bluuebunny/crossref_metadata_2025 huggingface dataset:
Benzo[a]pyrene diol‐epoxide (B[a]PDE) upregulates COX‐2 expression through MAPKs/AP‐1 and IKKβ/NF‐κB in mouse epidermal Cl41 cells
Authors: Ouyang Weiming , Ma Qian , Li Jingxia , Zhang Dongyun , Ding Jin , Huang Yi , Xing Mingzhao , Huang Chuanshu
Published: August 2006

Benzo[α]pyrene‐7,8‐diol‐9,10‐epoxide (B[a]PDE), the major metabolite of benzo[a]pyrene (B[a]P), shows an ultimate complete carcinogen in various animals and is a causative agent for human cancers. However, its effects on the activation of signal pathways and the expression of genes involved in its carcinogenic effect remain largely unknown. In this study, the effects of B[a]PDE on induction of cyclooxygenase (COX)‐2 and the signal pathways leading to the induction were investigated. Treatment of mouse epidermal Cl41 cells with B[a]PDE caused an increase in the expression of COX‐2 at both transcription and protein levels, while its parental compound B[a]P did not show significant inductive effect. The COX‐2 induction by B[a]PDE was dependent on the activation of mitogen‐activated protein kinases (MAPK)s/activation protein (AP)‐1 pathway, because inhibition of AP‐1 by either overexpression of TAM67 (dominant negative mutant of c‐jun), or pretreatment of cells with PD98059 (MEK1/2‐ERKs pathway inhibitor) or SB202190 (p38K inhibitor), markedly inhibited B[a]PDE‐induced COX‐2 expression. In addition, impairment of NF‐κB pathway by either NEMO‐BDBP (an NF‐κB specific inhibitor) or IκB kinase (IKK)β‐KM (dominant negative mutant of IKKβ) also caused marked reduction of COX‐2 induction by B[a]PDE. In contrast, inhibition of nuclear factor of activated T cells (NFAT) with FK506, did not show any effect on B[a]PDE‐induced COX‐2 expression. Collectively, these data indicate that exposure of Cl41 cells to B[a]PDE can induce COX‐2 expression by increasing its transcription, which requires the activation of MAPKs/AP‐1 and IKKβ/NF‐κB pathways, but not NFAT pathway. In view of the importance of COX‐2 in carcinogenesis, we anticipate that the induction of COX‐2 by B[a]PDE may coordinate its mutagenic effects to facilitate the development of skin cancer. © 2006 Wiley‐Liss, Inc.
Force steadiness, muscle activity, and maximal muscle strength in subjects with subacromial impingement syndrome
Authors: Bandholm Thomas , Rasmussen Lars , Aagaard Per , Jensen Bente Rona , Diederichsen Louise
Published: August 2006

We investigated the effects of the subacromial impingement syndrome (SIS) on shoulder sensory‐motor control and maximal shoulder muscle strength. It was hypothesized that both would be impaired due to chronic shoulder pain associated with the syndrome. Nine subjects with unilateral SIS who remained physically active in spite of shoulder pain and nine healthy matched controls were examined to determine isometric and isokinetic submaximal shoulder‐abduction force steadiness at target forces corresponding to 20%, 27.5%, and 35% of the maximal shoulder abductor torque, and maximal shoulder muscle strength (MVC). Electromyographic (EMG) activity was assessed using surface and intramuscular recordings from eight shoulder muscles. Force steadiness was impaired in SIS subjects during concentric contractions at the highest target force level only, with muscle activity largely unaffected. No between‐group differences in shoulder MVC were observed. The present data suggest that shoulder sensory‐motor control is only mildly impaired in subjects with SIS who are able to continue with upper body physical activity in spite of shoulder pain. Thus, physical activity should be continued by patients with SIS, if possible, to avoid the loss in neural and muscle functions associated with inactivity. Muscle Nerve, 2006
Negative impact of urinary incontinence on quality of life, a cross‐sectional study among women aged 49–61 years enrolled in the GAZEL cohort
Authors: Saadoun Karim , Ringa Virginie , Fritel Xavier , Varnoux Noëlle , Zins Marie , Bréart Gérard
Published: August 2006

Aims

The aim of the study was to analyze the relations between severity of urinary incontinence (UI), defined as involuntary loss of urine considered to be a hygienic or social problem, and quality of life (QoL) among middle‐aged French working women enrolled in a cohort study, while taking into account characteristics that may affect this relation.

Methods

Data came from self‐administered mail questionnaires completed by 2,640 women aged 49–61 years in the GAZEL cohort of utility company employees. The analysis considered social and demographic characteristics, lifestyle, hormone status, and body mass index. We used bivariate and multivariate analysis to study the associations between UI severity (measured by SANDVIK's index) and QoL scales (Contilife, specific for UI, and the generic Nottingham Health Profile).

Results

The sample included 556 women (21%) with UI. QoL alterations associated with UI severity were observed for all six Contilife dimensions (daily and effort activities, self‐image, emotional impact, sexuality, and well‐being) and two dimensions of the NHP (pain and physical mobility). These results remain after adjustment for age, BMI, and living arrangements.

Conclusions

UI affects QoL even among women from a nonclinical population, and the more severe the UI, the more harmful the effect. These results raise the question of whether UI in its severe forms should be considered a disability because of its negative effects on mobility in daily life. Neurourol. Urodynam. 25:696–702, 2006. © 2006 Wiley‐Liss, Inc.
Having a child to save a sibling: Reassessing risks and benefits of creating stem cell donors
Authors: Morgan Elaine R. , Girod Jennifer , Rinehart John S.
Published: August 2006

This manuscript assesses the risks, benefits, and ethical concerns regarding the use of assisted reproductive techniques (ART) to create a new donor for stem cell transplantation. We address ethical literature, the medical and psychosocial impact on patient, donor, family, and medical caregivers, and the appropriate decision‐making process. We conclude that the use of ART to create a stem cell donor can be ethically acceptable. The decision to conceive a donor has medical and psychosocial implications. The family is the appropriate decision‐maker and must consider risks and benefits to all parties with input from medical caregivers. Pediatr Blood Cancer 2007;48:249–253. © 2006 Wiley‐Liss, Inc.
A comparative analysis of functional outcomes in adolescents and young adults with lower‐extremity bone sarcoma
Authors: Ginsberg Jill P. , Rai Shesh N. , Carlson Claire A. , Meadows Anna T. , Hinds Pamela S. , Spearing Elena M. , Zhang Lijun , Callaway Lulie , Neel Michael D. , Rao Bhaskar N. , Marchese Victoria G.
Published: August 2006

Background

Comparison of functional mobility and quality of life is performed in patients with lower‐extremity bone sarcoma following either amputation, limb‐sparing surgery, or rotationplasty with four different types of outcome measures: (1) an objective functional mobility measure that requires patients to physically perform specific tasks, functional mobility assessment (FMA); (2) a clinician administered tool, Musculoskeletal Tumor Society Scale (MSTS); (3) a patient questionnaire, Toronto Extremity Salvage Scale (TESS); and (4) a health‐related quality of life (HRQL) measure, Short Form‐36 version 2 (SF‐36v.2).

Procedure

This is a prospective multi‐site study including 91 patients with lower‐extremity bone sarcoma following amputation, limb‐sparing surgery, or rotationplasty. One of three physical therapists administered the quality of life measure (SF‐36v.2) as well as a battery of functional measures (FMA, MSTS, and TESS).

Results

Differences between patients who had amputation, limb‐sparing surgery, or rotationplasty were consistently demonstrated by the FMA. Patients with limb sparing femur surgery performed better than those patients with an above the knee amputation but similarly to a small number of rotationplasty patients. Several of the more conventional self‐report measures were shown to not have the discriminative capabilities of the FMA in these cohorts.

Conclusion

In adolescents with lower‐extremity bone sarcoma, it may be advantageous to consider the use of a combination of outcome measures, including the FMA, for objective functional mobility assessment along with the TESS for a subjective measure of disability and the SF‐36v.2 for a quality‐of‐life measure. Pediatr Blood Cancer 2007;49:964–969. © 2006 Wiley‐Liss, Inc.
Mathematical modeling of interfacial polycondensation
Authors: Berezkin Anatoly V. , Khokhlov Alexei R.
Published: August 2006

The works on mathematical modeling of interfacial polycondensation are reviewed over the period since 1970s up to now. Attention is primarily paid to the techniques of local and macrokinetic modeling. Two approaches to the theoretical description of polycondensation have been formed up to date. The first one is based on analytical or semianalytical solution of differential balance equations using the stationary mass transfer approximation. The second one consists in numerical solution of the system of reaction–diffusion equations for the diffusion boundary layer of the reaction phase. The advantages and drawbacks of these approaches, specific features of their realization, basic results, as well as ways of combining these methods are discussed. A possibility of building a general model of interfacial polycondensation as a hierarchical combination of kinetic, local, and macrokinetic models is shown. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2698–2724, 2006
Mathematical modeling of crystallization analysis fractionation (Crystaf) of polyethylene
Authors: Anantawaraskul Siripon , Soares João B. P. , Jirachaithorn Preechathorn , Limtrakul Jumras
Published: August 2006

Four polyethylene samples (PE) with different molecular weight distributions (MWD) were analyzed by crystallization analysis fractionation (Crystaf) at several cooling rates to investigate the effect of MWD and cooling rate on their Crystaf profiles. Using these results, we developed a mathematical model for Crystaf that considers crystallization kinetic effects, which are ignored in all previous Crystaf models. The Crystaf model we proposed can fit the experimental Crystaf profiles of the 4 polyethylene resins very well. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2749–2759, 2006
Local order in polycarbonate glasses by 13C{19F} rotational‐echo double‐resonance NMR
Authors: Stueber Dirk , Mehta Anil K. , Chen Zhiyun , Wooley Karen L. , Schaefer Jacob
Published: August 2006

Nearest‐neighbor chain packing in a homogeneous blend of carbonate 13C‐labeled bisphenol A polycarbonate and CF3‐labeled bisphenol A polycarbonate has been characterized using a shifted‐pulse version of magic‐angle spinning 13C{19F} rotational‐echo double‐resonance (REDOR) NMR. Complementary NMR experiments have also been performed on a polycarbonate homopolymer containing the same 13C and 19F labels. In the blend, the 13C observed spin was at high concentration, and the 19F dephasing or probe spin was at low concentration. In this situation, an analysis in terms of a distribution of isolated heteronuclear pairs of spins is valid. A comparison of the results for the blend and homopolymer defines the NMR conditions under which higher concentrations of probe labels can be used and a simple analysis of the REDOR results is still valid. The nearest neighbors of a CF3 on one chain generally include a carbonate group on an adjacent chain. A direct interpretation of the REDOR total dephasing for the polycarbonate blend indicates that at least 75% of carbonate‐carbon 13C···F3 nearest neighbors are separated by a narrow distribution of distances 4.7 ± 0.3 Å. In addition, analysis of the variations in REDOR spinning‐sideband dephasing shows that most of the 13C···F3 dipolar vectors have a preferred orientation relative to the polycarbonate mainchain axis. This combination of distance and orientational constraints is interpreted in terms of local order in the packing of the carbonate group of one polycarbonate chain relative to the isopropylidene moiety in a neighboring chain. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2760–2775, 2006
Influence of molecular architecture of S–S/B–S triblock copolymers on rheological properties
Authors: Thunga M. , Staudinger U. , Satapathy B. K. , Weidisch R. , Abdel‐Goad M. , Janke A. , Knoll K.
Published: August 2006

The influence of middle and outer block composition of symmetric triblock copolymers consisting of a polystyrene–polybutadiene (S/B) random middle block and two polystyrene (PS) outer blocks on morphology and rheological behavior has been investigated. Master curves are obtained by shifting the experimental data measured at different temperatures using time‐temperature superposition principle, the validity of which was confirmed in the linear viscoelastic regime. The rheological properties are observed to be strongly influenced by the relative composition of the S‐SB‐S triblock copolymers. Increasing the S/B ratio from 1:1 to 1:2 in the middle block has lead to a change in morphology from wormlike to lamellar, which is also accompanied with broad and sharp tan δ peaks in the dynamic mechanical measurements, respectively. The storage and loss modulus have been observed to increase with the increase in PS contents in the outer blocks and PB content in the middle block. The triblock copolymer with wormlike structure showed terminal linear viscoelastic behavior, whereas the ones with lamellar morphology showed nonterminal flow behavior in the similar low‐frequency regime. The relaxation modulus (Gt) has been observed to increase four times when the S/B ratio is increased from 1:1 to 1:2, whereas it increases threefold when the PS‐content in the outer block was increased by just 8 wt %. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2776–2788, 2006
Predictors of spouses' provided support for patients receiving laparoscopic radical prostatectomy peri‐surgery
Authors: Knoll Nina , Burkert Silke , Peter Rosemeier Hans , Roigas Jan , Gralla Oliver
Published: August 2006

Close relationships are usually the most important source of social support. But even in close relationships, symptoms of distress in one or both partners may undermine support processes. Seventy‐seven patients receiving laparoscopic radical prostatectomy (44–73 years) and their spouses (38–72 years) provided data 1 day prior to surgery as well as 2 days and 2 weeks post‐surgery. Our assumption that the commonly found support‐eroding potential of receivers' depressive symptoms would not be evident during early stages of an acute crisis situation, such as major tumor surgery, tended to be supported by the data. However, depressive symptoms and degree of patient‐reported post‐operative pain were associated with a delayed decrease in spousal instrumental support provision 2 weeks after surgery. Spousal depression was largely unrelated to the provision of support. The present findings hint at the limits of a loved‐one's capacity to assist in times of need. Copyright © 2006 John Wiley & Sons, Ltd.
Physical impairment and social adaptation in adult survivors of childhood and adolescent rhabdomyosarcoma: a report from the Childhood Cancer Survivors Study
Authors: Punyko Judith A. , Gurney James G. , Scott Baker K. , Hayashi Robert J. , Hudson Melissa M. , Liu Yan , Robison Leslie L. , Mertens Ann C.
Published: August 2006

Background: Despite interest in the well‐being of adult survivors of childhood rhabdomyosarcoma (RMS), few studies have examined their health‐related quality of life (HRQOL). This study evaluated physical and social aspects of HRQOL among long‐term childhood RMS survivors relative to a sibling comparison group, and assessed whether physical impairment among RMS survivors adversely affected their ability to achieve adult life goals.

Methods: Using baseline data from the Childhood Cancer Survivor Study, we evaluated self‐reported physical impairment and social adaptation among 417 survivors of childhood RMS and 2685 siblings ⩾18 years of age at survey completion.

Results: Survivors were more likely than siblings to report physical impairment, characterized by: at least one medically diagnosed condition, limitations in the performance of routine activities, a health‐related inability to work or attend school, cancer‐related pain. Survivors were less likely than siblings to have completed high school, ever worked a job, or ever been married. The odds of completing high school were lower among survivors with performance limitations, a health‐related inability to work or attend school, or moderate to high levels of cancer‐related pain. Survivors who reported cancer‐related pain had an increased likelihood of ever being married.

Conclusions: The majority of adult survivors of pediatric RMS are successful in attaining adult life goals despite higher reported occurrence of physical impairment than their sibling counterparts. Additional studies are needed to advance our understanding of other aspects of HRQOL in this population of pediatric cancer survivors. Copyright © 2006 John Wiley & Sons, Ltd.
Protein under pressure: Molecular dynamics simulation of the arc repressor
Authors: Trzesniak Daniel , Lins Roberto D. , van Gunsteren Wilfred F.
Published: August 2006

Experimental nuclear magnetic resonance results for the Arc Repressor have shown that this dimeric protein dissociates into a molten globule at high pressure. This structural change is accompanied by a modification of the hydrogen‐bonding pattern of the intermolecular β‐sheet: it changes its character from intermolecular to intramolecular with respect to the two monomers. Molecular dynamics simulations of the Arc Repressor, as a monomer and a dimer, at elevated pressure have been performed with the aim to study this hypothesis and to identify the major structural and dynamical changes of the protein under such conditions. The monomer appears less stable than the dimer. However, the complete dissociation has not been seen because of the long timescale needed to observe this phenomenon. In fact, the protein structure altered very little when increasing the pressure. It became slightly compressed and the dynamics of the side‐chains and the unfolding process slowed down. Increasing both, temperature and pressure, a tendency of conversion of intermolecular into intramolecular hydrogen bonds in the β‐sheet region has been detected, supporting the mentioned hypothesis. Also, the onset of denaturation of the separated chains was observed. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations
Authors: Shehu Amarda , Clementi Cecilia , Kavraki Lydia E.
Published: August 2006

Characterizing protein flexibility is an important goal for understanding the physical–chemical principles governing biological function. This paper presents a Fragment Ensemble Method to capture the mobility of a protein fragment such as a missing loop and its extension into a Protein Ensemble Method to characterize the mobility of an entire protein at equilibrium. The underlying approach in both methods is to combine a geometric exploration of conformational space with a statistical mechanics formulation to generate an ensemble of physical conformations on which thermodynamic quantities can be measured as ensemble averages. The Fragment Ensemble Method is validated by applying it to characterize loop mobility in both instances of strongly stable and disordered loop fragments. In each instance, fluctuations measured over generated ensembles are consistent with data from experiment and simulation. The Protein Ensemble Method captures the mobility of an entire protein by generating and combining ensembles of conformations for consecutive overlapping fragments defined over the protein sequence. This method is validated by applying it to characterize flexibility in ubiquitin and protein G. Thermodynamic quantities measured over the ensembles generated for both proteins are fully consistent with available experimental data. On these proteins, the method recovers nontrivial data such as order parameters, residual dipolar couplings, and scalar couplings. Results presented in this work suggest that the proposed methods can provide insight into the interplay between protein flexibility and function. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations
Authors: Spiegel Katrin , De Grado William F. , Klein Michael L.
Published: August 2006

There is a pressing need for accurate force fields to assist in metalloprotein analysis and design. Recent work on the design of mimics of dimetal proteins highlights the requirements for activity. DF1 is a de novo designed protein, which mimics the overall fold and active site geometry of a series of diiron and dimanganese proteins. Specifically, the dimanganese form of DF1 is a mimic of the natural enzyme manganese catalase, which catalyzes the dismutation reaction of hydrogen peroxide into water and oxygen. During catalytic turnover, the active site has to accommodate both the reduced and the oxidized state of the dimanganese core. The biomimetic protein DF1 is only stable in the reduced form and thus not active. Furthermore, the synthetic protein features an additional bridging glutamate sidechain, which occupies the substrate binding site. The goal of this study is to develop classical force fields appropriate for design of such important dimanganese proteins. To this aim, we use a nonbonded model to represent the metal–ligand interactions, which implicitly takes into account charge transfer and local polarization effects between the metal and its ligands. To calibrate this approach, we compare and contrast geometric and dynamical properties of manganese catalase and DF1. Having demonstrated a good correspondence with experimental structural data, we examine the effect of mutating the bridging glutamate to aspartate (M1) and serine (M2). Classical MD based on the refined forcefield shows that these point mutations affect not only the immediate coordination sphere of the manganese ions, but also the relative position of the helices, improving the similarity to Mn‐catalase, especially in case ofM2. On the basis of these findings, classical molecular dynamics calculations with the active site parameterization scheme introduced herein seem to be a promising addition to the protein design toolbox. Proteins 2006; © 2006 Wiley‐Liss, Inc.
Team CIMAR's NaviGator: An unmanned ground vehicle for the 2005 DARPA grand challenge
Authors: Crane III Carl D. , Armstrong II David G. , Touchton Robert , Galluzzo Tom , Solanki Sanjay , Lee Jaesang , Kent Daniel , Ahmed Maryum , Montane Roberto , Ridgeway Shannon , Velat Steve , Garcia Greg , Griffis Michael , Gray Sarah , Washburn John , Routson Gregory
Published: August 2006

This paper describes the development of an autonomous vehicle system that participated in the 2005 DARPA Grand Challenge event. After a brief description of the event, the architecture, based on version 3.2 of the Department of Defense Joint Architecture for Unmanned Systems, and the design of the system are presented in detail. In particular, the “smart sensor” concept is introduced which provided a standardized means for each sensor to present data for rapid integration and arbitration. Information about the vehicle design, system localization, perception sensors, and the dynamic planning algorithms that were used is then presented in detail. Subsequently, testing results and performance results are presented. © 2006 Wiley Periodicals, Inc.
KAT‐5: Robust systems for autonomous vehicle navigation in challenging and unknown terrain
Authors: Trepagnier Paul G. , Nagel Jorge , Kinney Powell M. , Koutsougeras Cris , Dooner Matthew
Published: August 2006

KAT‐5 was the fourth vehicle to make history in DARPA's 2005 Grand Challenge, where for the first time ever, autonomous vehicles were able to travel through 100 miles of rough terrain at average speeds greater than 15 mph. In this paper, we describe the mechanisms and methods that were used to develop the vehicle. We describe the main hardware systems with which the vehicle was outfitted for navigation, computing, and control. We describe the sensors, the computing grid, and the methods that controlled the navigation based on the sensor readings. We also discuss the experiences gained in the course of the development and provide highlights of actual field performance. © 2006 Wiley Periodicals, Inc.
CajunBot: Architecture and algorithms
Authors: Lakhotia Arun , Golconda Suresh , Maida Anthony , Mejia Pablo , Puntambeker Amit , Seetharaman Guna , Wilson Scott
Published: August 2006

CajunBot, an autonomous ground vehicle and a finalist in the 2005 DARPA Grand Challenge, is built on the chassis of MAX IV, a six‐wheeled all‐terrain vehicle (ATV). Transformation of the ATV to an autonomous ground vehicle required adding drive‐by‐wire control, lidar sensors, an inertial navigation system (INS), and a computing system. Significant innovations in the core computational algorithms include an obstacle detection algorithm that takes advantage of shocks and bumps to improve visibility; a path planning algorithm that takes into account the vehicle's maneuverability limits to generate paths that are navigable at high speed; efficient data structures and algorithms that require just a single Intel Pentium 4 HT 3.2 GHz machine to handle all computations and a middleware layer that transparently distributes the computation to multiple machines, if desired. In addition, CajunBot also features support technologies, such as a simulator, playback of logged data, and live visualization on off‐board computers to aid in development, testing, and debugging. © 2006 Wiley Periodicals, Inc.
SciAutonics‐Auburn Engineering's low‐cost high‐speed ATV for the 2005 DARPA grand challenge
Authors: Travis William , Daily Robert , Bevly David M. , Knoedler Kevin , Behringer Reinhold , Hemetsberger Hannes , Kogler Jürgen , Kubinger Wilfried , Alefs Bram
Published: August 2006

This paper presents a summary of SciAutonics‐Auburn Engineering's efforts in the 2005 DARPA Grand Challenge. The areas discussed in detail include the team makeup and strategy, vehicle choice, software architecture, vehicle control, navigation, path planning, and obstacle detection. In particular, the advantages and complications involved in fielding a low budget all‐terrain vehicle are presented. Emphasis is placed on detailing the methods used for high‐speed control, customized navigation, and a novel stereo vision system. The platform chosen required a highly accurate model and a well‐tuned navigation system in order to meet the demands of the Grand Challenge. Overall, the vehicle completed three out of four runs at the National Qualification Event and traveled 16 miles in the Grand Challenge before a hardware failure disabled operation. The performance in the events is described, along with a success and failure analysis. © 2006 Wiley Periodicals, Inc.
The Golem Group/University of California at Los Angeles autonomous ground vehicle in the DARPA grand challenge
Authors: Mason Richard , Radford Jim , Kumar Deepak , Walters Robert , Fulkerson Brian , Jones Eagle , Caldwell David , Meltzer Jason , Alon Yaniv , Shashua Amnon , Hattori Hiroshi , Frazzoli Emilio , Soatto Stefano
Published: August 2006

This paper presents the Golem Group/University of California at Los Angeles entry to the 2005 DARPA Grand Challenge competition. We describe the main design principles behind the development of Golem 2, the race vehicle. The subsystems devoted to obstacle detection, avoidance, and state estimation are discussed in more detail. An overview of vehicle performance in the field is provided, including successes together with an analysis of the reasons leading to failures. © 2006 Wiley Periodicals, Inc.
Using a guided inquiry and modeling instructional framework (EIMA) to support preservice K‐8 science teaching
Authors: Schwarz Christina V. , Gwekwerere Yovita N.
Published: August 2006

This paper presents results from a study aimed at helping preservice elementary and middle school teachers incorporate model‐centered scientific inquiry into their science teaching practices. Specifically, the authors studied the effect of using a guided inquiry and modeling instructional framework (EIMA) and accompanying science methods instruction on preservice elementary teachers' science lesson design skills, scientific model use, and teaching orientations. Analysis of preservice teachers' pre–posttests, classroom artifacts, peer interviews, and lesson plans throughout the semester indicates that the framework successfully built on preservice teachers' prior instructional ideas, and that the majority of preservice teachers learned and used the framework in their lesson plans and teaching. Additionally, analysis of pre–posttest differences indicates an increase in posttest lesson plans that focused on engaging students in scientific inquiry using several kinds of models. Most importantly, the framework and accompanying instruction enabled two thirds of the class to move their teaching orientations away from discovery or didactic approaches toward reform‐based approaches such as conceptual change, inquiry, and guided inquiry. Results from this study show that using instructional frameworks such as EIMA can enable preservice teachers to socially construct, synthesize, and apply their knowledge for enacting reform‐oriented science teaching approaches such as model‐centered scientific inquiry. © 2006 Wiley Periodicals, Inc.Sci Ed91:158–186, 2007
An architecture for adaptive intrusion‐tolerant applications
Authors: Pal Partha , Rubel Paul , Atighetchi Michael , Webber Franklin , Sanders William H. , Seri Mouna , Ramasamy HariGovind , Lyons James , Courtney Tod , Agbaria Adnan , Cukier Michel , Gossett Jeanna , Keidar Idit
Published: August 2006

Applications that are part of a mission‐critical information system need to maintain a usable level of key services through ongoing cyber‐attacks. In addition to the well‐publicized denial of service (DoS) attacks, these networked and distributed applications are increasingly threatened by sophisticated attacks that attempt to corrupt system components and violate service integrity. While various approaches have been explored to deal with DoS attacks, corruption‐inducing attacks remain largely unaddressed. We have developed a collection of mechanisms based on redundancy, Byzantine fault tolerance, and adaptive middleware that help distributed, object‐based applications tolerate corruption‐inducing attacks. In this paper, we present the ITUA architecture, which integrates these mechanisms in a framework for auto‐adaptive intrusion‐tolerant systems, and we describe our experience in using the technology to defend a critical application that is part of a larger avionics system as an example. We also motivate the adaptive responses that are key to intrusion tolerance, and explain the use of the ITUA architecture to support them in an architectural framework. Copyright © 2006 John Wiley & Sons, Ltd.
MetaSockets: design and operation of runtime reconfigurable communication services
Authors: Sadjadi S. M. , McKinley P. K. , Kasten E. P. , Zhou Z.
Published: August 2006

This paper describes the internal architecture and operation of an adaptable communication component called the MetaSocket. MetaSockets are created using Adaptive Java, a reflective extension to Java that enables a component's internal architecture and behavior to be adapted at runtime in response to external stimuli. This paper describes how adaptive behavior is implemented in MetaSockets, as well as how MetaSockets interact with other adaptive components, such as decision makers and event mediators. Results of experiments on a mobile computing testbed demonstrate how MetaSockets respond to dynamic wireless channel conditions in order to improve the quality of interactive audio streams delivered to iPAQ handheld computers. Copyright © 2006 John Wiley & Sons, Ltd.
ISAMadapt: abstractions and tools for designing general‐purpose pervasive applications
Authors: Augustin I. , Yamin A. C. , da Silva L. C. , Real R. A. , Frainer G. , Geyer C. F. R.
Published: August 2006

The concept of pervasiveness provides the future of computing with an attractive perspective. However, software support for physical and logical mobility raises a set of new requirements and challenges for software production, creating demand for new types of applications, the so‐called pervasive applications, which express follow‐me semantics. The core of these challenges is a dynamic operating environment, which originates with the users' movement in different terminals and locations, and determines different execution contexts. For this envision to become a reality, developers must build applications that constantly adapt to a highly dynamic computing environment. Research works in pervasive computing have already addressed important issues, but they do not approach the problem of how to program general‐purpose pervasive systems. Pervasive applications are distributed, mobile, adaptive and consider context as a first‐order concept. To make the developers' task easier, we have introduced the software architecture called ISAM, which provides an integrated environment aimed at building pervasive applications composed of a development environment and an execution middleware. As part of our study within the ISAM project, we have been investigating how context‐awareness can be expressed at the programming language level with a basis on four main abstractions: context, adapters, adaptation commands, and adaptive behavior management policies. This paper introduces such abstractions, and presents some development and management tools anchored on an example application, which is under development. Copyright © 2006 John Wiley & Sons, Ltd.
End‐user programming of reconfigurable systems
Authors: Hague Rob , Robinson Peter
Published: August 2006

There is no ideal programming language. Each is better suited to some tasks rather than others. This is true not only for complete programs, but also for different stages such as architectural design, detailed implementation and maintenance. The situation is even more acute in the case of end‐user programming languages, which cater for a much more varied user population. It would therefore be advantageous to allow the same program to be viewed, and edited, in a number of different languages. We have developed a system, Lingua Franca, that provides this facility for end‐user programming languages in the setting of ubiquitous computing in the home. Copyright © 2006 John Wiley & Sons, Ltd.
A validation approach for neural network‐based online adaptive systems
Authors: Yerramalla Sampath , Fuller Edgar , Cukic Bojan
Published: August 2006

Traditional software validation methods cannot guarantee the safe behavior of online self‐adaptive systems. These systems are characterized by continual adaptation to changing environmental conditions. We present a novel methodology for validating adaptive software systems based ononline operational monitoring. The methodology inherits its theoretical underpinnings from the generic stability and convergence analysis ofLyapunov's theory. Lyapunov theory is well established in mathematics and control theory, but has not been used before for software validation. The presented validation technique is applied to a neural network‐based online self‐adaptive system,the intelligent flight control system. In this application, environmental changes include system failure modes, such as a stuck stabilator, broken aileron and/or rudder, sensor failure, etc. Our case study for validation is a specific online self‐adaptive system, the intelligent flight control that utilizes dynamic cell structures' neural networks to perform online adaptation. The theoretical foundation and practicability of the presented validation technique make the presented validation approach generally applicable to other types of online adaptive systems. Copyright © 2006 John Wiley & Sons, Ltd.
Using context and preferences to implement self‐adapting pervasive computing applications
Authors: Henricksen Karen , Indulska Jadwiga , Rakotonirainy Andry
Published: August 2006

Applications that exploit contextual information in order to adapt their behaviour to dynamically changing operating environments and user requirements are increasingly being explored as part of the vision of pervasive or ubiquitous computing. Despite recent advances in infrastructure to support these applications through the acquisition, interpretation and dissemination of context data from sensors, they remain prohibitively difficult to develop and have made little penetration beyond the laboratory. This situation persists largely due to a lack of appropriately high‐level abstractions for describing, reasoning about and exploiting context information as a basis for adaptation. In this paper, we present our efforts to address this challenge, focusing on our novel approach involving the use of preference information as a basis for making flexible adaptation decisions. We also discuss our experiences in applying our conceptual and software frameworks for context and preference modelling to a case study involving the development of an adaptive communication application. Copyright © 2006 John Wiley & Sons, Ltd.
Adapting workload distribution on software DSM clusters
Authors: Liu Yen‐Tso , Liang Tyng‐Yeu , Shieh Ce‐Kuen
Published: August 2006

Achieving an appropriate workload distribution is essential if user applications are to achieve a satisfactory performance on software distributed shared memory (SDSM) clusters. To address this problem, the present study develops a novel method for distributing program threads onto the individual computers of SDSM clusters. In contrast to alternative methods, the proposed approach takes account not only of processor speed and data‐sharing aspects, but also memory availability, such that application performance can be enhanced through the implementation of appropriate workload distributions. In addition, when distributing the program threads, the proposed method specifically chooses only those computers that can enhance the performance of the application, rather than simply distributing the threads to all the available nodes in the cluster. This location policy makes it possible to specify the appropriate node combinations that optimize program performance while simultaneously maximizing resource utilization. The proposed method is implemented on a testbed referred to as Teamster. The experimental results demonstrate that, compared to alternative methods, the proposed approach delivers a 20–30% improvement in the performance of the chosen test applications. Importantly, it is shown that the proposed method can efficiently specify proper node combinations for the applications. Copyright © 2006 John Wiley & Sons, Ltd.
The FRACTAL component model and its support in Java
Authors: Bruneton Eric , Coupaye Thierry , Leclercq Matthieu , Quéma Vivien , Stefani Jean‐Bernard
Published: August 2006

This paper presents FRACTAL, a hierarchical and reflective component model with sharing. Components in this model can be endowed with arbitrary reflective capabilities, from plain black‐box objects to components that allow a fine‐grained manipulation of their internal structure. The paper describes JULIA, a Java implementation of the model, a small but efficient runtime framework, which relies on a combination of interceptors and mixins for the programming of reflective features of components. The paper presents a qualitative and quantitative evaluation of this implementation, showing that component‐based programming in FRACTAL can be made very efficient. Copyright © 2006 John Wiley & Sons, Ltd.
A review of the psychosocial effects of false‐positive results on parents and current communication practices in newborn screening
Authors: Hewlett J. , Waisbren S. E.
Published: August 2006

As more states adopt expanded newborn screening for metabolic disorders, the overall number of false positives increases. False‐positive screening results have been associated with increased anxiety and stress in parents of infants who require follow‐up testing, even after the infant's good health is confirmed. This article reviews the literature on the negative impact of false‐positive newborn screening results on parents, along with a review of current communication practices for follow‐up screening. The results of this review suggest that parental stress and anxiety can be reduced with improved education and communication to parents, specifically at the time of follow‐up screening. Communication strategies with sample materials are proposed.
TAT gene mutation analysis in three Palestinian kindreds with oculocutaneous tyrosinaemia type II; characterization of a silent exonic transversion that causes complete missplicing by exon 11 skipping
Authors: Maydan G. , Andresen B. S. , Madsen P. P. , Zeigler M. , Raas‐Rothschild A. , Zlotogorski A. , Gutman A. , Korman S. H.
Published: August 2006

Deficiency of the hepatic cytosolic enzyme tyrosine aminotransferase (TAT) causes marked hypertyrosinaemia leading to painful palmoplantar hyperkeratoses, pseudodendritic keratitis and variable mental retardation (oculocutaneous tyrosinaemia type II or Richner–Hanhart syndrome). Parents may therefore seek prenatal diagnosis, but this is not possible by biochemical assays as tyrosine does not accumulate in amniotic fluid and TAT is not expressed in chorionic villi or amniocytes. Molecular analysis is therefore the only possible approach for prenatal diagnosis and carrier detection. To this end, we sought TAT gene mutations in 9 tyrosinaemia II patients from three consanguineous Palestinian kindreds. In two kindreds (7 patients), the only potential abnormality identified after sequencing all 12 exons and exon–intron boundaries was homozygosity for a silent, single‐nucleotide transversion c.1224G > T (p.T408T) at the last base of exon 11. This was predicted to disrupt the 5′ donor splice site of exon 11 and result in missplicing. However, as TAT is expressed exclusively in liver, patient mRNA could not be obtained for splicing analysis. A minigene approach was therefore used to assess the effect of c.1224G > T on exon 11 splicing. Transfection experiments with wild‐type and c.1224G > T mutant minigene constructs demonstrated that c.1224G > T results in complete exon 11 skipping, illustrating the utility of this approach for confirming a putative splicing defect when cDNA is unavailable. Homozygosity for a c.1249C > T (R417X) exon 12 nonsense mutation (previously reported in a French patient) was identified in both patients from the third kindred, enabling successful prenatal diagnosis of an unaffected fetus using chorionic villous tissue.
Measure of experimental pain using Rasch analysis
Authors: Decruynaere Céline , Thonnard Jean‐Louis , Plaghki Léon
Published: August 2006

Most common instruments used to assess the painfulness of nociceptive stimuli and the perception of such stimuli are ordinal. This property limits arithmetical operations and statistical procedures that can be applied on their numbers. The Rasch methodology provides mathematical procedures for transforming scores on an ordinal scale into measures on an interval scale. The present paper aims at presenting the basics of this methodology by applying it to the measurement of experimentally induced pain. Six blocks of seven CO2 laser heat stimuli varying in intensity were delivered on the hand of 100 healthy subjects. They rated their pain perception on a three‐level verbal rating scale (not painful, slightly painful, painful). One member of the family of Rasch models, the many‐facet model, was applied to the analysis of these ratings. The analysis provided linear measures of the painfulness for each intensity of stimulation, of the pain perception of each subject and of the painfulness of each successive block. All these measures are located on a single pain perception continuum. Advantages and disadvantages of this methodology will be discussed in terms of subsequent possible mathematical analyses, statistical tests and implications for experimental and clinical investigations.
Phosphatidylcholine‐specific phospholipase C, p53 and ROS in the association of apoptosis and senescence in vascular endothelial cells
Authors: Cheng Yizhe , Zhao Qitao , Liu Xia , Araki Satohiko , Zhang Shangli , Miao Junying
Published: August 2006

Previously, we found that phosphatidylcholine‐specific phospholipase C (PC‐PLC) participated in apoptosis signaling of vascular endothelial cells (VECs). Here, to explore whether PC‐PLC is involved in the association of apoptosis and senescence in VECs, we analyzed p53 expression and intracellular reactive oxygen species (ROS) levels in young and senescent VECs before and after inhibiting PC‐PLC activity. The results showed that suppressing PC‐PLC inhibited apoptosis and the elevation of p53 expression induced by apoptosis in young cells, but not in senescent cells, and that inhibiting PC‐PLC depressed intracellular ROS levels both in young and senescent cells. The data suggested that PC‐PLC was involved in the association of apoptosis and senescence. Its function might be closely related to the level of p53 in VECs.
Exocytosis of late endosomes does not directly contribute membrane to the formation of phagocytic cups or pseudopods in Dictyostelium
Authors: Charette Steve J. , Cosson Pierre
Published: August 2006

Exocytosis of late endocytic compartments in Dictyostelium has mostly been studied by live microscopy. Here we show that this exocytosis is accompanied by a complete fusion of late endosomes with the plasma membrane resulting in the transient formation of membrane microdomains that can be visualized by immunofluorescence in fixed cells. This permitted to demonstrate that fusion of late endocytic compartments with the cell surface does not occur in regions of the plasma membrane engaged in the formation of pseudopods, macropinosomes or phagosomes. Our results propose that exocytosis of late endosomes and actin‐driven membrane remodeling are mutually exclusive processes.
Deoxyribophosphate lyase activity of mammalian endonuclease VIII‐like proteins
Authors: Grin Inga R. , Khodyreva Svetlana N. , Nevinsky Georgy A. , Zharkov Dmitry O.
Published: August 2006

Base excision repair (BER) protects cells from nucleobase DNA damage. In eukaryotic BER, DNA glycosylases generate abasic sites, which are then converted to deoxyribo‐5′‐phosphate (dRP) and excised by a dRP lyase (dRPase) activity of DNA polymerase β (Polβ). Here, we demonstrate that NEIL1 and NEIL2, mammalian homologs of bacterial endonuclease VIII, excise dRP by β‐elimination with the efficiency similar to Polβ. DNA duplexes imitating BER intermediates after insertion of a single nucleotide were better substrates. NEIL1 and NEIL2 supplied dRPase activity in BER reconstituted with dRPase‐null Polβ. Our results suggest a role for NEILs as backup dRPases in mammalian cells.
Lipidomic strategies to study structural and functional defects of ABC‐transporters in cellular lipid trafficking
Authors: Schmitz Gerd , Liebisch Gerhard , Langmann Thomas
Published: August 2006

The majority of the human ATP‐binding cassette (ABC)‐transporters function in cellular lipid trafficking and in the regulation of membrane lipid composition associating their dysfunction with human disease phenotypes related to sterol, phospholipid and fatty acid homeostasis. Based on findings from monogenetic disorders, animal models, and in vitro systems, major clues on the expression, function and cellular localization of human ABC‐transporters have been gained. Here we review novel lipidomic technologies including quantitative mRNA expression monitoring by realtime RT‐PCR and DNA‐microarrays, lipid mass spectrometry, cellular fluorescence imaging and flow cytometry as promising tools to further define regulatory networks, lipid species patterns and subcellular domains important for ABC‐transporter‐mediated lipid trafficking.