bluuebunny/crossref_metadata_2025 huggingface dataset:
Following the dolphins: An ethnographic study of speech and language therapy with people with learning difficulties
Authors: van der Gaag Anna , Davies Philip
Published: November 2007

ABSTRACTS

The purpose of this study was to examine speech and language therapists' practices, and their perceptions of the knowledge and skills that they use in everyday clinical practice. The paper compares the knowledge and skills identified in a much larger consultative study of speech and language therapists' competence with the knowledge and skills identified by four speech and language therapists reflecting on a representative or ‘typical’ day in their working lives. This comparison between the outcome of a large survey and a more detailed ethnographic investigation of speech and language therapists' competence confirmed earlier reports that speech therapy appears to have a broad knowledge and skills base. Ethnographic analysis also revealed that this broad knowledge and skills base was, in the main, highly relevant to everyday clinical practices.

Le but de cette étude est d'examiner les thérapeutes du langage et de la parole dans l'exercice de leur métier, ainsi que la perception qu'ils ont de leur degré de connaissances et de savoir‐faire lors de la pratique clinique quotidienne. Une enquĉte consultative à grande échelle de la compétence des thérapeutes du langage et de la parole avait permis de définir leurs connaissances et leur savoir‐faire; la présente étude compare ces résultats avec la définition de la connaissance et du savoir‐faire qui ressort des réflections de quatre thérapeutes du langage et de la parole sur ce qui représentait une journée ‘typique’ de leur vie de travail. Cette comparaison entre les résultats d'une enquĉte à grande échelle et une analyse ethnographique plus restreinte de la compétence des thérapeutes du langage et de la parole confirme les rapports antérieurs, à savoir que l'orthophonie semble faire appel á une large gamme de connaissances et de savoir‐faire. L'analyse ethnographique révèle aussi que dans l'ensemble cette gamme est tout à fait en rapport avec la pratique clinique de tous les jours.

Ziel dieser Untersuchung war die Durchleuchtung der Therapiegewohnheiten von Sprachtherapeutinnen sowie ihrer eigenen Einschätzung der Kenntnisse und Fähigkeiten, die sie im klinischen Alltag einsetzen. Es werden die Kenntnisse und Fähigkeiten, die in einer viel größeren konsultativen Untersuchung der Kompetenz von Sprachtherapeutinnen identifiziert wurden, mit den Kenntnissen und Fähigkeiten verglichen, die vier Sprachtherapeutinnen identifizierten, denen die Aufgabe gegeben wurde, über einen ‘typischen Arbeitstag’ nachzudenken. Der Vergleich zwischen den Ergebnissen der großen Umfrage und dieser detaillierten ethnographischen Untersuchung bestätigte den früheren Befund, daß Sprach‐ und Sprechtherapie auf einem breiten Wissens‐ und Fähigkeitsfundament basiert. Die ethnographische Analyse zeigte außerdem, daß die breite Basis im großen und ganzen für den klinischen Alltag sehr relevant ist.
What makes a therapy? Some parameters of therapeutic intervention in aphasia
Authors: Byng Sally , Black Maria
Published: November 2007

ABSTRACTS

It has often been assumed that detailed analyses of aphasic impairments would be both necessary and sufficient for the development of remediation programmes. In this paper, we argue that the analysis of the impairment is a necessary but not sufficient precondition for therapy. Adequate remediation programmes require the development of an independent theory of therapy that provides a detailed specification of the different components of the therapeutic process. Therapy can be shown to have as many interacting components as the impairment itself. In this paper, we try to identify some of the components of the therapy process by comparing different therapy programmes that have been employed in the remediation of ‘mapping deficits' in agrammatism.

Il a souvent été supposé qu'il était nécessaire et suffisant de faire des analyses en détail des troubles acquis aphasiques pour mettre au point des programmes thérapeutiques. Nous soutenons dans cet article que l'analyse du trouble acquis est une condition nécessaire, mais non suffisante. Les programmes correctifs dignes de ce nom nécessitent la mise au point d'une théorie de la thérapie qui soit indépendante et qui puisse fournir des spécifications détaillées des différents composants du procédé thérapeutique. La thérapie se révèle avoir autant de composants agissant les uns sur les autres que le trouble acquis lui même. Nous essayons dans cet article d'identifier certains composants du procédé thérapeutique en comparant les différents programmes thérapeutiques qui ont été employés pour remédier aux ‘déficits de stratégie’ de l'agrammatisme.

Es is oft angenommen wird, daß die detaillierte Analyse aphasischer Behinderungen sowohl notwendig als auch ausreichend für die Entwicklung von remedialen Programmen sei. Hier wird argumentiert, daß eine solche Analyse zwar eine notwendige jedoch keine ausreichende Voraussetzung für die Therapie sei. Effektive Behandlungsprogramme bedürfen der Entwicklung einer unabhängigen Theorie der Therapie, die eine detaillierte Spezifikation der unterschiedlichen Komponenten des therapeutischen Prozesses einschließt. Es kann gezeigt werden, daß eine Therapie so viele miteinander verzahnte Komponenten wie die Behinderung selbst hat. Wir versuchen, einige Komponenten des Therapieprozesses zu identifizieren, indem wir verschiedene Therapieprogramme vergleichen, die zur Behandlung von Projektionsdefiziten (‘mapping deficits') bei Agrammatismus eingesetzt worden sind.
Lexical‐semantic deficits following right hemisphere damage: evidence from verbal fluency tasks
Authors: Varley Rosemary
Published: November 2007

ABSTRACTS

The evidence of lexical‐semantic deficits following right, non‐language‐dominant hemisphere injury was assessed using word (or verbal) fluency tests. Two groups of subjects (non‐brain‐damaged controls and right hemisphere‐damaged patients) were indistinguishable in their performances on convergent lexical tasks. Subjects completed verbal fluency tasks by five semantic criteria. The brain‐damaged subjects produced significantly fewer responses on two of the categories and demonstrated fewer lexical retrieval strategies. The results were interpreted as evidence that lexical‐semantic knowledge is largely intact following right‐hemisphere damage, and that apparent lexical deficits result from failure to use lexical knowledge flexibly, suggesting that right‐hemisphere language disorders may stem from broader cognitive failures.

Partant de l'idée que certaines lésions de l'hémisphère droit, non dominant du point de vue linguistique, occasionnent des déficits lexico‐sémantiques, l'on a utilisé ici des tests de degré de fluidité d'utilisation de mots (ou fluidité verbale). Deux groupes de sujets (des sujets de contrôle sans lésion du cerveau, et des patients dont l'hémisphère droit était atteint) ont eu un comportement identique lors de tests lexicaux convergeants. On leur a fait subir des tests de fluidité verbale en fonction de cinq critères sémantiques. Ceux dont le cerveau était atteint ont fourni des réponses significativement moins nombreuses dans deux catégories et ont utilisé moins de stratégies pour trouver les mots. L'interprétation des résultats donne à penser que la connaissance lexico‐sémantique reste dans une grande mesure intacte après une lésion de l'hémisphère droit, et que les déficits lexicaux qu'on aperçoit résultent d'une incapacité à utiliser la connaissance lexicale avec suffisamment de flexibilité, ce qui suggère que les troubles du langage relatifs à l'hémisphère droit proviennent d'insuffisances cognitives plus vastes.

Indizien lexiko‐semantischer Mängel in der Folge von Hirnschäden auf der nichtsprachlich‐dominanten Seite wurden mit Wortgewandtheitstests bewertet. Zwei Gruppen (eine Kontrollgruppe ohne Hirnschäden und Patienten mit Schäden der rechten Hirnhälfte) waren in ihrer Leistung bei konvergenten lexikalischen Aufgaben nicht zu unterscheiden. Die Versuchspersonen (Vpn.) führten Wortgewandtheitsaufgaben nach fünf semantischen Kriterien durch. Die hirngeschädigten Vpn. gaben signifikant weniger Antworten bei zwei der Kategorien und zeigten weniger Wortfind‐ungsstrategien. Die Ergebnisse wurden als Zeichen dafür interpretiert, daß lexikalisch‐semantisches Wissen nach Schädigung der rechten Hirnhälfte weitgehend erhalten bleibt und das scheinbare lexikalische Mängel aus der inflexiblen Benutzung lexikalischen Wissens resultiert. Hieraus kann abgeleitet werden, daß Sprachmängel bei Schäden an der rechten Hirnhälfte möglicherweise von breiter angelegten kognitiven Mängeln herrühren.
AAC systems*: obstacles to effective use
Authors: Murphy Joan , Marková Ivana , Collins Sarah , Moodie Eleanor
Published: November 2007

ABSTRACTS

This paper investigates some of the issues which contribute to the lack of use of Augmentative and Alternative Communication (AAC) systems. It presents findings from a two‐year research study which examined the communication of 93 adolescent and adult AAC users with cerebral palsy and 186 of their communication partners. The methods of data collection were questionnaires, interviews and field notes. The results show that some of the obstacles to effective use of AAC systems include lack of availability and accessibility of AAC systems, communication partners' lack of knowledge of AAC systems, insufficient amount of therapy provided, type of vocabulary in AAC systems and gther modes of communication available to AAC user.

Cet article examine certains problèmes qui contribuent au manque d'utilisation des systèmes de Communication Augmentative et Alternative (abréviation anglaise: AAC). Il présente les résultats de deux ans de recherches sur l'usage de l'AAC par 93 adolescents et adultes souffrant de paralysie cérébrale et par 186 de leurs partenaires en communication. La collecte des données s'est faite au moyen de questionnaires, les interviews et notes prises sur le terrain. Les résultats montrent que parmi les obstacles à un usage effectif des systèmes d'AAC on peut citer leur manque de disponibilité et d'accessibilité le manque de connaissance de l'AAC de la part des partenaires en communication, l'insuffisance de la thérapie, le type de vocabulaire des systèmes AAC et la présence d'autres modes de communication à la disposition de l'usager.

In diesem Aufsatz werden einige Punkte erörtert, die zu mangelnden Einsatz unterstützender und alternativen Kommunikationssysteme (AAC = augmentative and alternative communication systems) beitragen. Es werden Ergebnisse aus einer zwei jährigen Studie präsentiert, die das Kommunikationsverhalter von 93 pubertären und erwachsenen AAC‐Benutzern mit spasticher Motorstörungen und 186 ihrer Kommunikationspartner untersuchte. Die Datenerhebungsmethoden bestanden aus Fragebögen, Gesprächer und Feldnotizen. Die Ergebnisse zeigen, daß Hindernisse gegen der effektiven Einsatz von AAC‐Systemen unter anderem darin bestehen, daß sie schwer erhältlich und schwer zugänglich sind, daß die Kommunikationspartner wenig darüber wissen, daß zu wenig Therapie geboten wird. Probleme entstehen auch durch das Vokabular, das in AAC‐Systemen und anderen Kommunikationsmodi verwendet werden, die dem AAC‐Benutzer zur Verfügung stehen.
Using a quantitative measure of communicative environment to compare two psychogeriatric day care settings
Authors: Armstrong Linda , Woodgates Sarah
Published: November 2007

ABSTRACTS

The importance of the relationship between the physical and interpersonal environment and the maintenance and enhancement of communication in the ageing institutionalised population is well‐documented in the literature. This study aimed to evaluate the communicative environment in two different day care settings for people with dementia by the recording and structuring of observations made of sampled conversations. The data collected were considered quantitatively in order to compare the two settings. The findings of the study can be applied to clinical and everyday practice, through the suggestion of practical ideas for physical and/or social environmental modification.

L'on dispose d'une documentation abondante sur l'importance de la relation entre les environ‐nements physique et interpersonnel d'une part, et le maintien et L'amélioration de la communication chez les vieillards vivant dans des établissements d'autre part. Le but de cette étude est d'évaluer l'environnement communicatif dans deux situations de soins de jour pour des vieillards souffrant de démence sénile. L'on a procédé à l'enregistrement d'un échantillonnage de conversations et à la structuration des observations recueillies sur ces conversations. Une étude quantitative a permis de comparer les deux situations. Les résultats peuvent servir à la pratique de soins en clin‐ique et de jour, grâce à la suggestion d'idés pratiques pour modifier l'environnement physique et/ou social.

Die Bedeutung der Beziehung zwischen der physischen und zwischenmenschlichen Ungebung und der Erhaltung und Verbesserung der Kommunikation unter alternden Menschen in Heimen ist in der Literatur gut dokummentiert. Der Ziel dieser Studie war, die Kommunikationsungebung von Menschen mit Altersdementia in zwei verschiedenen Tagespflegestätten durch die Registrierung und Struktursierung der Gesprächen gemachten Beobachtungen. Die gesammelten Daten wurden zum Vergleich der zwei Umgebungen quantitiv analysiert. Praktische Vorschläge für die Veränderung der physischen und/ober der sozialen Umgebung ermöglichen die Ubertragung der Ergebnisse auf die klinische und alltägliche Betreungspraxis.
Acquisition of speech, pre‐ and post‐cochlear implantation: longitudinal studies of a congenitally deaf infant
Authors: Robinshaw Helen M.
Published: November 2007

ABSTRACTS

This paper details the process of speech acquisition by the first British, congenitally deaf infant (without additional handicaps) to be fitted with a multi‐channel cochlear implant. The infant's phonologic and phonetic level development using, firstly, acoustic hearing aids and, secondly, a cochlear implant, is thoroughly detailed by use of video‐ and audio‐recorded data, taken at weekly intervals and across a variety of contexts. The paper examines the benefit of early implantation for spoken language development and notes the utility of Ling's model of speech acquisition for the habilitation of young, congenitally deaf implant recipients.

L’ article décrit en détail le processus d'acquisition du langage par le premier enfant britannique sourd congénital qui a reçu un implant cochléaire à canaux multiples. L'enfant ne souffrait d'aucun handicap supplémentaire. Des enregistrements sonores et sur vidéos faits chaque semaine et recouvrant tout un ensemble de contextes ont permis de décrire point par point son développement phonétique et phonologique, au début grâce à des appareils acoustiques et ensuite grâce à l'implant cochléaire. L'article analyse l'avantage qu'il y a à procéder très tòt à des implants pour assurer le développement de la parole, et il examine l'utilité du modele de Ling de l'acquisition du langage pour l'habilitation de jeunes sourds congénitaux qui reçoivent des implants.

Dieser Aufsatz beschreibt den Spracherwerbsprozeß des ersten britischen, gehörlos geborenen Kindes (ohne weitere Behinderungen), das ein mehrkanaliges Cochlearimplantat belommen hat. Die phonetische und phonologische Entwicklung des Kindes, zunächst mit akustischen Hörgeräten, dann mit Cochlearimplantat, wird anhand von Video‐ und Audioaufzeichnungen, die in Abständen von einer Woche in einer Vielzahl underschiedlicher Kontexte gemacht wurden, eingehend dargelegt. Die Vorteile früher Implantation für die Sprechentwicklung und der Nutzen von Lings Spracherwerbsmodell für die Habilitation junger kongenital gehörloser Implantatsempfänger werden erörtert.
Use of the Arizona Battery for Communication Disorders of Dementia in the UK
Authors: Armstrong Linda , Borthwick Sheena E. , Bayles Kathryn A. , Tomoeda Cheryl K.
Published: November 2007

ABSTRACTS

The Arizona Battery for Communication Disorders of Dementia (ABCD) (Bayles & Tomoeda, 1993) was given to groups of young and old normal subjects and to subjects with moderate Alzheimer's disease in the UK. Very few significant differences were found between their raw scores and those of the original standardisation sample in the USA, which makes the ABCD an appropriate test to use in the UK. Although some subjects commented on several of the test stimuli, cultural differences in pictures and vocabulary did not produce notable effects on test performance and so alterations to test materials are not required for the test to be used in the UK.

La Batterie de Tests de l'Arizona pour les Troubles de le Communication (sigle anglais: ABCD) (Bayles & Tomoeda, 1993) a été administrée en Grande‐Bretagne à des sujets normaux jeunes et vieux, ainsi qu'à des sujets atteints modérément de la Maladie d'Alzheimer. L'on a trouvé très peu de différences significatives entre leurs niveaux bruts de performances et ceux de l'échantillon de standardisation originel provenant des Etats‐Unis, ce qui démontre que l'ABCD peut très bien s'utiliser en Grande‐Bretagne. Meme si certains sujets ont fait des réflexions sur quelques stimuli du test, les différences culturelles concernant les images et le vocabulaire n'ont pas produit d'effets notables sur les résultats, de sorte que l'on n'a pas besoin de modifier les matériaux du test pour l'utiliser en Grande‐Bretagne.

The Arizona Battery for Communication Disorders of Dementia (ABCD) wurde in Großbritannien bei Gruppen von jungen und alten Normalpersonen und bei Personen mit mittelschwerer Alzheimererkrankung angewandt. Sehr wenige signifikante Unterschiede wurden zwischen diesen Rohdaten und denen der ursprünglichen Standardisierungsstichproben in den USA gefunden. Dieses Ergebnis bestätigt, daß die ABCD ein für Großbritannien geeigneter Test ist. Während einige Personen Bemerkungen über mehrere Teststimuli machten, hatten kulturelle Unterschiede in den‐Bildern und im Wortschatz keine bemerkenswerten Folgen für die Testleistung. Deshalb sind Veränderungen der Testmaterialien für den Einsatz in Großbritannien nicht erforderlich.
Singers' and non‐singers' vocal health, vocal behaviours, and attitudes towards voice and singing: indirect findings from a questionnaire
Authors: Sapir Shimon , Mathers‐Schmidt Barbara , Larson George W.
Published: November 2007

ABSTRACTS

A vocal health questionnaire was administered in three locations in the USA to female university singers and non‐singers. The responses of 70 singers and 89 non‐singers were analysed. The questionnaire solicited background information as well as information about vocal health and symptoms, vocally abusive speech habits, attitudes toward singing and vocal health, feelings about the voice, and general affective/dysphoric tendencies. There were marked, sometimes diametric, differences between singers' and non‐singers' responses, attesting to the unique attitude and heightened sensivity and concern of singers regarding voice, singing and vocal health.

Un questionnaire sur l'état de leur Système vocal a été administré dans trois sites universitaires américains à des femmes universitaires, dont certaines chantaient et d'autres ne chantaient pas. L'on a analysé les réponses de 70 des premières et 89 des secondes. Les questions portaient sur leurs antécédents, et également sur l'état de leur voix, leurs symptômes vocaux, leurs habitudes néfastes pour leur voix, leurs attitudes envers le chant et la santé vocale, leurs sentiments à propos de la voix, et leurs tendances générates affectives/dysphoriques. Des différences marquées, parfois diamétralement opposées sont apparues entre les réponses de celles qui chantaient et celles qui ne chantaient pas, ce qui atteste de l'attitude particulière des premières, et de leur sensibilité accrue envers la voix, le chant et l'état de leurs cordes vocales.

Ein Fragebogen zur Stimmhygiene wurde an drei Orten in den USA einerseits an Gesangsstudentinnen und andererseits an Studentinnen anderer Fächer verteilt. Der Fragebogen zielte auf Basisinformation und auf Information zur Stimmgesundheit und Symptome, zu stimmschädigenden Sprechgewohnheiten, zur Haltung gegenüber dem Singen und der Stimmgesundheit, zu Gefühlen über die Stimme und zu allgemeinen affektiven/dysphärischen Tendenzen. Es zeigten sich klare, manchmal diametrale Gegensätze zwischen den Antworten der Sängerinnen und der Nicht‐Sängerinnen, die von der einzigartigen Haltung und der erhöten Sensitivität und Sorge von Sängerinnen bezüglich der Stimme, des Singens und der Stimmgesundheit zeugen.
Chronic pulmonary thromboembolism in a patient with a fontan circulation: Percutaneous management
Authors: Dehghani Payam , Collins Nicholas , Horlick Eric , Benson Lee
Published: November 2007

Chronic pulmonary embolism is a common complication in patients with Fontan circulations. When anticoagulation is ineffective and surgery is contraindicated, percutaneous techniques may be considered. The authors report the first case of successful catheter intervention in a 30‐year‐old woman with a Fontan circulation who presented with NYHA class IV symptoms and chronic and complete obstruction of her left pulmonary artery. © 2007 Wiley‐Liss, Inc.
Preparation of combined extract of cell wall and cytosol antigens of Candida albicans for immunoblot analysis
Authors: Dojnov Biljana , Božić Nataša , Bulajić Nina , Vujčić Zoran
Published: November 2007

Immunoblot analysis is not in wide use for diagnosis of invasive candidiasis, mostly because the procedure is not standardized and hence not reliable. This work describes a standardized method for C. albicans antigen extract preparation and immunochemical detection. The major improvement of the method is the preparation of combined antigen extract—consisting of the cell wall and cytosol antigens. The fungal cells and lysis buffer were mixed at a 1:3 ratio and disintegrated by ultrasound for six cycles of one minute each. After centrifugation, cytosol antigens were obtained in the supernatant and cell wall antigens were in the precipitate. Precipitate was dissolved in lysis buffer with 2% sodium dodecyl sulfate (SDS) and boiled at 100°C for 2 min. After centrifugation, the supernatant was combined with the previous one, so the extract of the combined antigens was obtained in the mixture. With those combined antigen extracts and with sera of three different groups of patients, immunoblot analysis showed sensitivity of 90.2%, specificity of 84.4%, and accuracy of 88.0%. J. Clin. Lab. Anal. 21:406–412, 2007. © 2007 Wiley‐Liss, Inc.
Flexibility in the ABC transporter MsbA: Alternating access with a twist
Authors: Ward Andrew , Reyes Christopher L. , Yu Jodie , Roth Christopher B. , Chang Geoffrey
Published: November 2007

ATP-binding cassette (ABC) transporters are integral membrane proteins that translocate a wide variety of substrates across cellular membranes and are conserved from bacteria to humans. Here we compare four x-ray structures of the bacterial ABC lipid flippase, MsbA, trapped in different conformations, two nucleotide-bound structures and two in the absence of nucleotide. Comparison of the nucleotide-free conformations of MsbA reveals a flexible hinge formed by extracellular loops 2 and 3. This hinge allows the nucleotide-binding domains to disassociate while the ATP-binding half sites remain facing each other. The binding of the nucleotide causes a packing rearrangement of the transmembrane helices and changes the accessibility of the transporter from cytoplasmic (inward) facing to extracellular (outward) facing. The inward and outward openings are mediated by two different sets of transmembrane helix interactions. Altogether, the conformational changes between these structures suggest that large ranges of motion may be required for substrate transport.
Breaking the diffraction barrier outside of the optical near-field with bright, collimated light from nanometric apertures
Authors: Stark Peter R. H. , Halleck Allison E. , Larson Dale N.
Published: November 2007

The optical diffraction limit has been the dominant barrier to achieving higher optical resolution in the fields of microscopy, photolithography, and optical data storage. We present here an approach toward imaging below the diffraction barrier. Through the exposure of photosensitive films placed a finite and known distance away from nanoscale, zero-mode apertures in thin metallic films, we show convincing, physical evidence that the propagating component of light emerging from these apertures shows a very strong degree of collimation well past the maximum extent of the near-field (λ
0
/4n–λ
0
/2n). Up to at least 2.5 wavelengths away from the apertures, the transmitted light exhibits subdiffraction limit irradiance patterns. These unexpected results are not explained by standard diffraction theory or nanohole-based “beaming” rationalizations. This method overcomes the diffraction barrier and makes super-resolution fluorescence imaging practical.
Short Article: Emotional and Neutral Scenes in Competition: Orienting, Efficiency, and Identification
Authors: Calvo Manuel G. , Nummenmaa Lauri , Hyönä Jukka
Published: November 2007

To investigate preferential processing of emotional scenes competing for limited attentional resources with neutral scenes, prime pictures were presented briefly (450 ms), peripherally (5.2° away from fixation), and simultaneously (one emotional and one neutral scene) versus singly. Primes were followed by a mask and a probe for recognition. Hit rate was higher for emotional than for neutral scenes in the dual- but not in the single-prime condition, and A′ sensitivity decreased for neutral but not for emotional scenes in the dual-prime condition. This preferential processing involved both selective orienting and efficient encoding, as revealed, respectively, by a higher probability of first fixation on—and shorter saccade latencies to—emotional scenes and by shorter fixation time needed to accurately identify emotional scenes, in comparison with neutral scenes.
Short Article: Spatial Exploration Patterns Determine Navigation Efficiency: Trade-off between Memory Demands and Distance Travelled
Authors: Makany Tamas , Redhead Edward S. , Dror Itiel E.
Published: November 2007

A total of 41 participants explored a novel square-shaped environment containing five identical boxes each hiding a visually distinct object. After an initial free exploration the participants were required to locate the objects first in a predetermined and subsequently in an optional order task. Two distinct exploration strategies emerged: Participants explored either along the main axes of the room (axial), or in a more spatially spread, circular pattern around the edges of the room (circular). These initial exploration strategies influenced the optimality of spatial navigation performance in the subsequent optional order task. The results reflect a trade-off between memory demands and distance efficiency. The more sequential axial strategy resulted in fewer demands on spatial memory but required more distance to be travelled. The circular strategy was more demanding on memory but required less subsequent travelling distance. The findings are discussed in terms of spatial knowledge acquisition and optimality of strategy representations.
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
Authors: Ye Kai , Anton Feenstra K. , Heringa Jaap , IJzerman Adriaan P. , Marchiori Elena
Published: November 2007

Motivation: Identification of residues that account for protein function specificity is crucial, not only for understanding the nature of functional specificity, but also for protein engineering experiments aimed at switching the specificity of an enzyme, regulator or transporter. Available algorithms generally use multiple sequence alignments to identify residue positions conserved within subfamilies but divergent in between. However, many biological examples show a much subtler picture than simple intra-group conservation versus inter-group divergence.

Results: We present multi-RELIEF, a novel approach for identifying specificity residues that is based on RELIEF, a state-of-the-art Machine-Learning technique for feature weighting. It estimates the expected ‘local’ functional specificity of residues from an alignment divided in multiple classes. Optionally, 3D structure information is exploited by increasing the weight of residues that have high-weight neighbors. Using ROC curves over a large body of experimental reference data, we show that (a) multi-RELIEF identifies specificity residues for the seven test sets used, (b) incorporating structural information improves prediction for specificity of interaction with small molecules and (c) comparison of multi-RELIEF with four other state-of-the-art algorithms indicates its robustness and best overall performance.

Availability: A web-server implementation of multi-RELIEF is available at www.ibi.vu.nl/programs/multirelief. Matlab source code of the algorithm and data sets are available on request for academic use.

Contact:  elena@few.vu.nl

Supplementary information: Supplemenmtary data are available at Bioinformatics online
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment
Authors: Deforche K. , Camacho R. , Van Laethem K. , Lemey P. , Rambaut A. , Moreau Y. , Vandamme A.-M.
Published: November 2007

Motivation: HIV-1 antiviral resistance is a major cause of antiviral treatment failure. The in vivo fitness landscape experienced by the virus in presence of treatment could in principle be used to determine both the susceptibility of the virus to the treatment and the genetic barrier to resistance. We propose a method to estimate this fitness landscape from cross-sectional clinical genetic sequence data of different subtypes, by reverse engineering the required selective pressure for HIV-1 sequences obtained from treatment naive patients, to evolve towards sequences obtained from treated patients. The method was evaluated for recovering 10 random fictive selective pressures in simulation experiments, and for modeling the selective pressure under treatment with the protease inhibitor nelfinavir.

Results: The estimated fitness function under nelfinavir treatment considered fitness contributions of 114 mutations at 48 sites. Estimated fitness correlated significantly with the in vitro resistance phenotype in 519 matched genotype-phenotype pairs (R2 = 0.47 (0.41 − 0.54)) and variation in predicted evolution under nelfinavir selective pressure correlated significantly with observed in vivo evolution during nelfinavir treatment for 39 mutations (with FDR = 0.05).

Availability: The software is available on request from the authors, and data sets are available from http://jose.med.kuleuven.be/∼kdforc0/nfv-fitness-data/.

Contact:  annemie.vandamme@uz.kuleuven.be

Supplementary information: Supplementary data are available at Bioinformatics online.
Computational epigenetics
Authors: Bock Christoph , Lengauer Thomas
Published: November 2007

Epigenetic research aims to understand heritable gene regulation that is not directly encoded in the DNA sequence. Epigenetic mechanisms such as DNA methylation and histone modifications modulate the packaging of the DNA in the nucleus and thereby influence gene expression. Patterns of epigenetic information are faithfully propagated over multiple cell divisions, which makes epigenetic regulation a key mechanism for cellular differentiation and cell fate decisions. In addition, incomplete erasure of epigenetic information can lead to complex patterns of non-Mendelian inheritance. Stochastic and environment-induced epigenetic defects are known to play a major role in cancer and ageing, and they may also contribute to mental disorders and autoimmune diseases. Recent technical advances such as ChIP-on-chip and ChIP-seq have started to convert epigenetic research into a high-throughput endeavor, to which bioinformatics is expected to make significant contributions. Here, we review pioneering computational studies that have contributed to epigenetic research. In addition, we give a brief introduction into epigenetics—targeted at bioinformaticians who are new to the field—and we outline future challenges in computational epigenetics.

Contact:  cbock@mpi-inf.mpg.de
KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours
Authors: Draghici Sorin , Tarca Adi L. , Yu Longfei , Ethier Stephen , Romero Roberto
Published: November 2007

Motivation: The BioArray Software Environment (BASE) is a very popular MIAME-compliant, web-based microarray data repository. However in BASE, like in most other microarray data repositories, the experiment annotation and raw data uploading can be very timeconsuming, especially for large microarray experiments.

Results: We developed KUTE (Karmanos Universal daTabase for microarray Experiments), as a plug-in for BASE 2.0 that addresses these issues. KUTE provides an automatic experiment annotation feature and a completely redesigned data work-flow that dramatically reduce the human–computer interaction time. For instance, in BASE 2.0 a typical Affymetrix experiment involving 100 arrays required 4 h 30 min of user interaction time forexperiment annotation, and 45 min for data upload/download. In contrast, for the same experiment, KUTE required only 28 min of user interaction time for experiment annotation, and 3.3 min for data upload/download.

Availability:  http://vortex.cs.wayne.edu/kute/index.html

Contact:  sod@cs.wayne.edu
Detection of L1, infectious virions and anti-L1 antibody in domestic rabbits infected with cottontail rabbit papillomavirus
Authors: Hu Jiafen , Budgeon Lynn R. , Cladel Nancy M. , Culp Timothy D. , Balogh Karla K. , Christensen Neil D.
Published: November 2007

Shope papillomavirus or cottontail rabbit papillomavirus (CRPV) is one of the first small DNA tumour viruses to be characterized. Although the natural host for CRPV is the cottontail rabbit (Sylvilagus floridanus), CRPV can infect domestic laboratory rabbits (Oryctolagus cuniculus) and induce tumour outgrowth and cancer development. In previous studies, investigators attempted to passage CRPV in domestic rabbits, but achieved very limited success, leading to the suggestion that CRPV infection in domestic rabbits was abortive. The persistence of specific anti-L1 antibody in sera from rabbits infected with either virus or viral DNA led us to revisit the questions as to whether L1 and infectious CRPV can be produced in domestic rabbit tissues. We detected various levels of L1 protein in most papillomas from CRPV-infected rabbits using recently developed monoclonal antibodies. Sensitive in vitro infectivity assays additionally confirmed that extracts from these papillomas were infectious. These studies demonstrated that the CRPV/New Zealand White rabbit model could be used as an in vivo model to study natural virus infection and viral life cycle of CRPV and not be limited to studies on abortive infections.
Time-course studies of 14-3-3 protein isoforms in cerebrospinal fluid and brain of primates after oral or intracerebral infection with bovine spongiform encephalopathy agent
Authors: Yutzy Barbara , Holznagel Edgar , Coulibaly Cheick , Stuke Andreas , Hahmann Uwe , Deslys Jean-Philippe , Hunsmann Gerhard , Löwer Johannes
Published: November 2007

Experimental transmission of bovine spongiform encephalopathy (BSE) to cynomolgus monkeys (Macaca fascicularis) is an animal model for variant Creutzfeldt–Jakob disease (vCJD). The presence of 14-3-3 proteins in cerebrospinal fluid (CSF) samples indicates neuronal destruction and is therefore used as a clinical biomarker. However, time-course studies using 14-3-3 proteins have not been performed until now in simian vCJD. The main goals of this study were to determine isoform patterns, to examine kinetics and to correlate the clinical course with the occurrence of this biomarker in simian vCJD. In monkeys dosed intracerebrally with BSE, the earliest clinical sign of illness was a drop in body weight that was detected months before the onset of mild neurological signs. Macaques dosed orally or intracerebrally with BSE developed neurological signs 4.3 (3.7–4.6) and 4.8 (2.9–6.0) years post-infection, respectively. 14-3-3β- and -γ-positive CSF samples were found around the time of onset of mild neurological signs, but not earlier. In contrast, 14-3-3ϵ and -ηisoforms were not detectable. 14-3-3 levels increased with time and were positively correlated with the degree of neurological symptoms. Post-mortem examination of brain samples revealed a positive correlation between PrPresand 14-3-3ϵ levels. Interestingly, florid plaques characteristic of human vCJD could not be detected in diseased monkeys. It was concluded that analysis of 14-3-3 proteins in CSF is a reliable tool to characterize the time course of brain degeneration in simian vCJD. However, there are differences in the clinical course between orally and intracerebrally infected animals that may influence the detection of other biomarkers.
Baculovirus envelope fusion proteins F and GP64 exploit distinct receptors to gain entry into cultured insect cells
Authors: Westenberg Marcel , Uijtdewilligen Peter , Vlak Just M.
Published: November 2007

Group II nucleopolyhedroviruses (NPVs), e.g. Helicoverpa armigera (Hear) NPV and Spodoptera exigua (Se) MNPV (multiple NPV), lack a GP64-like protein that is present in group I NPVs, e.g. Autographa californica (Ac)MNPV, but have an unrelated envelope fusion protein named F. Three AcMNPV viruses were constructed by introducing AcMNPV gp64, HearNPV f or SeMNPV f genes, respectively, into a gp64-negative AcMNPV bacmid. Sf21 cells were incubated with different amounts of inactivated budded virus to occupy receptors and were subsequently infected with a fixed amount of infectious virus to compete for attachment. The results suggest that GP64 and F act on their own and use different receptors, while the two different F proteins exploit the same receptor. Additionally, gp64-null AcMNPV pseudotyped with baculovirus F was, in contrast to GP64, unable to transduce mammalian cells, indicating that mammalian cells do not possess baculovirus F protein receptors despite the structural similarity of baculovirus F to vertebrate viral fusion proteins.
Recurrent Deletions of Puroindoline Genes at the GrainHardnessLocus in Four Independent Lineages of Polyploid Wheat
Authors: Li Wanlong , Huang Li , Gill Bikram S.
Published: November 2007

Polyploidy is known to induce numerous genetic and epigenetic changes but little is known about their physiological bases. In wheat, grain texture is mainly determined by the Hardness (Ha) locus consisting of genes Puroindoline a (Pina) and b (Pinb). These genes are conserved in diploid progenitors but were deleted from the A and B genomes of tetraploid Triticum turgidum (AB). We now report the recurrent deletions of Pina-Pinb in other lineages of polyploid wheat. We analyzed the Ha haplotype structure in 90 diploid and 300 polyploid accessions of Triticum and Aegilops spp. Pin genes were conserved in all diploid species and deletion haplotypes were detected in all polyploid Triticum and most of the polyploid Aegilops spp. Two Pina-Pinb deletion haplotypes were found in hexaploid wheat (Triticum aestivum; ABD). Pina and Pinb were eliminated from the G genome, but maintained in the A genome of tetraploid Triticum timopheevii (AG). Subsequently, Pina and Pinb were deleted from the A genome but retained in the Am genome of hexaploid Triticum zhukovskyi (AmAG). Comparison of deletion breakpoints demonstrated that the Pina-Pinb deletion occurred independently and recurrently in the four polyploid wheat species. The implications of Pina-Pinb deletions for polyploid-driven evolution of gene and genome and its possible physiological significance are discussed.
Defects and rework in new build: an analysis of the phenomenon and drivers
Authors: Sommerville James
Published: November 2007

Purpose

The purpose of this paper is to look at the continued media attention surrounding defects, and the resulting “rework”, in new build projects, especially homes.

Design/methodology/approach

This paper evaluates the literature on defects and rework in new build projects, with an emphasis on housing, and identifies a number of issues within the underlying research agenda.

Findings

Suggestions are put forward as to how predictor models may be focused to drive impetus for the development of a greater number of analytical tools which industry participants can use to characterize, model, evaluate and inform, decisions about defects and rework.

Research limitations/implications

The house‐building segment of the construction industry is important since it is clearly outward facing and monitored by a range of interested stakeholders. The findings of this study will hopefully provide impetus to the search for alternative approaches to be taken to the elimination or reduction in new house defects.

Originality/value

There is a lack of information on defects and rework management models that the industry may utilize when considering how to minimize the occurrence and impact of defects and rework on future developments. As such, there is a need for a model(s) and approach(es) which help to eliminate or mitigate the underlying characteristics of defects and rework. In particular, there is relatively little research on defects and rework that focuses specifically on measurement and modelling and reduction in new housing.
Understanding Gandhian dialectics
Authors: Ghosh B.N.
Published: November 2007

Purpose

The aim of the present paper is to deal with a conceptual category. The basic purpose of this paper is to lay bare the meaning and implications of Gandhian dialectics.

Design/methodology/approach

The analysis of the paper is somewhat abstract and depends on the metaphysical approach that deals with philosophical issues.

Findings

Gandhian dialectics can be interpreted in at least six different senses, and in many ways, is found to be well comparable with many aspects of dialectics that are used in the contemporary Marxist political economy.

Originality/value

Never before the concept of Gandhian dialectics has been elaborated by any researcher. Gandhian political economy applies implicitly the dialectical method in the analysis of social interactions and change.
Political correctness and the economics of higher education
Authors: Block Walter , Dauterive Jerry
Published: November 2007

Purpose

It is the contention of this paper that the state of siege on the part of students against academics and administrators of the 1960s has been replaced by one led by university administrators who are now waging a war of “political correctness” against students and faculty. These administrators were in large part the radicals of the 1960s. The present paper attempts to analyze the effects of government involvement in this industry on this phenomenon and the role of free speech rights in the presence and absence of marketplace considerations.

Design/methodology/approach

Discusses political correctness and the economics of higher education.

Findings

The contention is that competition brings about a better product at a lower price, and that the educational sector is no exception to this general rule. If free enterprise were allowed to operate in this context, much of these difficulties would disappear.

Originality/value

The paper offers insights into today's higher education industry and how economic analysis can explain the current “state of siege” on university campuses.
Navigating trans‐atlantic deals: warranties, disclosure and material adverse change
Authors: Phillips John , Runnicles Julian , Schwartz Jeffery
Published: November 2007

Purpose

The purpose of this paper is to explore certain remaining differences in the underlying legal considerations and the differing customs and practices of US and UK mergers and acquisitions in relation to certain issues.

Design/methodology/approach

A review was undertaken of the leading cases in the UK and various states of the USA and custom and practice in the UK and USA, in each case in relation to the following areas: representations and warranties; disclosure; the effect of the buyer's knowledge; repetition of warranties/representations; and material adverse change.

Findings

Although the historical differences between UK and US mergers and acquisitions are diminishing as the frequency of trans‐atlantic transactions increases, there remain certain variances which have important implications for the allocation of risk between a buyer and seller in any trans‐atlantic merger or acquisition.

Originality/value

This paper is useful for professional advisers acting in connection with a trans‐atlantic merger or acquisition and for buyers and sellers contemplating such transactions.
Financial Ombudsman's statutory powers
Authors: Gray Joanna
Published: November 2007

Purpose

This paper aims to report and comment on a successful High Court challenge by financial advisory firms via the financial Ombudsman.

Design/methodology/approach

The paper's approach is to outline the facts and explain the decision.

Findings

Although the industry will welcome this decision, the FSA and the Ombudsman may not and the comments made by Mr Justice Lewison recognise what may be an eternal tension between “regulatory” redress schemes in the financial services industry and the courts and the common law.

Originality/value

The paper provides a useful commentary on a decision that has some considerable significance to the financial services industry.
Public communication about home burglary prevention in Belgium
Authors: Gelders Dave , Peeraer Hans , Goossens Jelle
Published: November 2007

Purpose

The purpose of this paper is to gain insight into the content, format and evaluation of printed public communication from police officers and governments regarding home burglary prevention in Belgium.

Design/methodology/approach

The content and format in this paper is analyzed through content analysis of 104 printed communication pieces in the Belgian province of Flemish‐Brabant in 2005. The evaluation is analyzed through five focus group interviews among professionals and common citizens.

Findings

The paper finds that police zones significantly differ in terms of communication efforts. The media mix is not diverse with poor collaboration between police officers and government information officers, while intermediaries (i.e. architects) are rarely used, culminating in poor targeted communication.

Research limitations/implications

The paper shows that only printed communication is analyzed and more large‐scale empirical research is desired.

Practical implications

The paper shows that a richer media mix, more targeted communication, more national communication support and additional dialogue between and training of police officers and communication with professionals are advisable.

Originality/value

This paper combines two empirical studies and methods (content analysis and focus group interviews), resulting in a series of recommendations for further inquiry and future action.