the Library
Authors: Serebriiskii Ilya
Published: May 2010

INTRODUCTION

An important element in the characterization of the function of a protein is the identification of other proteins with which it interacts. A powerful genetic strategy for this purpose, termed the “yeast two-hybrid system,” uses transcriptional reporters in yeast to indirectly reflect the interaction between two proteins. The term “two-hybrid” derives from the two classes of chimeric, or “hybrid,” proteins used in each screen. The first, commonly referred to as the “bait,” is a fusion of a protein of interest “x” with a DNA-binding domain (DBD-x). The second, sometimes called the “prey,” is a fusion of a cDNA library “y” to a transcriptional activation domain (AD-y). Together, DBD-x and AD-y provide the basis of the detection system. The two-hybrid approach has gained wide popularity because of the relative ease and speed with which it can be used to identify novel protein-protein interactions and to analyze known interactions. The second stage of the method, described in this protocol, includes the transformation of yeast with a cDNA library, followed by library characterization. It can be performed in parallel with construction of a bait protein (stage 1).
Yeast Two-Hybrid System for Studying Protein-Protein Interactions--Stage 3: Screen for Interacting Proteins
Authors: Serebriiskii Ilya
Published: May 2010

INTRODUCTION

An important element in the characterization of the function of a protein is the identification of other proteins with which it interacts. A powerful genetic strategy for this purpose, termed the “yeast two-hybrid system,” uses transcriptional reporters in yeast to indirectly reflect the interaction between two proteins. The term “two-hybrid” derives from the two classes of chimeric, or “hybrid,” proteins used in each screen. The first, commonly referred to as the “bait,” is a fusion of a protein of interest “x” with a DNA-binding domain (DBD-x). The second, sometimes called the “prey,” is a fusion of a cDNA library “y” to a transcriptional activation domain (AD-y). Together, DBD-x and AD-y provide the basis of the detection system. The two-hybrid approach has gained wide popularity because of the relative ease and speed with which it can be used to identify novel protein-protein interactions and to analyze known interactions. Once the bait strain has been made and characterized (stage 1) and the library strain has been transformed and frozen in aliquots (stage 2), the next step is to mate the two strains. Stage 3 of the method, described here, details the mating and screening of the cDNA library for positive interactors.
Yeast Two-Hybrid System for Studying Protein-Protein Interactions--Stage 4: Isolation of Library Plasmid Insert and Second Confirmation of Positive Interactions
Authors: Serebriiskii Ilya
Published: May 2010

INTRODUCTION

An important element in the characterization of the function of a protein is the identification of other proteins with which it interacts. A powerful genetic strategy for this purpose, termed the “yeast two-hybrid system,” uses transcriptional reporters in yeast to indirectly reflect the interaction between two proteins. The term “two-hybrid” derives from the two classes of chimeric, or “hybrid,” proteins used in each screen. The first, commonly referred to as the “bait,” is a fusion of a protein of interest “x” with a DNA-binding domain (DBD-x). The second, sometimes called the “prey,” is a fusion of a cDNA library “y” to a transcriptional activation domain (AD-y). Together, DBD-x and AD-y provide the basis of the detection system. The two-hybrid approach has gained wide popularity because of the relative ease and speed with which it can be used to identify novel protein-protein interactions and to analyze known interactions. Stage 4, described here, outlines a series of first-order and subsequent control experiments designed to establish whether an interacting protein is likely to be biologically significant. The number of positive interactions obtained will vary drastically from bait to bait. Subsequent processing methods will depend on the number initially obtained and on the preference of the individual investigator.
Visualizing Fetal Mouse Great Blood Vessels by Plastic Casting: Figure 1.
Authors: Liu Chengyu , Martin Jim
Published: May 2010

INTRODUCTION

In this protocol, the great vessels of the mouse are visualized by injecting colored plastic solutions directly into the heart, thereby filling the vessels. The plastic solidifies to create a stable cast that is then revealed by removing the mouse tissues with a caustic. This protocol can be modified for casting the vasculature of other organs by altering the delivery of the liquid plastic. For example, plastic casts of the maternal and fetal vasculature of the placenta can be generated.
DNA Isolation from Rat Tail or Ear
Authors: Cuppen Edwin
Published: May 2010

INTRODUCTION

This protocol describes a rapid procedure for isolating DNA from rat tail or ear punches. The simplest version of the protocol can be scaled for use in 96-well (deep-well) plates. The quality of the DNA is sufficient for any polymerase chain reaction (PCR)-based genotyping approach.
Dynamic Balancing of Spherical 4R Linkages
Authors: Moore Brian , Schicho Josef , Gosselin Clément M.
Published: May 2010

A mechanism, which, for any motion, does not apply reaction forces on the base, is said to be statically or force balanced. It is moment balanced or dynamically balanced if, moreover, it does not apply torques on the base. In this paper, an approach to determine the complete set of statically balanced spherical four-bar linkages is presented. Furthermore, it is shown that for all possible design parameters, it is not possible to dynamically balance such linkages.
Instant-Center Based Force Transmissivity and Singularity Analysis of Planar Linkages
Authors: Simionescu P. A. , Talpasanu I. , Di Gregorio R.
Published: May 2010

The instant centers of velocity (ICs) of most planar mechanisms can be determined as the intersection of the lines of centers, also known as Aronhold–Kennedy lines, along which the ICs of three distinct links in relative motion are located. It is shown how these intersections can be kept track of in matrix form, very suitable to algorithmic implementation on a computer. Solving for the coordinates of the actual instant centers can be also cast in matrix form. Moreover, the singularity and force transmissivity of the mechanism are reflected in the condition numbers of these matrices and the degree of dispersion of the secondary instant centers i.e., the instant centers that cannot be found by inspection.
A Unified Approach to Direct Kinematics of Some Reduced Motion Parallel Manipulators
Authors: Zsombor-Murray P. J. , Gfrerrer A.
Published: May 2010

After discussing the Study point transformation operator, a unified way to formulate kinematic problems, using “points moving on planes or spheres” constraint equations, is introduced. Application to the direct kinematics problem solution of a number of different parallel Schönflies motion robots is then developed. Certain not widely used but useful tools of algebraic geometry are explained and applied for this purpose. These constraints and tools are also applied to some special parallel robots called “double triangular” to show that the approach is flexible and universally pertinent to manipulator kinematics in reducing the complexity of some previously achieved solutions. Finally a novel two-legged Schönflies architecture is revealed to emphasize that good design is not only essential to good performance but also to easily solve kinematic models. In this example architecture, with double basally actuated legs so as to minimize moving mass, the univariate polynomial solution turns out to be simplest, i.e., of degree 2.
Slider-Cranks as Compatibility Linkages for Parametrizing Center-Point Curves
Authors: Myszka David H. , Murray Andrew P.
Published: May 2010

In synthesizing a planar 4R linkage that can achieve four positions, the fixed pivots are constrained to lie on a center-point curve. It is widely known that the curve can be parametrized by a 4R compatibility linkage. In this paper, a slider-crank is presented as a suitable compatibility linkage to generate the center-point curve. Furthermore, the center-point curve can be parametrized by the crank angle of a slider-crank linkage. It is observed that the center-point curve is dependent on the classification of the slider-crank. Lastly, a direct method to calculate the focus of the center-point curve is revealed.
Analytical and Experimental Assessment of Some Novel Variable-Valve-Actuation Mechanisms
Authors: Gecim Burak , Raghavan Madhusudan
Published: May 2010

We describe our analytical and experimental works on three novel variable valve actuation systems. These include a mechanical variable-lift and duration concept, a hydraulic-lost-motion variable-lift system, and a valve-deactivation mechanism with unique features. These devices differ in their complexity and versatility but offer a spectrum of design solutions applicable to a range of products. The strengths and weaknesses of these different approaches are discussed and analyzed, and some test results are presented.
On the Dynamic Properties of Rigid-Link Flexible-Joint Parallel Manipulators in the Presence of Type 2 Singularities
Authors: Briot Sébastien , Arakelian Vigen
Published: May 2010

In our previous work (2008, “Optimal Force Generation in Parallel Manipulators for Passing through the Singular Positions,” Int. J. Robot. Res., 27(8), pp. 967–983), the dynamic properties of rigid-link parallel manipulators, in the presence of type 2 singularities, have been studied. It was shown that any parallel manipulator can pass through the singular positions without perturbation of motion if the wrench applied on the end-effector by the legs and external efforts of the manipulator are orthogonal to the twist along the direction of the uncontrollable motion. This condition was obtained using the symbolic approach based on the inverse dynamics and the study of the Lagrangian of a general rigid-link parallel manipulator. It was validated by experimental tests carried out on the prototype of a four-degrees-of-freedom parallel manipulator. However, it is known that the flexibility of the mechanism may not always be neglected. Indeed, joint flexibility is the main source contributing to the overall manipulator flexibility and it leads to the trajectory distortion. Therefore, in this paper, the condition for passing through a type 2 singularity of parallel manipulators with flexible joints is studied. The suggested technique is illustrated by the example of a 5R parallel manipulator with flexible joints. It is shown that passing through singularity is possible if the 12th-order polynomial trajectory planning is applied. The obtained results are validated by the numerical simulations carried out using the ADAMS software.
Determining the Number of Inverse Kinematic Solutions of a Constrained Parallel Mechanism Using a Homotopy Algorithm
Authors: Newkirk Jeremy T. , Watson Layne T. , Stanišić Michael M.
Published: May 2010

This paper numerically determines the number of real-valued inverse kinematic solutions to a constrained parallel mechanism composed of three triangular platforms. The base and middle platforms are connected by three fixed-length legs, while the middle and distal platforms are connected by three variable length legs that extend out of the fixed-length legs in a collinear fashion. All legs are connected to the platforms via spherical joints at the corners. This mechanism is intended to replicate the motion of a human shoulder girdle. The constrained parallel mechanism has a multivalued solution to the inverse kinematics problem. A homotopy method was used to numerically compute the inverse kinematic solutions for over 100 cases. Each case was filtered for the number of real-valued solutions. The maximum number of real solutions was found to be 8, but in some cases there were fewer solutions.
Design of a Bio-Inspired Spherical Four-Bar Mechanism for Flapping-Wing Micro Air-Vehicle Applications
Authors: McDonald Matt , Agrawal Sunil K.
Published: May 2010

The design of flapping-wing micro air-vehicles presents many engineering challenges. As observed by biologists, insects and birds exhibit complex three-dimensional wing motions. It is believed that these unique patterns of wing motion create favorable aerodynamic forces that enable these species to fly forward, hover, and execute complex motions. From the perspective of micro air-vehicle applications, extremely light-weight designs that accomplish these motions of the wing, using just a single or a few actuators, are preferable. This paper presents a method to design a spherical four-bar flapping mechanism that approximates a given spatial flapping motion of a wing, considered to have favorable aerodynamics. A spherical flapping mechanism was then constructed and its aerodynamic performance was compared to the original spatially moving wing using an instrumented robotic flapper with force sensors.
PERFORMANCE OF BRIDGES WITH SOLID AND PERFORATED PARAPETS IN RESISTING TSUNAMI ATTACKS
Authors: LAU TZE LIANG , LUKKUNAPRASIT PANITAN , RUANGRASSAMEE ANAT , OHMACHI TATSUO
Published: May 2010

Tsunamis have damaged bridges with various configurations to different extents. This paper reports an experimental investigation of the tsunami loads on two types of bridge configurations, namely bridges with solid and perforated parapets. The results reveal that the maximum forces acting on the bridge deck with 60% perforated parapets are about 17% lower than the one with solid parapets. However, the percentage of force reduction is found to be smaller than the percentage of perforation area in the parapets. It is also noted that the perforated parapets in the bridge deck can substantially reduce the tsunami forces acting on it throughout the force time-history. Hence, as far as the horizontal forces are concerned, the experimental results indicate that the bridge with perforation in parapets would suffer less damage as compared to the one with solid parapets because of the smaller energy input into the structure.
CALIBRATION OF TSUNAMI LOADING ON A DAMAGED BUILDING
Authors: LUKKUNAPRASIT PANITAN , RUANGRASSAMEE ANAT , STITMANNAITHUM BOONCHAI , CHINTANAPAKDEE CHATPAN , THANASISATHIT NUTTAWUT
Published: May 2010

The survival of a large number of buildings in southern Thailand with minor structural damage under 2–6 m inundation heights above the ground in the 2004 Indian Ocean tsunami tragedy suggests that it is necessary to calibrate the formulas stipulated by FEMA-55 [2000] for computing tsunami loadings. In this study, the weather monitoring building of the Meteorological station at Takua Pa, Phang Nga is used as the case study. The building suffered only minor structural damage to the columns and girders. However, most of the nonstructural members such as infill brick panels were damaged, except a few which contributed to significant reserve strength against the tsunami attack. The FEMA-55 loading is calibrated with the actual building performance from a field load test. The maximum velocity that occurred at the site in that event is assessed, and a velocity suitable for computation of tsunami load for southern Thailand is recommended.
RECOVERY CURVES FOR HOUSING RECONSTRUCTION IN SRI LANKA AFTER THE 2004 INDIAN OCEAN TSUNAMI
Authors: MURAO OSAMU , NAKAZATO HIDEAKI
Published: May 2010

On the 26th of December 2004, the Tsunami damaged to five provinces in Sri Lanka and more than 40,000 people were displaced, lost, or killed within a short time. After the tsunami, the Government provided three types of houses for the victims (temporary shelters, transitional houses, and permanent houses). The authors conducted several field surveys and interviews in the damaged area to investigate the recovery conditions, and obtained dataset, which had been collected for 13 months since December 2004 by Rebuilding and Development Agency. It shows the construction status of transitional house and permanent house in the damaged areas. This paper demonstrates recovery curves for the transitional houses and the permanent houses. With the aim of constructing post-earthquake recovery curves for Sri Lanka, the factors of time (months) and completion ratio of building construction are used. The obtained curves quantitatively clarify the regional differences in the completion dates and processes of construction. The proposed quantitative methodology will be used for other damaged countries due to the 2004 Indian Ocean Tsunami. It means that this kind of analysis is essential for investigating post-disaster recovery process because it enables comparative studies of urban/rural planning among different types of post-disaster recovery processes throughout the world.
DAMAGE AND RECONSTRUCTION OF LIFELINES IN PHANG NGA PROVINCE, THAILAND AFTER THE 2004 INDIAN OCEAN EARTHQUAKE AND TSUNAMI
Authors: TAKADA SHIRO , KUWATA YASUKO , PINTA ARUN
Published: May 2010

The Indian Ocean earthquake and tsunami occurred in December 2004 caused destructive damage to Phang Nga Province, Thailand. We carried out two times of interview surveys about 1 and 3 years after the event to administrative bodies and lifeline companies for getting the information on lifeline damage, restoration and reconstruction situation, and summarized the basic concept of reconstruction plan of tsunami suffered towns considering lifeline restoration. On the other hand, as for the comparison of reconstruction problems, the lifelines recovery is reviewed at Aonae district in Okushiri Island after the 1993 Hokkaido-Nansei-oki earthquake. As the result, the difference of the process of reconstruction of town and lifelines has been revealed and the importance of preparing of the reconstruction plan before the event under the consideration of a long-term city planning is pointed out.
COMPLEMENTARY ENSEMBLE EMPIRICAL MODE DECOMPOSITION: A NOVEL NOISE ENHANCED DATA ANALYSIS METHOD
Authors: YEH JIA-RONG , SHIEH JIANN-SHING , HUANG NORDEN E.
Published: May 2010

The phenomenon of mode-mixing caused by intermittence signals is an annoying problem in Empirical Mode Decomposition (EMD) method. The noise assisted method of Ensemble EMD (EEMD) has not only effectively resolved this problem but also generated a new one, which tolerates the residue noise in the signal reconstruction. Of course, the relative magnitude of the residue noise could be reduced with large enough ensemble, it would be too time consuming to implement. An improved algorithm of noise enhanced data analysis method is suggested in this paper. In this approach, the residue of added white noises can be extracted from the mixtures of data and white noises via pairs of complementary ensemble IMFs with positive and negative added white noises. Though this new approach yields IMF with the similar RMS noise as EEMD, it effectively eliminated residue noise in the IMFs. Numerical experiments were conducted to demonstrate the new approach and also illustrate the problems of mode splitting and translation.
INTRINSIC MODE FUNCTIONS OF EARTHQUAKE SLIP DISTRIBUTION
Authors: RAGHU KANTH S. T. G.
Published: May 2010

In this paper, empirical mode decomposition technique is used to analyze the spatial slip distribution of five past earthquakes. It is shown that the finite fault slip models exhibit five empirical modes of oscillation. The last intrinsic mode is positive and characterizes the non-stationary mean of the slip distribution. This helps in splitting the spatial variability of slip into trend and the remaining modes sum as the fluctuation in the data. The fluctuation component indicates that it can be modeled as an anisotropic random field. Important parameters of this random field have been estimated. The effect of these modes on ground motion is presented by simulating both acceleration and displacement time histories.
AN ANATOMY OF ECONOMIC GROWTH IN TAIWAN
Authors: KONG TUAN-YUEN , CHU YUN-PENG , HSU CHIN-FU , HUANG NORDEN E.
Published: May 2010

This paper revises Sedgley's model of innovation-driven endogenous growth and applies it to the case of Taiwan. The methods of empirical mode decomposition (EMD) and constrained vector error correction (VEC model or VECM) are used in the process. The EMD is used to filter out very short term fluctuations in growth, while the VECM is used to detect the various factors that affect economic growth, including human capital, public and private capital, knowledge capital and public institutions (the index of protection of property rights). It is the first attempt to include such a rich set of factors affecting economic growth at least for the studies of Taiwan.
THE TIME-DEPENDENT INTRINSIC CORRELATION BASED ON THE EMPIRICAL MODE DECOMPOSITION
Authors: CHEN XIANYAO , WU ZHAOHUA , HUANG NORDEN E.
Published: May 2010

A Time-Dependent Intrinsic Correlation (TDIC) method is introduced. This new approach includes both auto- and cross-correlation analysis designed especially to analyze, capture and track the local correlations between nonlinear and nonstationary time series pairs. The approach is based on Empirical Mode Decomposition (EMD) to decompose the nonlinear and nonstationary data into their intrinsic mode functions (IMFs) and uses the instantaneous periods of the IMFs to determine a set of the sliding window sizes for the computation of the running correlation coefficients for multi-scale data. This new method treats the selection of the sliding window sizes as an adaptive process determined by the data itself, not a "tuning" process. Therefore, it gives an intrinsic correlation analysis of the data. Furthermore, the multi-window approach makes the new method applicable to complicated data from multi-scale phenomena. The synthetic and time series from real world are used to demonstrate conclusively that the new approach is far more superior over the traditional method in its ability to reveal detailed and subtle correlations unavailable through any other methods in existence. Thus, the TDIC represents a major advance in statistical analysis of data from nonlinear and nonstationary processes.
Transcriptional Regulation of thersbVPromoter Controlling Stress Responses to Ethanol, Carbon Limitation, and Phosphorous Limitation inBacillus subtilis
Authors: Choi Soo-Keun , Saier Milton H.
Published: May 2010

TheσB-dependent promoter in front of thersbVgene ofBacillus subtilisis induced∼5-fold in response to (1) the addition of 4% ethanol, (2) carbon starvation, and (3) phosphorous starvation. Binding sites for the global carbon and nitrogen regulators, CcpA and TnrA, were mutated, and the consequences of their loss and that of CcpA or TnrA were studied usingrsbV-lacZfusions. These responses proved to be dependent on CcpA, TnrA, and their putative binding sites upstream of the promoter. Induction in response to glucose limitation was largely abolished by loss of CcpA or the upstream region, while induction in response to phosphorous limitation was largely abolished only by the upstream mutations. The results suggest that CcpA directly influences the carbon starvation response and that both proteins exert indirect effects on all three stress responses. The integrity of the DNA sequence is important for all three responses.
Determination of Reference Chemical Potential Using Molecular Dynamics Simulations
Authors: Jatkar Krishnadeo , Lee Jae W. , Lee Sangyong
Published: May 2010

A new method implementing molecular dynamics (MD) simulations for calculating the reference properties of simple gas hydrates has been proposed. The guest molecules affect interaction between adjacent water molecules distorting the hydrate lattice, which requires diverse values of reference properties for different gas hydrates. We performed simulations to validate the experimental data for determining , the chemical potential difference between water and theoretical empty cavity at the reference state, for structure II type gas hydrates. Simulations have also been used to observe the variation of the hydrate unit cell volume with temperature. All simulations were performed using TIP4P water molecules at the reference temperature and pressure conditions. The values were close to the experimental values obtained by the Lee-Holder model, considering lattice distortion.
Genome-Wide Identification and Analysis of the Chicken Basic Helix-Loop-Helix Factors
Authors: Liu Wu-yi , Zhao Chun-jiang
Published: May 2010

Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ‘‘orphans’’. A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.
Normal Human Gingival Epithelial Cells SenseC. parapsilosisby Toll-Like Receptors and Module Its Pathogenesis through Antimicrobial Peptides and Proinflammatory Cytokines
Authors: Bahri Raouf , Curt Sèverine , Saidane-Mosbahi Dalila , Rouabhia Mahmoud
Published: May 2010

This study was designed to investigate the interaction betweenC. parapsilosisand human epithelial cells using monolayer cultures and an engineered human oral mucosa (EHOM).C. parapsilosiswas able to adhere to gingival epithelial cells and to adopt the hyphal form in the presence of serum. Interestingly, when cultured onto the engineered human oral mucosa (EHOM),C. parapsilosisformed small biofilm and invaded the connective tissue. Following contact withC. parapsilosis, normal human gingival epithelial cells expressed high levels of Toll-like receptors (TLR)-2, -4, and -6, but not TLR-9 mRNA. The upregulation of TLRs was paralleled by an increase of IL-1β, TNFα, and IFNγmRNA expression, suggesting the involvement of these cytokines in the defense against infection withC. parapsilosis. The active role of epithelial cells in the innate immunity againstC. parapsilosisinfection was enhanced by their capacity to express high levels of human beta-defensin-1, -2, and -3. The upregulation of proinflammatory cytokines and antimicrobial peptide expression may explain the growth inhibition ofC. parapsilosisby the gingival epithelial cells. Overall results provide additional evidence of the involvement of epithelial cells in the innate immunity againstC. parapsilosisinfections.
Da Vinci Robot-Assisted Transoral Odontoidectomy for Basilar Invagination
Authors: Lee John Y.K. , Lega Bradley , Bhowmick Deb , Newman Jason G. , O’Malley, Jr. Bert W. , Weinstein Greg S. , Grady M. Sean , Welch William C.
Published: May 2010

The transoral approach is an effective way to decompress the craniocervical junction due to basilar invagination. This approach has been described and refined, but significant limitations and technical challenges remain. Specifically, should the transoral route be used for intradural pathology, such as a meningioma, or should an inadvertent durotomy occur during extradural dissection, achieving a watertight closure of the dura in such a deep and narrow working channel is limited with the current microscopic and endoscopic techniques. Even closure of the posterior pharyngeal mucosa can be challenging, and problems with wound dehiscence encountered in some case series may be attributable to this difficulty. These problems, and the corollary aversion to the procedure felt by many neurosurgeons, led our group to investigate an alternative approach.
Evaluation of the Psychological Status in Seasonal Allergic Rhinitis Patients
Authors: Lv Xiaofei , Xi Lin , Han Demin , Zhang Luo
Published: May 2010

Objective: To investigate the psychological status of Chinese adults with seasonal allergic rhinitis (SAR) in the allergic season, and evaluate the effects of nasal symptoms on their psychological status. Methods: The Symptom Checklist 90 (SCL-90) or Self-Reporting Inventory was employed to analyze the psychological status of 337 SAR patients. Results: The SCL-90 scores of the SAR patients were statistically higher than those of nonallergic adults in terms of somatization, depression, anxiety, hostility and psychosis. No statistical discrepancies existed in gender or age, the impact of disease course was limited to somatization, compulsion and phobic disorders and the impact of the educational level was that the lower the level of education, the more obvious the hostility. The behavior of somatization, compulsion, depression and anxiety in patients with a history of eczema or asthma was much more obvious than in patients without such a history. Nasal obstruction had a conspicuous impact on somatization, compulsion, interpersonal sensitivity, depression, anxiety and psychosis, while nasal itching contributed to somatization, depression and anxiety. Conclusion: The psychological status of SAR patients is evidently worse than that of nonallergic adults. Symptoms such as nasal obstruction and nasal itching had an obvious impact on the psychological status of the patients.
Classification and Surgical Management of Localized Attic Cholesteatoma: Single-Institution Experience and Follow-Up
Authors: Zhang Zhi Gang , Chen Sui Jun , Sun Wei , Zheng Yi Qing
Published: May 2010

Objectives: To present an effective system for the evaluation and surgical management of localized attic cholesteatoma, as well as describing the follow-up of patients treated at our institution. Study Design: Retrospective review of single-institution experience. Methods: A total of 71 patients (71 ears) with localized attic cholesteatoma received atticotomies. Further surgical management was then carried out according to the extent of the cholesteatoma and whether the malleoincudal joint was preserved (type I) or not (type II). There were 27 type I patients and 44 type II patients. In all 71 patients, the lateral wall of epitympanum was rebuilt with tragal cartilage. The healing of the lateral wall of the attic and the tympanic membrane as well as the recovery of hearing level were assessed after the operation. Results: The follow-up periods lasted 3–6 years, with an average of 4.5 years. The healing of the lateral wall of the epitympanum was satisfactory in all 71 patients. According to pure tone audiometry conducted after the operation, the air-bone gap was <10 dB in 43 patients, <20 dB in 23 patients, <30 dB in 4 patients, and >30 dB in only 1 patient. No vertigo or tinnitus was experienced after the operation. Conclusions: The surgical management of localized attic cholesteatoma should be planed according to the extent of the cholesteatoma and especially the condition of the malleoincudal joint. In order to prevent a subsequent retraction pocket of the attic, it is important to rebuild the lateral wall of the attic with cartilage after clearing the cholesteatoma.
Hyaluronic Acid Hydrogel Sustains the Delivery of Dexamethasone across the Round Window Membrane
Authors: Borden Robert C. , Saunders James E. , Berryhill Wayne E. , Krempl Greg A. , Thompson David M. , Queimado Lurdes
Published: May 2010

Background: The use of intratympanic (IT) steroids for the treatment of inner ear disorders is promising, but the clinical challenges of prolonged middle ear drug application have proven burdensome, and a sustainable delivery system is yet to be developed. Method: In this study, a guinea pig model was used to determine if dexamethasone in combination with a hyaluronic-acid (HA)-based hydrogel is an efficient, stable and sustainable dexamethasone delivery system to the inner ear. For each animal, right and left middle ear bullae were randomly selected to be filled with dexamethasone alone or dexamethasone-HA (Dex-HA) gel. Perilymph samples were collected at different time points and dexamethasone levels were determined using an ELISA. Results: Dexamethasone was measurable in the perilymph samples up to 72 h after treatment. At 24 h after treatment, the perilymph dexamethasone concentrations were significantly higher (p = 0.01) in the ears treated with Dex-HA gel than in those treated with dexamethasone alone. While the perilymph dexamethasone concentration had decreased at 48 h after treatment with Dex-HA gel, the levels were still higher than those observed at 24 h in ears treated with dexamethasone alone. A high variability in dexamethasone concentration was observed between the samples, and the variability between matched ears receiving different treatments was remarkably lower than the variability within each treatment group, suggesting that individual parameters might play a major role in perilymph dexamethasone concentration. There was no statistically significant correlation between dexamethasone concentration and sex, weight or laterality. Conclusions: Our results show that the Dex-HA gel used in this study provides an effective and sustained dexamethasone release mechanism that might be utilized to treat conditions such as sudden sensorineural hearing loss. This could potentially reduce the morbidity and costs associated with IT treatment.
Convergence and Stability of Quantized Hopfield Networks Operating in a Fully Parallel Mode
Authors: Calabuig Daniel , Monserrat Jose F. , Cardona Narcís
Published: May 2010

Hopfield neural networks (HNNs) have proven useful in solving optimization problems that require fast response times. However, the original analog model has an extremely high implementation complexity, making discrete implementations more suitable. Previous work has studied the convergence of discrete-time and quantized-neuron models but has limited the analysis to either two-state neurons or serial operation mode. Nevertheless, two-state neurons have poor performance, and serial operation modes lose fast convergence, which is characteristic of analog HNNs. This letter is the first in the field analyzing the convergence and stability of quantized Hopfield networks (QHNs)—with more than two states—operating in fully parallel mode. Moreover, this letter presents some further analysis on the energy minimization of this type of network. The main conclusion drawn is that QHNs operating in fully parallel mode always converge to a stable state or a cycle of length two and any stable state is a local minimum of the energy.