bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real time traffic information and its impacts on route switching behavior of expressway drivers
Authors: Jou Rong‐Chang , Lam Soi‐Hoi , Weng Mei‐Chuan , Chen Chih‐Cheng 
Published: January 2010

AbstractNon‐quantifiable factors (e.g. perceived, attitudinal and preferential factors) have not been investigated fully in past transportation studies, which has raised questions on the predictive capabilities of the models. In this study, Structure Integration Models, with one of their sub‐models, Measurement Equation, are combined with latent variables, which are integrated with another sub‐model, Structural Equation. The estimated latent variables are used as explanatory variables in decision models. As a result, the explanatory and predictive capabilities of the models are enhanced. The models can then be used to describe the various behaviors of travelers of different types of transportation systems in a more accurate way. In this study, the Structure Integration Model was applied to study the impacts of real‐time traffic information on the route‐switching behavior of road users on the Sun Yat‐Sen expressway, Taiwan. At present, the real‐time traffic information provided on this expressway includes radio traffic reports and changeable message signs. The results of this study can facilitate the provision of traffic information on highways.
Sensitivity analysis on stochastic equilibrium transportation networks using genetic algorithm
Authors: Ceylan Halim , Bell Michael G. H. 
Published: January 2010

AbstractThis study deals with the sensitivity analysis of an equilibrium transportation networks using genetic algorithm approach and uses the bi‐level iterative sensitivity algorithm. Therefore, integrated Genetic Algorithm‐TRANSYT and Path Flow Estimator (GATPFE) is developed for signalized road networks for various level of perceived travel time in order to test the sensitivity of perceived travel time error in an urban stochastic road networks. Level of information provided to drivers correspondingly affects the signal timing parameters and hence the Stochastic User Equilibrium (SUE) link flows. When the information on road system is increased, the road users try to avoid conflicting links. Therefore, the stochastic equilibrium assignment concept tends to be user equilibrium. The GATPFE is used to solve the bi‐level problem, where the Area Traffic Control (ATC) is the upper‐level and the SUE assignment is the lower‐level. The GATPFE is tested for six‐junction network taken from literature. The results show that the integrated GATPFE can be applied to carry out sensitivity analysis at the equilibrium network design problems for various level of information and it simultaneously optimize the signal timings (i.e. network common cycle time, signal stage and offsets between junctions).
The simple platoon advancement model of its technologies applied to vehicle control at signalised intersections
Authors: Clement Stuart , Taylor Michael 
Published: January 2010

AbstractThe Simple Platoon Advancement (SPA) Model describes a conceptual system whose principal objective is to increase the throughput of vehicles at signalised intersections. This is achieved through a novel combination of Intelligent Transport System (ITS) technologies including Automatic Cruise Control, Lane Departure Avoidance, and Collision Avoidance. These are combined in SPA so that vehicles are progressed through signalised intersections under automated control. All of the vehicles in a stationary queue are moved instantly at the start‐of‐green as a closely‐spaced platoon. Dispersion occurs after all vehicles are in motion. Throughput of the SPA model is determined analytically and comparisons are made between the SPA model and a valid representation of current road traffic behaviour. These comparisons show that theoretically a SPA system can progress nearly twice as many vehicles past the stopline as can be seen in today's road network. Other benefits of a conceptual SPA system are improved safety and a reduction in delay per vehicle.
The importance of information flows temporal attributes for the efficient scheduling of dynamic demand responsive transport services
Authors: Diana Marco 
Published: January 2010

AbstractThe operation of a demand responsive transport service usually involves the management of dynamic requests. The underlying algorithms are mainly adaptations of procedures carefully designed to solve static versions of the problem, in which all the requests are known in advance. However there is no guarantee that the effectiveness of an algorithm stays unchanged when it is manipulated to work in a dynamic environment. On the other hand, the way the input is revealed to the algorithm has a decisive role on the schedule quality. We analyze three characteristics of the information flow (percentage of real‐time requests, interval between call‐in and requested pickup time and length of the computational cycle time), assessing their influence on the effectiveness of the scheduling process.
Estimation of a time‐dependent origin‐destination matrix for congested highway networks
Authors: Cheung W. M. , Wong S. C. , Tong C. O. 
Published: January 2010

AbstractThis paper presents a time‐dependent origin‐destination (O‐D) matrix estimation procedure embedded with a dynamic traffic assignment model, in which the predictive dynamic user optimal conditions in congested networks are maintained. Two solution algorithms are proposed, namely: an iterative (ITR) scheme and a method of successive averages (MSA) scheme. It is found that the MSA scheme outperforms the ITR scheme. As a prior O‐D matrix is an important input for the problem, its quality is essential for the reliability of the matrix estimation procedure. Empirical constraints are set in relation to the quality of the prior O‐D matrix for the estimation procedure. Numerical examples are used to demonstrate the effectiveness of the proposed methodology.
Homocysteine metabolism and its relation to health and disease
Authors: Williams Kelly T. , Schalinske Kevin L. 
Published: January 2010

AbstractHomocysteine is a metabolic intermediate in methyl group metabolism that is dependent on a number of nutritional B‐vitamin cofactors. An emerging aspect of homocysteine metabolism is its relation to health and disease. Perturbations of homocysteine metabolism, particularly intracellular and subsequently circulating accumulation of homocysteine (i.e., hyperhomocysteinemia), are associated with vascular disease risk, as well as other pathologies. However, intervention with B‐vitamin supplementation has been shown to successfully restore normal homocysteine concentrations, but without concomitant reductions in disease risk. Thus, the mechanistic relation between homocysteine balance and disease states, as well as the value of homocysteine management, remains an area of intense investigation.
Fibrillar peptide gels in biotechnology and biomedicine
Authors: Jung Jangwook P. , Gasiorowski Joshua Z. , Collier Joel H. 
Published: January 2010

AbstractPeptides, peptidomimetics, and peptide derivatives that self‐assemble into fibrillar gels have received increasing interest as synthetic extracellular matrices for applications in 3D cell culture and regenerative medicine. Recently, several of these fibrillizing molecules have been functionalized with bioactive components and chemical features such as cell‐binding ligands, degradable sequences, drug eluting compounds, and cross‐linkable groups, thereby producing gels that can reliably display multiple factors simultaneously. This capacity for incorporating precise levels of many different biological and chemical factors is advantageous given the natural complexity of cell–matrix interactions that many current biomaterial strategies seek to mimic. In this review, recent efforts in the area of fibril‐forming peptide materials are described, and advantages of biomaterials containing multiple modular elements are outlined. In addition, a few hurdles and open questions surrounding fibrillar peptide gels are discussed, including issues of the materials' structural heterogeneity, challenges in fully characterizing the diversity of their self‐assembled structures, and incomplete knowledge of how the materials are processed in vivo. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94: 49–59, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Self‐assembly of peptide amphiphiles: From molecules to nanostructures to biomaterials
Authors: Cui Honggang , Webber Matthew J. , Stupp Samuel I. 
Published: January 2010

AbstractPeptide amphiphiles are a class of molecules that combine the structural features of amphiphilic surfactants with the functions of bioactive peptides and are known to assemble into a variety of nanostructures. A specific type of peptide amphiphiles are known to self‐assemble into one‐dimensional nanostructures under physiological conditions, predominantly nanofibers with a cylindrical geometry. The resultant nanostructures could be highly bioactive and are of great interest in many biomedical applications, including tissue engineering, regenerative medicine, and drug delivery. In this context, we highlight our strategies for using molecular self‐assembly as a toolbox to produce peptide amphiphile nanostructures and materials and efforts to translate this technology into applications as therapeutics. We also review our recent progress in using these materials for treating spinal cord injury, inducing angiogenesis, and for hard tissue regeneration and replacement. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94:1–18, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Protein‐ and peptide‐modified synthetic polymeric biomaterials
Authors: Krishna Ohm D. , Kiick Kristi L. 
Published: January 2010

AbstractThis review presents an overview on bio‐hybrid approaches of integrating the structural and functional features of proteins and peptides with synthetic polymers and the resulting unique properties in such hybrids, with a focus on bioresponsive/bioactive systems with biomaterials applications. The review is divided in two broad sections. First, we describe several examples of bio‐hybrids produced by combining versatile synthetic polymers with proteins/enzymes and drugs that have resulted in (1) hybrid materials based on responsive polymers, (2) responsive hydrogels based on enzyme‐catalyzed reactions, protein–protein interactions and protein–drug sensing, and (3) dynamic hydrogels based on conformational changes of a protein. Next, we present hybrids produced by combining synthetic polymers with peptides, classified based on the properties of the peptide domain: (1) peptides with different conformations, such as α‐helical, coiled‐coil, and β‐sheet; (2) peptides derived from structural protein domains such as silk, elastin, titin, and collagen; and (3) peptides with other biofunctional properties such as cell‐binding domains and enzyme‐recognized degradation domains. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94:32–48, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Polysaccharide‐modified synthetic polymeric biomaterials
Authors: Baldwin Aaron D. , Kiick Kristi L. 
Published: January 2010

AbstractThis review presents an overview of polysaccharide‐conjugated synthetic polymers and their use in tissue‐engineered scaffolds and drug‐delivery applications. This topic will be divided into four categories: (1) polymeric materials modified with non‐mammalian polysaccharides such as alginate, chitin, and dextran; (2) polymers modified with mammalian polysaccharides such as hyaluronan, chondroitin sulfate, and heparin; (3) multi‐polysaccharide‐derivatized polymer conjugate systems; and (4) polymers containing polysaccharide‐mimetic molecules. Each section will discuss relevant conjugation techniques, analysis, and the impact of these materials as micelles, particles, or hydrogels used in in‐vitro and in‐vivo biomaterial applications. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94:128–140, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Molecular biomimetics: GEPI‐based biological routes to technology
Authors: Tamerler Candan , Khatayevich Dmitriy , Gungormus Mustafa , Kacar Turgay , Oren E. Emre , Hnilova Marketa , Sarikaya Mehmet 
Published: January 2010

AbstractIn nature, the viability of biological systems is sustained via specific interactions among the tens of thousands of proteins, the major building blocks of organisms from the simplest single‐celled to the most complex multicellular species. Biomolecule‐material interaction is accomplished with molecular specificity and efficiency leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, Mother Nature developed molecular recognition by successive cycles of mutation and selection. Molecular specificity of probe‐target interactions, e.g., ligand‐receptor, antigen–antibody, is always based on specific peptide molecular recognition. Using biology as a guide, we can now understand, engineer, and control peptide‐material interactions and exploit them as a new design tool for novel materials and systems. We adapted the protocols of combinatorially designed peptide libraries, via both cell surface or phage display methods; using these we select short peptides with specificity to a variety of practical materials. These genetically engineered peptides for inorganics (GEPI) are then studied experimentally to establish their binding kinetics and surface stability. The bound peptide structure and conformations are interrogated both experimentally and via modeling, and self‐assembly characteristics are tested via atomic force microscopy. We further engineer the peptide binding and assembly characteristics using a computational biomimetics approach where bioinformatics based peptide‐sequence similarity analysis is developed to design higher generation function‐specific peptides. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems in a wide‐range of applications from tissue engineering, disease diagnostics, and therapeutics to various areas of nanotechnology where integration is required among inorganic, organic and biological materials. Here, we describe lessons from biology with examples of protein‐mediated functional biological materials, explain how novel peptides can be designed with specific affinity to inorganic solids using evolutionary engineering approaches, give examples of their potential utilizations in technology and medicine, and, finally, provide a summary of challenges and future prospects. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94:78–94, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Potential allosteric modulators of the proteasome activity
Authors: Jankowska E. , Gaczynska M. , Osmulski P. , Sikorska E. , Rostankowski R. , Madabhushi S. , Tokmina‐Lukaszewska M. , Kasprzykowski F. 
Published: January 2010

AbstractProteasome, consisting of a tube‐shaped proteolytic core particle and attached to it regulatory modules, is a multifunctional enzymatic complex essential for the ubiquitin‐proteasome metabolic pathway. Due to its immense involvement in regulation of cellular physiology, the proteasome is an acknowledged anticancer drug target and potential target to treat inflammatory or degenerative diseases. So far, competitive inhibitors of the core particle gain most consideration as drugs. We postulate that noncompetitively‐acting small‐molecule compounds would provide excellent means to precisely regulate actions of the proteasome. In this study, we evaluated five short peptides based on sequences of two proteins known to interact with the core proteasome: HIV‐1 Tat and PA28/REG activator. We performed Circular Dichroism (CD), Fourier Transformed Infrared Spectroscopy (FTIR), and Nuclear Magnetic Resonance (NMR) analysis, supplemented by MD simulations, and tested influence of the peptides on performance of the core particle active sites and functioning of regulatory modules. We found that PP2‐containing Tat peptides are noncompetitive inhibitors of the core, interfering with the actions of PA28αβ activator. In addition, at low concentrations the turn‐prone Tat2 is able to activate the latent core. The random coil‐structured PA28‐derived peptides display only weak or nondetectable direct effects on the core activities, exhibiting, however, a positive cooperation with activity‐enhancing actions of PA28αβ. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 481–495, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Vibrational spectroscopic studies of newly developed synthetic biopolymers
Authors: Bista Rajan K. , Bruch Reinhard F. , Covington Aaron M. 
Published: January 2010

AbstractVibrational spectroscopic techniques such as near‐infrared (NIR), Fourier transform infrared (FTIR), and Raman spectroscopy are valuable diagnostic tools that can be used to elucidate comprehensive structural information of numerous biological samples. In this review article, we have highlighted the advantages of nanotechnology and biophotonics in conjunction with vibrational spectroscopic techniques in order to understand the various aspects of new kind of synthetic biopolymers termed as polyethylene glycol (PEG)ylated lipids. In contrast to conventional phospholipids, these novel lipids spontaneously form liposomes or nanovesicles upon hydration, without the supply of external activation energy. The amphiphiles considered in this study differ in their hydrophobic acyl chain length and contain different units of PEG hydrophilic headgroups. We have further explored the thermotropic phase behaviors and associated changes in the conformational order/disorder of such lipids by using variable‐temperature FTIR and Raman spectroscopy. Phase transition temperature profiles and correlation between various spectral indicators have been identified by either monitoring the shifts in the vibrational peak positions or plotting vibrational peak intensity ratios in the CH stretching region as a function of temperature. To supplement our observations of phase transformations, a thermodynamic approach known as differential scanning calorimetry (DSC) has been applied and revealed a good agreement with the infrared and Raman spectroscopic data. Finally, the investigation of thermal properties of lipids is extremely crucial for numerous purposes, thus the results obtained in this work may find application in a wide variety of studies including the development of PEGylated lipid based drug and substances delivery vehicles. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 403–417, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Model peptide‐based system used for the investigation of metal ions binding to histidine‐containing polypeptides
Authors: Murariu Manuela , Dragan Ecaterina Stela , Drochioiu Gabi 
Published: January 2010

AbstractThe reaction of histidine‐containing polypeptides with toxic and essential metals and the molecular mechanism of complexation has yet to be determined, particularly with respect to the conformational changes of the interacting macromolecules. Therefore, a system of oligopeptides containing histidine residues in various positions of Ala or Gly sequences has been designed and used in heavy metal comparatively binding experiments. The role of spacing residues (Gly and Ala repeats) in selecting the various conformations was investigated. The newly synthesized peptides and metal ion adducts have been characterized by Fourier transform infrared spectroscopy (FTIR) as well as electrospray ion trap mass spectrometry (ESI–MS) and circular dichroism (CD). The analysis of CD‐spectra of the four peptides in water revealed that the secondary structure depends much on the position of each amino acid in the peptide backbone. Our peptides system reveals various binding mechanisms of metal ions to peptides depending on the position of histidine residue and the corresponding conformations of Ala or Gly sequences. Biological and medical consequences of conformational changes of metal‐bound peptides are further discussed. Thus, the binding of heavy metals to four peptides may serve as a model system with respect to the conformational consequences of the metal addition on the amino acid repeats situated in prion protein. © 2010 Wiley Periodicals, Inc. Biopolymers 93:497–508, 2010.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Photoregulated assembly/disassembly of DNA‐templated protein arrays using modified oligonucleotide carrying azobenzene side chains
Authors: Hachikubo You , Iwai Sosuke , Uyeda Taro Q.P. 
Published: January 2010

AbstractDNA‐templated self‐assembly of nanomaterials provides great potential for applications including biosensors, nanoelectronics, and programmable and autonomous molecular machines. To switch or regulate the activities of those nanobiotechnological devices, non‐invasive methods to assemble and disassemble specific nanoscale components are needed. Here, we describe photocontrol of assembly of DNA‐templated protein arrays in solution, by using photo‐controlled duplex formation of oligonucleotides carrying azobenzene. As a proof of concept prototype, we designed a one‐dimensional protein array system that consists of a scaffold of DNA and two kinds of anchor DNA that were conjugated with fluorescent proteins (CFP and YFP, respectively). The scaffold DNA was modified to carry multiple azobenzene side chains so that the hybridization involving the scaffold DNA is regulated by photoirradiation through conformational changes of the azobenzene moieties. Melting temperatures of duplex made of the modified DNA scaffold and an anchor oligonucleotide were shifted significantly and reversibly by UV and visible photoirradiation (difference of Tm was 34.8°C in 150 mM potassium acetate). Measurements of Förster resonance energy transfer between CFP and YFP showed that the assembly of the protein array system was also changed by photoirradiation. Such non‐invasive and reversible method to control assembly/disassembly of multiple, specific proteins in a DNA‐templated protein array system would provide many functions for nanobiotechnological devices such as on/off switches and the ability to change the configuration reversibly. Biotechnol. Bioeng. 2010; 106: 1–8. © 2010 Wiley Periodicals, Inc.