bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do glial cells control pain?
Authors: Suter Marc R. , Wen Yeong-Ray , Decosterd Isabelle , Ji Ru-Rong 
Published: April 2008

AbstractManagement of chronic pain is a real challenge, and current treatments that focus on blocking neurotransmission in the pain pathway have resulted in limited success. Activation of glial cells has been widely implicated in neuroinflammation in the CNS, leading to neurodegeneration in conditions such as Alzheimer's disease and multiple sclerosis. The inflammatory mediators released by activated glial cells, such as tumor necrosis factor-α and interleukin-1β not only cause neurodegeneration in these disease conditions, but also cause abnormal pain by acting on spinal cord dorsal horn neurons in injury conditions. Pain can also be potentiated by growth factors such as brain-derived growth factor and basic fibroblast growth factor, which are produced by glia to protect neurons. Thus, glial cells can powerfully control pain when they are activated to produce various pain mediators. We review accumulating evidence that supports an important role for microglial cells in the spinal cord for pain control under injury conditions (e.g. nerve injury). We also discuss possible signaling mechanisms, in particular mitogen-activated protein kinase pathways that are crucial for glial-mediated control of pain. Investigating signaling mechanisms in microglia might lead to more effective management of devastating chronic pain.
Snow Cover in South Dakota: Statistical analysis of spatiotemporal diversity
Authors: Shmagin Boris , Johnston Carol 
Published: April 2008

AbstractSnow distribution and accumulation influence many human activities and the dynamic sustainability of ecological systems. Snow cover distribution analysis is a second research step towards creating a Atlas of Climate and Water Resources for SD (temperature analysis was presented last year). We analyzed the regional diversity of monthly total snowfall based on long-term data obtained from the High Plains Regional Climate Center for South Dakota. Multidimensional statistical methods were used, and the results presented for the State of South Dakota.The sets of initial matrixes were compiled with snow observations for the state. The first type of initial matrix of time series {Xt*n}, where t = number of years (67) and n = number of meteorological stations (25), contains 25 stations with mutual observational interval (1931-1998) of 67 winters. The second type of initial matrix {Xt*m}, where t = number of years (67) and m = number of months in a year, included seven initial matrixes.Statistical analysis allowed us to differentiate weather stations by temporal trends and spatial distribution for the time intervals 1931-1998. The average annual sum of total monthly snowfall (October-May) ranged from 25.5 to 53.5 inches for 25 stations trough this time interval. The most variable stations (Bowman Court House, Alexandria, Colony, Gordon, Clark, hot Springs and Eureka) were determined; their seasonality was described (the most variable months and correlation among months during period of snowfall) and their seasonal regime determined.
MUSIC - Multisimulation Coordinator: Request For Comments
Authors: Ekeberg Örjan , Djurfeldt Mikael 
Published: April 2008

AbstractMUSIC is an API allowing large scale neuron simulators using MPI internally to exchange data during runtime. MUSIC provides mechanisms to transfer massive amounts of event information and continuous values from one parallel application to another. Special care has been taken to ensure that existing simulators can be adapted to MUSIC. In particular, MUSIC handles data transfer between applications that use different time steps and different data allocation strategies. This RFC - Request For Comments - document invites comments on the proposed design and prototype specifications.
Classroom-Based Language Goals and Intervention for Children Who Use AAC: Back to Basics
Authors: Binger Cathy 
Published: April 2008

Abstract
When working with a preschool or school-aged child who uses aided AAC, much of the speech-language pathologist's (SLP's) focus is commonly on the AAC tools that the child is using. SLPs will often talk with educators and parents about the technology itself, and sometimes, many of the child's IEP goals center around use of the AAC technologies. Many educators (and sometimes even SLPs), however, are often reluctant to use technologies with which they are not comfortable. In the midst of all of the complications that come with technology use, it can be helpful to remember that AAC technologies are simply tools that provide the child with access to language. Most children who use AAC experience language deficits (e.g., Binger & Light, in press), and the purpose of AAC is to provide the child with a means of overcoming these language deficits. Given these facts, the goals, objectives, and intervention techniques that SLPs use with children who use AAC should not, in many cases, be very different from the goals and techniques for children who primarily rely on speech to communicate. In other words, it is important to put the language back into speech-language pathology, when working with children who use AAC. To illustrate these points, three cases of children who use AAC and who have very different profiles are presented below, with example language goals and intervention techniques that may be used with each child.
AAC in the Schools: Current Issues and Future Directions
Authors: Fallon Karen A. 
Published: April 2008

Abstract
For students with complex communication needs, positive educational outcomes are heavily dependent on support services that facilitate access to AAC technologies, the acquisition of literacy skills, and access to the academic curriculum within supportive classroom communities. Although the AAC research literature documents continuous progress in the quality and effectiveness of school-based services, by many indicators the field has a distance to go in pursuit of excellence in AAC service delivery. In reflecting upon the current state of school-based practice, several important factors emerge as critical to the success of students who require AAC, including the expertise of practicing professionals, effective collaborations of service-delivery teams, and the availability of empirical studies to guide practitioners. This article examines key issues affecting AAC service delivery in the schools and discusses critical clinical and research needs in the areas of personnel preparation, collaborative team building, and the provision of quality AAC services. Suggestions for the development and refinement of best practices are also explored in a discussion of future directions for school-based AAC services.
The Changing “Face” of Aphasia Therapy
Authors: Lee Jaime B. , Cherney Leora R. 
Published: April 2008

Abstract

Purpose:
Clinicians and researchers are searching for cost effective ways to deliver intensive aphasia treatment. The purpose of this article is to describe one method of providing less costly but intensive treatment via a computer software program called AphasiaScripts
TM
.

Method:
First, we describe the unique, interactive computer software program developed for individuals with aphasia to practice conversations that have been individually scripted for them. In AphasiaScripts
TM
, an avatar serves as the virtual therapist or conversational partner. The simplicity of the user interface allows the person with aphasia to quickly learn how to use the program and to manage the level of supportive cueing needed. Second, we clarify the role of the speech-language pathologist in the light of new technology that allows the person with aphasia to practice these conversations intensively and independently.

Conclusions:
AphasiaScripts
TM
serves as an example of a software program that makes use of advanced computer technology, yet still requires the clinical expertise of the speech-language pathologist.
Think Tank Deliberates Future Directions for the Social Approach to Aphasia
Authors: Simmons-Mackie Nina , Conklin Jamie , Kagan Aura 
Published: April 2008

Abstract

Purpose
: This article describes the rationale and outcome of an international meeting held to explore evidence related to social approaches to aphasia intervention.

Method
: A think tank and conference took place in Toronto, Canada, in September 2007 with the purpose of mobilizing a process of collaboration to document and collect evidence related to social approaches to aphasia. Using a framework called “Living with Aphasia: Framework for Outcome Measurement” (A-FROM), meeting participants worked to identify evidence available in the literature related to social approaches, identify gaps in evidence, and establish a plan to move forward in the process of establishing a comprehensive evidence base.

Results
: A preliminary summary of evidence was defined according to A-FROM domains, and weaknesses and gaps were identified. Concrete directions for the future were set forth as action plans.

Conclusions:
This report on the outcomes of the international think tank serves as an invitation to those interested in furthering the evidence for social approaches to aphasia to become involved in a collaborative process of evaluating and collecting evidence.
Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists
Authors: Hackenberg Michael , Matthiesen Rune 
Published: April 2008

Abstract
Motivation: The ontological analysis of the gene lists obtained from DNA microarray experiments constitutes an important step in understanding the underlying biology of the analyzed system. Over the last years, many other high-throughput techniques emerged, covering now basically all ‘omics’ fields. However, for some of these techniques the generally used functional ontologies might not be sufficient to describe the biological system represented by the derived gene lists. For a more complete and correct interpretation of these experiments, it is important to extend substantially the number of annotations, adapting the ontological analysis to the new emerging techniques.
Results: We developed Annotation-Modules, which offers an improvement over the current tools in two critical aspects. First, the underlying annotation database implements features from many different fields like gene regulation and expression, sequence properties, evolution and conservation, genomic localization and functional categories—resulting in about 60 different annotation features. Second, it examines not only single annotations but also all the combinations, which is important to gain insight into the interplay of different mechanisms in the analyzed biological system.
Availability: http://web.bioinformatics.cicbiogune.es/AM/AnnotationModules.php
Contact: mlhackenberg@gmail.com
TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
Authors: Tusnády Gábor E. , Kalmár Lajos , Hegyi Hédi , Tompa Péter , Simon István 
Published: April 2008

Abstract
Summary: The TOPDOM database is a collection of domains and sequence motifs located consistently on the same side of the membrane in α-helical transmembrane proteins. The database was created by scanning well-annotated transmembrane protein sequences in the UniProt database by specific domain or motif detecting algorithms. The identified domains or motifs were added to the database if they were uniformly annotated on the same side of the membrane of the various proteins in the UniProt database. The information about the location of the collected domains and motifs can be incorporated into constrained topology prediction algorithms, like HMMTOP, increasing the prediction accuracy.
Availability: The TOPDOM database and the constrained HMMTOP prediction server are available on the page http://topdom.enzim.hu
Contact: tusi@enzim.hu; lkalmar@enzim.hu
A Genome-Wide Functional Investigation into the Roles of Receptor-Like Proteins in Arabidopsis
Authors: Wang Guodong , Ellendorff Ursula , Kemp Ben , Mansfield John W. , Forsyth Alec , Mitchell Kathy , Bastas Kubilay , Liu Chun-Ming , Woods-Tör Alison , Zipfel Cyril , de Wit Pierre J.G.M. , Jones Jonathan D.G. , Tör Mahmut , Thomma Bart P.H.J. 
Published: April 2008

AbstractReceptor-like proteins (RLPs) are cell surface receptors that typically consist of an extracellular leucine-rich repeat domain, a transmembrane domain, and a short cytoplasmatic tail. In several plant species, RLPs have been found to play a role in disease resistance, such as the tomato (Solanum lycopersicum) Cf and Ve proteins and the apple (Malus domestica) HcrVf2 protein that mediate resistance against the fungal pathogens Cladosporium fulvum, Verticillium spp., and Venturia inaequalis, respectively. In addition, RLPs play a role in plant development; Arabidopsis (Arabidopsis thaliana) TOO MANY MOUTHS (TMM) regulates stomatal distribution, while Arabidopsis CLAVATA2 (CLV2) and its functional maize (Zea mays) ortholog FASCINATED EAR2 regulate meristem maintenance. In total, 57 RLP genes have been identified in the Arabidopsis genome and a genome-wide collection of T-DNA insertion lines was assembled. This collection was functionally analyzed with respect to plant growth and development and sensitivity to various stress responses, including susceptibility toward pathogens. A number of novel developmental phenotypes were revealed for our CLV2 and TMM insertion mutants. In addition, one AtRLP gene was found to mediate abscisic acid sensitivity and another AtRLP gene was found to influence nonhost resistance toward Pseudomonas syringae pv phaseolicola. This genome-wide collection of Arabidopsis RLP gene T-DNA insertion mutants provides a tool for future investigations into the biological roles of RLPs.
Structure and dynamics of de novo proteins from a designed superfamily of 4‐helix bundles
Authors: Go Abigail , Kim Seho , Baum Jean , Hecht Michael H. 
Published: April 2008

AbstractLibraries of de novo proteins provide an opportunity to explore the structural and functional potential of biological molecules that have not been biased by billions of years of evolutionary selection. Given the enormity of sequence space, a rational approach to library design is likely to yield a higher fraction of folded and functional proteins than a stochastic sampling of random sequences. We previously investigated the potential of library design by binary patterning of hydrophobic and hydrophilic amino acids. The structure of the most stable protein from a binary patterned library of de novo 4‐helix bundles was solved previously and shown to be consistent with the design. One structure, however, cannot fully assess the potential of the design strategy, nor can it account for differences in the stabilities of individual proteins. To more fully probe the quality of the library, we now report the NMR structure of a second protein, S‐836. Protein S‐836 proved to be a 4‐helix bundle, consistent with design. The similarity between the two solved structures reinforces previous evidence that binary patterning can encode stable, 4‐helix bundles. Despite their global similarities, the two proteins have cores that are packed at different degrees of tightness. The relationship between packing and dynamics was probed using the Modelfree approach, which showed that regions containing a high frequency of chemical exchange coincide with less well‐packed side chains. These studies show (1) that binary patterning can drive folding into a particular topology without the explicit design of residue‐by‐residue packing, and (2) that within a superfamily of binary patterned proteins, the structures and dynamics of individual proteins are modulated by the identity and packing of residues in the hydrophobic core.
Cysteine 155 plays an important role in the assembly of Mycobacterium tuberculosis FtsZ
Authors: Jaiswal Richa , Panda Dulal 
Published: April 2008

AbstractThe assembly of FtsZ plays an important role in bacterial cell division. Mycobacterium tuberculosis FtsZ (MtbFtsZ) has a single cysteine residue at position 155. We have investigated the role of the lone cysteine residue in the assembly of MtbFtsZ using different complimentary approaches, namely chemical modification by a thiol‐specific reagent 5,5′‐dithiobis‐(2‐nitrobenzoic acid) (DTNB) or a cysteine‐chelating agent HgCl2, and site‐directed mutagenesis of the cysteine residue. HgCl2 strongly reduced the polymerized mass of MtbFtsZ while it had no detectable effect on the polymerization of Escherichia coli FtsZ, which lacks a cysteine residue. HgCl2 inhibited the protofilamentous assembly of MtbFtsZ and induced the aggregation of the protein. Further, HgCl2 perturbed the secondary structure of MtbFtsZ and increased the binding of a hydrophobic probe 1‐anilinonaphthalene‐8‐sulfonic acid (ANS) with MtbFtsZ, indicating that the binding of HgCl2 altered the conformation of MtbFtsZ. Chemical modification of MtbFtsZ by DTNB also decreased the polymerized mass of MtbFtsZ. Further, the mutagenesis of Cys‐155 to alanine caused a strong reduction in the assembly of MtbFtsZ. Under assembly conditions, the mutated protein formed aggregates instead of protofilaments. Far‐UV CD spectroscopy and ANS binding suggested that the mutated MtbFtsZ has different conformation than that of the native MtbFtsZ. The effect of the mutation or chemical modification of Cys‐155 on the MtbFtsZ assembly has been explained considering its location in the MtbFtsZ crystal structure. The results together suggest that the cysteine residue (Cys‐155) of MtbFtsZ plays an important role in the assembly of MtbFtsZ into protofilaments.
Conformational gating of dimannose binding to the antiviral protein cyanovirin revealed from the crystal structure at 1.35 Å resolution
Authors: Fromme Raimund , Katiliene Zivile , Fromme Petra , Ghirlanda Giovanna 
Published: April 2008

AbstractCyanovirin (CV‐N) is a small lectin with potent HIV neutralization activity, which could be exploited for a mucosal defense against HIV infection. The wild‐type (wt) protein binds with high affinity to mannose‐rich oligosaccharides on the surface of gp120 through two quasi‐symmetric sites, located in domains A and B. We recently reported on a mutant of CV‐N that contained a single functional mannose‐binding site, domain B, showing that multivalent binding to oligomannosides is necessary for antiviral activity. The structure of the complex with dimannose determined at 1.8 Å resolution revealed a different conformation of the binding site than previously observed in the NMR structure of wt CV‐N. Here, we present the 1.35 Å resolution structure of the complex, which traps three different binding conformations of the site and provides experimental support for a locking and gating mechanism in the nanoscale time regime observed by molecular dynamics simulations.
Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis
Authors: Wu Dalei , Hu Tiancen , Zhang Liang , Chen Jing , Du Jiamu , Ding Jianping , Jiang Hualiang , Shen Xu 
Published: April 2008

AbstractAlanine racemase (Alr) is an important enzyme that catalyzes the interconversion of L‐alanine and D‐alanine, an essential building block in the peptidoglycan biosynthesis. For the small size of the Alr active site, its conserved substrate entryway has been proposed as a potential choice for drug design. In this work, we fully analyzed the crystal structures of the native, the D‐cycloserine‐bound, and four mutants (P219A, E221A, E221K, and E221P) of biosynthetic Alr from Escherichia coli (EcAlr) and studied the potential roles in substrate orientation for the key residues involved in the substrate entryway in conjunction with the enzymatic assays. Structurally, it was discovered that EcAlr is similar to the Pseudomonas aeruginosa catabolic Alr in both overall and active site geometries. Mutation of the conserved negatively charged residue aspartate 164 or glutamate 165 at the substrate entryway could obviously reduce the binding affinity of enzyme against the substrate and decrease the turnover numbers in both D‐ to L‐Ala and L‐ to D‐Ala directions, especially when mutated to lysine with the opposite charge. However, mutation of Pro219 or Glu221 had only negligible or a small influence on the enzymatic activity. Together with the enzymatic and structural investigation results, we thus proposed that the negatively charged residues Asp164 and Glu165 around the substrate entryway play an important role in substrate orientation with cooperation of the positively charged Arg280 and Arg300 on the opposite monomer. Our findings are expected to provide some useful structural information for inhibitor design targeting the substrate entryway of Alr.
Influence of methylmalonyl‐CoA mutase alleles on resistance to bovine tuberculosis in the European wild boar (Sus scrofa)
Authors: Naranjo V. , Acevedo‐Whitehouse K. , Vicente J. , Gortazar C. , de la Fuente J. 
Published: April 2008

SummaryAn association study was carried out to examine the influence of methylmalonyl‐CoA mutase (MUT) polymorphisms on the susceptibility of a well‐studied wild boar population from southern Spain to develop bovine tuberculosis (bTB). To this end, we examined polymorphisms at a closely linked dinucleotide microsatellite flanking exon 2 of the MUT gene in 37 wild boars with bTB and 36 non‐infected individuals. The microsatellite showed low polymorphism in the studied population, with only three alleles (MUTm‐A, MUTm‐B and MUTm‐C) found, in contrast to the 11 alleles previously reported for domestic pigs. Our case–control study showed that the MUTm‐B allele was associated with disease in a dominant pattern (odds ratio = 3.36; 95% CI = 1.05–10.72; P = 0.04), while the MUTm AA genotype appeared to have a protective effect against bTB infection (odds ratio = 4.33; 95% CI = 1.20–14.96; P = 0.02). Interestingly, infected wild boars heterozygous for MUTm AB are at an advantage (11‐fold) to contain the systemic spread of the disease when compared to other genotypes, implying that a balanced polymorphism may be present in the population. These results strengthen previous observations regarding the importance of the MUT gene on bTB resistance in wild boars and indicate that polymorphisms at this locus will influence the risk of acquiring and maintaining bTB in the studied population.