bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ion-acoustic solitary waves in a multi-species magnetized plasma consisting of non-thermal and isothermal electrons
Authors: ISLAM SKANARUL , BANDYOPADHYAY A. , DAS K. P. 
Published: April 2008

AbstractThe Korteweg–de Vries–Zakharov–Kuznetsov (KdV-ZK) equation describes the nonlinear behaviour of long-wavelength weakly nonlinear ion-acoustic waves propagating obliquely to an external uniform (space independent) static (time independent) magnetic field in a plasma consisting of warm adiabatic ions and a superposition of two distinct population of electrons, one due to Cairns et al. (1995Geophys. Res. Lett.22, 2709), which generates the fast energetic electrons, and the other the well-known Maxwell–Boltzman distributed electrons. It is found that the compressive or rarefactive nature of the ion-acoustic solitary wave solution of the KdV-ZK equation does not depend on the ion temperature if σc<0 or σc>1, where σcis a function of β1,nscand σsc. This β1is the non-thermal parameter associated with the non-thermal velocity distribution function of electrons (Cairns et al.),nscis the ratio of the unperturbed number density of the isothermal electrons to that of the non-thermal electrons and σscis the ratio of the average temperature of the non-thermal electrons to that of the isothermal electrons. The KdV-ZK equation describes compressive or rarefactive ion-acoustic solitary wave according to whether σc<0 or σc>1. When 0 ≤ σc≤ 1, the KdV-ZK equation describes compressive or rarefactive ion-acoustic solitary wave according to whether σ>σcor σ<σc, where σ is the ratio of the average temperature of ions to the effective temperature of electrons. If σ takes the value σcwith 0 ≤ σc≤ 1, the coefficient of the nonlinear term of the KdV-ZK equation vanishes and for this case the nonlinear evolution equation of the ion-acoustic wave is a modified KdV-ZK (MKdV-ZK) equation. It is found that the four-dimensional parameter space, originated from the physically admissible values of the four-parameters β1, σ, σscandnscof the present extended plasma system, can be decomposed into five mutually disjoint subsets with respect to the critical values of the different parameters, and the nonlinear behaviour of the same ion acoustic wave in those subsets can be described by different modified KdV-ZK equations. A general method of perturbation of the dependent variables has been developed to obtain the different evolution equations. The applicability of the different evolution equations and their solitary wave solutions (along with the conditions for their existence) have been investigated analytically and graphically.
Connexin and pannexin mediated cell–cell communication
Authors: Scemes Eliana , Suadicani Sylvia O. , Dahl Gerhard , Spray David C. 
Published: April 2008

AbstractIn this review, we briefly summarize what is known about the properties of the three families of gap junction proteins, connexins, innexins and pannexins, emphasizing their importance as intercellular channels that provide ionic and metabolic coupling and as non-junctional channels that can function as a paracrine signaling pathway. We discuss that two distinct groups of proteins form gap junctions in deuterostomes (connexins) and protostomes (innexins), and that channels formed of the deuterostome homologues of innexins (pannexins) differ from connexin channels in terms of important structural features and activation properties. These differences indicate that the two families of gap junction proteins serve distinct, complementary functions in deuterostomes. In several tissues, including the CNS, both connexins and pannexins are involved in intercellular communication, but have different roles. Connexins mainly contribute by forming the intercellular gap junction channels, which provide for junctional coupling and define the communication compartments in the CNS. We also provide new data supporting the concept that pannexins form the non-junctional channels that play paracrine roles by releasing ATP and, thus, modulating the range of the intercellular Ca2+-wave transmission between astrocytes in culture.
The effects of aging, injury and disease on microglial function: a case for cellular senescence
Authors: Miller Kelly R. , Streit Wolfgang J. 
Published: April 2008

AbstractNeuroinflammation resulting from chronic reactive microgliosis is thought to contribute to age-related neurodegeneration, as well as age-related neurodegenerative diseases, specifically Alzheimer's disease (AD). Support of this theory comes from studies reporting a progressive, age-associated increase in microglia with an activated phenotype. Although the underlying cause(s) of this microglial reactivity is idiopathic, an accepted therapeutic strategy for the treatment of AD is inhibition of microglial activation using anti-inflammatory agents. Although the effectiveness of anti-inflammatory treatment for AD remains equivocal, microglial inhibition is being tested as a potential treatment for additional neurodegenerative disorders including amyotrophic lateral sclerosis and Parkinson's disease. Given the important and necessary functions of microglia in normal brain, careful evaluation of microglial function in the aged brain is a necessary first step in targeting more precise treatment strategies for aging-related neurodegenerative diseases. Studies from our laboratory have shown multiple age-related changes in microglial morphology and function that are suggestive of cellular senescence. In this manuscript, we review current knowledge of microglia in the aging brain and present new, unpublished work that further supports the theory that microglia experience an age-related decline in proliferative function as a result of cellular senescence.
Augmentative and Alternative Communication: Assessment in the Schools
Authors: Proctor Lisa A. , Oswalt Jill 
Published: April 2008

Abstract
The purpose of this article is to review augmentative and alternative communication (AAC) assessment issues in the schools. Initially, the article discusses the role and responsibilities of school-based speech-language pathologists in the assessment of children with complex communication needs. Next, the article briefly reflects on the importance of teaming in device selection for children with AAC needs. The main portion of the article provides information on assessment tools and resources related to comprehensive assessment for children with complex communication needs. This includes information on assessment of speech production and the relevance in AAC assessment. This is followed by tools and resources for receptive language and expressive language assessment. Also included in this main section is information on tools that examine academic and social participation. Finally, information on literacy assessment for student with complex communication needs is provided. The intent of the article is to provide the reader with a brief overview of assessment tools and resources for children with complex communication needs.
Communication Partner Interventions for Students Who Use AAC
Authors: Kent-Walsh Jennifer 
Published: April 2008

Abstract
Research indicates that the communication skills of partners significantly influence the success of communicative interactions with individuals who use AAC. Frequently, partners have been reported to not provide supportive opportunities for communication when interacting with individuals who use AAC. In turn, individuals who use AAC have been documented to often be passive communicators, particularly when they are at the beginning stages of developing communicative competence. Given the importance of effective communication skills in the school environment, it is essential that speech-language pathologists consider conducting partner interventions when working with school-age children with AAC needs. This article provides practical suggestions for speech-language pathologists by exploring (a) the range of communication partners who may benefit from partner interventions, (b) examples of interaction skills that can be targeted through partner interventions, and (c) a suggested protocol for communication partner interventions. By providing interventions for communication partners who are complimentary to interventions provided directly, it is possible for school SLPs to strengthen their approach to improving communication and educational outcomes for children with AAC needs.
Professional Preparedness for Provision of Auditory Oral Programs to Children With Hearing Loss: Results of a Survey
Authors: Luckhurst Joan A. 
Published: April 2008

AbstractAdvances in technology have facilitated development of auditory-oral skills in greater numbers of children who are deaf. In addition, mainstream educational placements are increasing for this population. Since success in the mainstream is largely dependent upon development of oral communication skills, it is imperative that professionals working with these children have competence in auditory-oral methodology. The present study investigated professionals' perceptions of preparedness to develop and implement auditory-oral programs. Professionals using an auditory-oral approach were asked about their perceived levels of knowledge and skills, pre-service training, and on-the-job factors that contributed to their competence to provide auditory-oral programs to children who are deaf. Classification tables, chi-square, and qualitative analyses were used to determine professionals' perceptions of preparedness and to identify significant differences among professional groups (i.e., speech-language pathologists, teachers of the deaf, audiologists), as well as specific aspects of pre-service and occupational training that promoted knowledge and skills. Results indicated that a significant number of professionals in all groups feel unprepared. Specific group differences and needed components for adequate preparation are discussed. Suggestions for further study are presented.
Telepractice Aural Habilitation for School-Age Children
Authors: Duncan Jill 
Published: April 2008

Abstract
This paper examines telepractice aural habilitation for school-age children delivered via videoconferencing. It identifies issues, concerns, and successful teaching behaviors and strategies employed in this unique environment. The paper concludes with a description of the Royal Institute for Deaf and Blind Children’s Teleschool and a case study of a 16-year-old cochlear implant user who has received intercontinental auditory-verbal therapy via videoconferencing for 24 months.
Cortical Stimulation and Aphasia: The State of the Science
Authors: Cherney Leora R. 
Published: April 2008

AbstractPurpose:Biological approaches to aphasia rehabilitation involve procedures aimed to alter brain anatomy and physiology so that language function can be restored. One such approach is the application of electrical stimulation to the cerebral cortex to facilitate brain plasticity and enhance stroke recovery.Method:This article discusses the rationale for the application of cortical stimulation and reviews three different methods of delivering cortical brain stimulation — repetitive transcranial magnetic stimulation (rTMS), transcranial direct current stimulation (tDCS), and epidural cortical stimulation. Each of these methods has been applied to the rehabilitation of language after stroke, and some of the key studies that have addressed the use of cortical stimulation as a potential treatment for post-stroke aphasia are described.Conclusions:Pilot results suggest a potential role for cortical stimulation as an adjuvant strategy in aphasia rehabilitation. Further investigation of each method of stimulation and its impact on language recovery is warranted. Suggestions for the direction of future research are discussed.
Typicality Treatment for Naming Deficits in Aphasia: Why Does It Work?
Authors: Kiran Swathi 
Published: April 2008

AbstractPurpose:The present paper provides a review of a recent treatment approach for alleviating naming deficits in patients with aphasia. This is an example of a treatment that is theoretically based and supported by behavioral evidence from normal adult language processing.Method:First, a theoretical basis for naming deficits in patients with aphasia is provided. Then, current options for semantic-based treatment of naming deficits are reviewed. Previous work from our laboratory indicates that training atypical examples of semantic categories resulted in generalization to untrained typical examples, whereas training typical examples did not result in generalization to untrained atypical examples.The usefulness of the typicality treatment approach is discussed in the context of recent studies from our laboratory that have examined this approach across a variety of semantic categories, including animate categories (e.g., birds), inanimate categories (e.g., furniture), well-defined categories such as “shapes,” and goal derived categories such as “things to have in a garage sale.”Conclusions:We suggest that the success of the treatment seemingly relies on the stringent selection of typical/atypical examples and on highlighting the variation of semantic features of the trained category as part of the treatment protocol.
RNAplex: a fast tool for RNA–RNA interaction search
Authors: Tafer Hakim , Hofacker Ivo L. 
Published: April 2008

Abstract
Motivation: Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. Additionally ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncRNAs is a lengthy task as tools for cofolding RNA molecules like RNAcofold and RNAup are too slow for genome-wide search. Tools like RNAhybrid that neglects intramolecular interactions have runtimes proportional to 𝒪(m · n), albeit with a large prefactor. Still in many cases the need for even faster methods exists.
Results: We present a new program, RNAplex, especially designed to quickly find possible hybridization sites for a query RNA in large RNA databases. RNAplex uses a slightly different energy model which reduces the computational time by a factor 10–27 compared to RNAhybrid. In addition a length penalty allows to focus the target search on short highly stable interactions.
Availability: RNAplex can be downloaded at http://www.tbi.univie.ac.at/~htafer/
Contact: ivo@tbi.univie.ac.at
Supplementary information: Supplementary data are available at Bioinformatics online.
RUPTURED POLLEN GRAIN1, a Member of the MtN3/saliva Gene Family, Is Crucial for Exine Pattern Formation and Cell Integrity of Microspores in Arabidopsis
Authors: Guan Yue-Feng , Huang Xue-Yong , Zhu Jun , Gao Ju-Fang , Zhang Hong-Xia , Yang Zhong-Nan 
Published: April 2008

AbstractDuring microsporogenesis, the microsporocyte (or microspore) plasma membrane plays multiple roles in pollen wall development, including callose secretion, primexine deposition, and exine pattern determination. However, plasma membrane proteins that participate in these processes are still not well known. Here, we report that a new gene, RUPTURED POLLEN GRAIN1 (RPG1), encodes a plasma membrane protein and is required for exine pattern formation of microspores in Arabidopsis (Arabidopsis thaliana). The rpg1 mutant exhibits severely reduced male fertility with an otherwise normal phenotype, which is largely due to the postmeiotic abortion of microspores. Scanning electron microscopy examination showed that exine pattern formation in the mutant is impaired, as sporopollenin is randomly deposited on the pollen surface. Transmission electron microscopy examination further revealed that the primexine formation of mutant microspores is aberrant at the tetrad stage, which leads to defective sporopollenin deposition on microspores and the locule wall. In addition, microspore rupture and cytoplasmic leakage were evident in the rpg1 mutant, which indicates impaired cell integrity of the mutant microspores. RPG1 encodes an MtN3/saliva family protein that is integral to the plasma membrane. In situ hybridization analysis revealed that RPG1 is strongly expressed in microsporocyte (or microspores) and tapetum during male meiosis. The possible role of RPG1 in microsporogenesis is discussed.
RDC‐assisted modeling of symmetric protein homo‐oligomers
Authors: Wang Xu , Bansal Sonal , Jiang Mei , Prestegard James H. 
Published: April 2008

AbstractProtein oligomerization serves an important function in biological processes, yet solving structures of protein oligomers has always been a challenge. For solution NMR, the challenge arises both from the increased size of these systems and, in the case of homo‐oligomers, from ambiguities in assignment of intra‐ as opposed to intersubunit NOEs. In this study, we present a residual dipolar coupling (RDC)‐assisted method for constructing models of homo‐oligomers with purely rotational symmetry. Utilizing the fact that one of the principal axes of the tensor describing the alignment needed for RDC measurement is always parallel to the oligomer symmetry axis, it is possible to greatly restrict possible models for the oligomer. Here, it is shown that, if the monomer structure is known, all allowed dimer models can be constructed using a grid search algorithm and evaluated based on RDC simulations and the quality of the interface between the subunits. Using the Bacillus subtilis protein YkuJ as an example, it is shown that the evaluation criteria based on just two sets of NH RDCs are very selective and can unambiguously produce a model in good agreement with an existing X‐ray structure of YkuJ.
Side chain substitution benchmark for peptide/MHC interaction
Authors: Knapp Bernhard , Omasits Ulrich , Schreiner Wolfgang 
Published: April 2008

AbstractThe prediction of T‐cell epitopes is an essential part in virtual immunology. Apart from sequence‐based techniques, which achieve good results but fail to give insight into the binding behavior of a certain peptide binding to a major histocompatibility complex, structure‐based approaches are another important technique. An essential step is the correct placement of the side chains for a given peptide in cases where no experimental data for the structure are available. To our knowledge, no benchmark for side chain substitution in the area of HLA has been reported in the literature. Here, we present a comparison of five different tools (SCWRL, SCATD, SPDBV, SCit, IRECS) applicable for side chain substitution. Each tool is tested on 29 different HLA‐A2 structures with experimentally known side chain positions. Parts of the benchmark are correctness, reliability, runtime, and usability. For validation, the root mean square deviations between X‐ray structures and predicted structures are used. All tools show different strengths and weaknesses.
Applicability of cord blood‐derived unrestricted somatic stem cells in tissue engineering concepts
Authors: Degistirici Ö. , Jäger M. , Knipper A. 
Published: April 2008

Abstract.  Objectives: Cell‐based tissue engineering concepts are becoming an important therapeutic alternative in the treatment of traumatic or chronic skeletal diseases. Here, we have evaluated cord blood‐derived unrestricted somatic stem cells (USSCs) for use in bone and cartilage repair strategies. Methods and results: This type of somatic stem cell can be generated from cord blood with a current rate of 29% and we have documented excellent proliferation potential to high passage numbers. The cells have an initial population doubling time of 39 h, which slightly decreased with increasing passage number, but cells maintained their proliferation abilities up to passage 23. Cells clearly differentiated towards chondrogenic, adipogenic and osteogenic lineage as shown by reverse transcription‐polymerase chain reaction as well as by histological, biochemical and immunohistochemical stains. Differentiation potential of USSCs was observed at passage 6, passage 15 and passage 21. In addition, USSCs showed increased secretion of vascular endothelial growth factor (VEGF) during osteogenic differentiation, as well as expression of key markers of angiogenesis such as vascular endothelial growth factor receptor‐2 and platelet/endothelial cell adhesion molecule. Conclusions: USSCs when transplanted into a bone defect might support the repair process not only by pure remineralization but also by installation of angiogenic environment.
Food allergy QoL questionnaire for children aged 0–12 years: content, construct, and cross‐cultural validity
Authors: DunnGalvin A. , De BlokFlokstra B. M. J. , Burks A. W. , Dubois A. E. J. , Hourihane J. O'B. 
Published: April 2008

SummaryBackground
To date, there is no food allergy‐specific questionnaire that allows parents to report children's health‐related QoL (HRQL) from the child's perspective.Objective
The aim of this study was to develop a sensitive, multi‐dimensional measure to assess parental perception of HRQL in children aged 0–12 years with food allergy.Methods
The Food Allergy QoL – Parent Form (FAQLQ‐PF) was developed and validated in four stages: (1) item generation using focus groups, expert opinion, and literature review; (2) item reduction, using clinical impact and factor analysis; (3) internal and test–retest reliability and construct validity were evaluated using relevant scales of the Child Health Questionnaire (CHQ)‐28 and the disease‐specific food allergy independent measure (FAIM); and (4) cross‐cultural and content validity was examined by administering the questionnaire in a US sample.Results
Stage 1: Saturation was reached at 110 items. Stage 2: The reduced instrument has 14 items for children <4 years and 26 and 30 items for children aged 4–6 years and 7–12 years, respectively. Factor analysis revealed three subscales: emotional impact, food anxiety, and social and dietary limitations, accounting for 68% of the variance. Stage 3: Cronbach's α >0.7 for subscales and total score. Construct validity was demonstrated by significant correlations between relevant scales of the CHQ‐28 and FAQLQ‐PF subscales (r=0.69–0.77, P<0.01), and between FAQLQ‐PF subscales and the FAIM. Sensitivity was shown by significant within‐group differences in a sample of 124 food‐allergic children. Stage 4: The FAQLQ‐PF was validated in a sample of US children, Cronbach's α >0.7 for subscales and total score. Construct validity was demonstrated by significant correlations between FAQLQ‐PF and the FAIM (parent report) and between the FAQLQ‐PF and the FAIM (child report). No differences were observed between the US and Irish scores.Conclusion
The FAQLQ‐PF is psychometrically robust, with excellent reliability and validity.