bluuebunny/crossref_metadata_2025_split huggingface dataset:
The physical principles of energy transduction in chloroplast thylakoid membranes
Authors: Thorne S. W. , Duniec J. T. 
Published: March 2009

Photosynthesis in green plants or algae may be represented by an overall equation:The energy necessary to promote this overall reaction is derived from light through absorption by pigment molecules — chiefly the chlorophylls.Photosynthesis occurs in chloroplasts - subcellular organelles in which all the chlorophyll pigments are located. The chloroplasts comprise membranous, structures, and can be classified into two types. To the first type belong chloroplasts with appressed stacks of lamellar membranes, termed grana. These chloroplasts occur in mesophyll cells (C3plants). The second type of chloroplasts are those with lamellar membranes that do not form the grana structures; they occur in bundle sheath cells of maize and other monocotyledons (C4plants, Hatch & Slack, 1970). In algae a greater diversity of structure occurs (Kirk & Tilney-Basset, 1978). Fluorescence microscopy indicates that chlorophyll molecules are localized mainly in the grana membrane regions of mesophyll-type chloroplasts and uniformly throughout the bundle sheath cells (Spencer & Wildman, 1962). Mesophyll chloroplasts are flattened saucer-shaped organelles (20 or more in each cell) of between 5000 and 10000 nm in diameter, and of thickness 1000–2000 nm, whilst the individual grana are each of the order of 300–500 nm in diameter. The available evidence suggests that individual lamellar membranes are arranged to form vesicles, or sacks where the internal space is completely delimited from the external space. These individual closed membrane structures were termed thylakoids (Menke, 1962).
Biped gait generation based on parametric excitation by knee-joint actuation
Authors: Harata Yuji , Asano Fumihiko , Luo Zhi-Wei , Taji Kouichi , Uno Yoji 
Published: March 2009

SUMMARYRestoration of mechanical energy dissipating on impact at the ground is necessary for sustainable gait generation. Parametric excitation is one approach to restore the mechanical energy. Asano et al. (“Parametric excitation mechanisms for dynamic bipedal walking,” IEEE International Conference on Robotics and Automation (2005) pp. 611–617.) applied parametric excitation to a biped robot with telescopic-legs, in which up-and-down motion restores total mechanical energy like playing on the swing. In this paper, parametric excitation principle is applied to a kneed biped robot with only knee actuation and it is shown that the robot walks successively without hip actuation. We also examine influences of several parameters and reference trajectory on walking performance.
The effect of vaccination on undetected persistence of foot-and-mouth disease virus in cattle herds and sheep flocks
Authors: SCHLEY D. , PATON D. J. , COX S. J. , PARIDA S. , GUBBINS S. 
Published: March 2009

SUMMARYThe importance of carrier animals (those in whom virus persists after recovery from disease or acute infection) and their potential role in the spread of disease remain open questions within foot-and-mouth disease epidemiology. Using simple probabilistic models we attempt to quantify the effect of emergency vaccination – and especially the time of application – on the likely number of such animals, using data from challenge experiments on both cattle and sheep to determine the probability of persistence in diseased and subclinically infected animals. We show that the number of persistently infected animals in a group is predominantly determined by the number of animals initially infected on premises – the high variability of which ultimately limits the accuracy of any predictions of carrier numbers based upon transmission models. Furthermore, results suggest that, within a cattle herd, carrier numbers may be increased if challenge occurs shortly after vaccination. We show that the quality of inspection is the principal factor influencing whether or not carrier herds occur and that, by reducing clinical signs, the application of vaccination in regularly checked stock also results in an increase in undetected persistently infected animals. Where clinical detection would be poor regardless of the use of vaccination (i.e. particularly in sheep), vaccination will result in a reduction in the probability of a group containing undetected carriers: otherwise there is a benefit only if vaccination is applied sufficiently far in advance of any challenge. The implications of the results for serosurveillance are discussed, including the requisite test sensitivity and practices for successful implementation.
Culturally and Linguistically Diverse Populations: Serving GLBT Families in Our Schools
Authors: Frazier Ashley M. 
Published: March 2009

Abstract
School speech-language pathologists (SLPs) are increasingly likely to serve children of gay, lesbian, bisexual, and transgender (GLBT) parents or GLBT students as cultural and societal changes create growth in the population and increased willingness to disclose sexual orientation. The American Speech-Language-Hearing Association (ASHA) has a progressive nondiscrimination statement that includes sexual orientation as a protected status and strongly urges the membership to develop cultural competence as a matter of ethical service delivery. The purpose of this article is to describe cultural competence in relation to GLBT culture, discuss GLBT parent and student cultural issues as they are important in parent-school or student-school relations, and to provide suggestions for increasing sensitivity in these types of interactions. A list of resources is provided.
Comparisons of stuttering frequency during and after speech initiation in unaltered feedback, altered auditory feedback and choral speech conditions
Authors: Saltuklaroglu Tim , Kalinowski Joseph , Robbins Mary , Crawcour Stephen , Bowers Andrew 
Published: March 2009

Background: Stuttering is prone to strike during speech initiation more so than at any other point in an utterance. The use of auditory feedback (AAF) has been found to produce robust decreases in the stuttering frequency by creating an electronic rendition of choral speech (i.e., speaking in unison). However, AAF requires users to self‐initiate speech before it can go into effect and, therefore, it might not be as helpful as true choral speech during speech initiation.Aims: To examine how AAF and choral speech differentially enhance fluency during speech initiation and in subsequent portions of utterances.Methods & Procedures: Ten participants who stuttered read passages without altered feedback (NAF), under four AAF conditions and under a true choral speech condition. Each condition was blocked into ten 10 s trials separated by 5 s intervals so each trial required ‘cold’ speech initiation. In the first analysis, comparisons of stuttering frequencies were made across conditions. A second, finer grain analysis involved examining stuttering frequencies on the initial syllable, the subsequent four syllables produced and the five syllables produced immediately after the midpoint of each trial.Outcomes & Results: On average, AAF reduced stuttering by approximately 68% relative to the NAF condition. Stuttering frequencies on the initial syllables were considerably higher than on the other syllables analysed (0.45 and 0.34 for NAF and AAF conditions, respectively). After the first syllable was produced, stuttering frequencies dropped precipitously and remained stable. However, this drop in stuttering frequency was significantly greater (approximately 84%) in the AAF conditions than in the NAF condition (approximately 66%) with frequencies on the last nine syllables analysed averaging 0.15 and 0.05 for NAF and AAF conditions, respectively. In the true choral speech condition, stuttering was virtually (approximately 98%) eliminated across all utterances and all syllable positions.Conclusions & Implications: Altered auditory feedback effectively inhibits stuttering immediately after speech has been initiated. However, unlike a true choral signal, which is exogenously initiated and offers the most complete fluency enhancement, AAF requires speech to be initiated by the user and ‘fed back’ before it can directly inhibit stuttering. It is suggested that AAF can be a viable clinical option for those who stutter and should often be used in combination with therapeutic techniques, particularly those that aid speech initiation. The substantially higher rate of stuttering occurring on initiation supports a hypothesis that overt stuttering events help ‘release’ and ‘inhibit’ central stuttering blocks. This perspective is examined in the context of internal models and mirror neurons.
The barriers perceived to prevent the successful implementation of evidence‐based practice by speech and language therapists
Authors: O'Connor Siobhan , Pettigrew Catharine M. 
Published: March 2009

Background: There is currently a paucity of research investigating what speech and language therapists, in particular, perceive are the greatest barriers to implementing evidence‐based practice.Aims: The purpose of this study was to investigate the perceived barriers that are faced by speech and language therapists in southern Ireland when attempting to implement evidence‐based practice.Methods & Procedures: A 34‐item questionnaire was sent to 39 therapists working in several counties in southern Ireland. The survey received an 82.1% (n = 32) response rate.Outcomes & Results: The results of the study indicated that certain barriers are perceived to prevent evidence‐based practice being implemented successfully. The most significant barrier affecting evidence‐based practice implementation was reported to be a lack of time to read research (71.9%). Additional barriers that were found to be the most significant were the research having methodological inadequacies (62.5%) and insufficient time to implement new ideas (59.4%). Other important factors identified as being significant barriers to the implementation of evidence‐based practice were those associated with the quality and presentation of the research, workplace setting, and lack of skills of the therapist. Associations between specific barriers and workplace setting or grade were also investigated. Some possible reasons for these barriers and the implications for clinical practice are also discussed.Conclusions & Implications: This small study suggests that therapists agreed that evidence‐based practice is essential to the practice of speech and language therapy. There are, however, barriers in place that are perceived to prevent its successful implementation. It is hoped that because these barriers have been identified, individual clinicians and organizations can be proactive in aiming to provide an evidence‐based service to their clients.
Functional asymmetry in a simple coincidence‐anticipation task: Effects of handedness
Authors: Rodrigues Paula Cristina , Vasconcelos Olga , Barreiros João , Barbosa Ricardo , Trifilio Fábio 
Published: March 2009

AbstractRight‐ and left‐handed performance presents different degrees of manual functional asymmetry, because left‐handers usually present lower asymmetry in several tasks. Thus, we asked 27 right‐handed and 33 left‐handed male and female adolescents to perform a coincidence‐anticipation task. Absolute, constant, and variable errors were calculated for each participant, for the preferred and non‐preferred hand, as well as the performance asymmetry index. Results demonstrated that: (i) right‐ and left‐handers performed to a similar level; (ii) both right‐ and left‐handers were less variable when using their left hand; (iii) males were more accurate and less variable than their female counterparts. Although handedness failed to show a significant effect, our results demonstrate that both performing hand and gender have an influence on coincidence timing ability. The gender‐related effect lends support to the idea that differences exist in the neural mechanisms of visuospatial processing between the sexes, and the performing hand‐related effect is supposed to reflect the right hemisphere advantage in movement planning.
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data
Authors: Kirk Paul D. W. , Stumpf Michael P. H. 
Published: March 2009

AbstractMotivation: Although widely accepted that high-throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved. Here, we present a parametric bootstrapping approach for time-course data, in which Gaussian process regression (GPR) is used to fit a probabilistic model from which replicates may then be drawn. This approach implicitly allows the time dependence of the data to be taken into account, and is applicable to a wide range of problems.Results: We apply GPR bootstrapping to two datasets from the literature. In the first example, we show how the approach may be used to investigate the effects of data uncertainty upon the estimation of parameters in an ordinary differential equations (ODE) model of a cell signalling pathway. Although we find that the parameter estimates inferred from the original dataset are relatively robust to data uncertainty, we also identify a distinct second set of estimates. In the second example, we use our method to show that the topology of networks constructed from time-course gene expression data appears to be sensitive to data uncertainty, although there may be individual edges in the network that are robust in light of present data.Availability: Matlab code for performing GPR bootstrapping is available from our web site: http://www3.imperial.ac.uk/theoreticalsystemsbiology/data-software/Contact: paul.kirk@imperial.ac.uk, m.stumpf@imperial.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation
Authors: Thomas Alun 
Published: March 2009

Abstract
Motivation: Efficient models for genetic linkage disequilibrium (LD) are needed to enable appropriate statistical analysis of the dense, genome-wide single nucleotide polymorphism assays currently available.
Results: Estimation of graphical models for LD within a restricted class of decomposable models is shown to be possible using computer time and storage that scale linearly with the number of loci. Programs for estimation and for simulating from these models on a whole-genome basis are described and provided.
Availability: Java classes and source code for IntervalLD and GeneDrops are freely available over the internet at http://bioinformatics.med.utah.edu/∼alun.
Contact: alun@genepi.med.utah.edu
A concanavalin A-like lectin domain in the CHS1/LYST protein, shared by members of the BEACH family
Authors: Burgess Agathe , Mornon Jean-Paul , de Saint-Basile Geneviève , Callebaut Isabelle 
Published: March 2009

Abstract
CHS1/LYST, the causative protein of the Chediak–Higashi syndrome (CHS), belongs to the BEACH (named after BEige And Chediak–Higashi) family, which includes various large proteins sharing the same C-terminal domain architecture [a PH (Pleckstrin homology)–BEACH domain followed by WD repeats). Members of the BEACH family are generally defined as vesicle-trafficking regulatory proteins, but their functions remain to be determined at the molecular level.
Here, using a panel of sensitive methods of sequence analysis, we show that the N-terminal regions of BEACH proteins contain an as yet not described domain, which shares striking similarities with clostridial neurotoxins and defines a novel family within the concanavalin A (ConA)-like lectin superfamily. These results suggest that the BEACH ConA-like lectin domain could be involved in oligosaccharide binding associated with protein traffic and sorting along the secretory pathway, especially in relation with components of the vesicle fusion machinery.
Contact: isabelle.callebaut@impmc.jussieu.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Clinical efficacies of topical agents for the treatment of seborrheic dermatitis of the scalp: A comparative study
Authors: SHIN Hyoseung , KWON Oh Sang , WON Chong Hyun , KIM Beom Joon , LEE Yang Won , CHOE Yong Beom , AHN Kyu Joong , EUN Hee Chul 
Published: March 2009

ABSTRACTPrevious studies have shown that topical steroid and shampoo containing zinc pyrithione provide clinical benefits for treatment of scalp seborrheic dermatitis. But the clinical efficacy of topical tacrolimus, a newly developed calcineurin inhibitor on seborrheic dermatitis, is not well investigated yet. We wanted to compare the clinical efficacy of topical tacrolimus with that of conventional treatment (zinc pyrithione shampoo and topical betamethasone) for treatment of seborrheic dermatitis of the scalp. Patients with seborrheic dermatitis of the scalp were randomly allocated to receive topical betamethasone, topical tacrolimus or zinc pyrithione shampoo. Some patients were instructed to continue the treatments for 8 weeks and the others to discontinue the treatments at week 4. We evaluated the efficacy using a clinical severity score, dandruff score and sebum secretion at baseline, week 4 and week 8. All treatment groups showed significant improvements in clinical assessment after 4 weeks. While the patients treated by zinc pyrithione improved continuously even after cessation of the treatment, the patients treated by betamethasone lotion or tacrolimus ointment were aggravated clinically. Topical tacrolimus was as effective as topical betamethasone, and showed more prolonged remission than topical betamethasone. To treat seborrheic dermatitis of the scalp, we think that the combination therapy of topical steroid or topical tacrolimus, and zinc pyrithione is recommended.
Candidate genes for cannabis use disorders: findings, challenges and directions
Authors: Agrawal Arpana , Lynskey Michael T. 
Published: March 2009

ABSTRACTAim Twin studies have shown that cannabis use disorders (abuse/dependence) are highly heritable. This review aims to: (i) review existing linkage studies of cannabis use disorders and (ii) review gene association studies, to identify potential candidate genes, including those that have been tested for composite substance use disorders and (iii) to highlight challenges in the genomic study of cannabis use disorders.Methods Peer‐reviewed linkage and candidate gene association studies are reviewed.Results Four linkage studies are reviewed: results from these have homed in on regions on chromosomes 1, 3, 4, 9, 14, 17 and 18, which harbor candidates of predicted biological relevance, such as monoglyceride lipase (MGLL) on chromosome 3, but also novel genes, includingELTD1[epidermal growth factor (EGF), latrophilin and seven transmembrane domain containing 1] on chromosome 1. Gene association studies are presented for (a) genes posited to have specific influences on cannabis use disorders:CNR1,CB2,FAAH,MGLL,TRPV1andGPR55and (b) genes from various neurotransmitter systems that are likely to exert a non‐specific influence on risk of cannabis use disorders, e.g.GABRA2,DRD2andOPRM1.Conclusions There are challenges associated with (i) understanding biological complexity underlying cannabis use disorders (including the need to study gene–gene and gene–environment interactions), (ii) using diagnostic versus quantitative phenotypes, (iii) delineating which stage of cannabis involvement (e.g. use versus misuse) genes influence and (iv) problems of sample ascertainment.
Influence of experimental warming and shading on host–parasitoid synchrony
Authors: KLAPWIJK MAARTJE J. , GRÖBLER B. CHRIS , WARD KIMBERLEY , WHEELER DAVID , LEWIS OWEN T. 
Published: March 2009

AbstractAs the climate warms, many species are showing altered phenology patterns, potentially disrupting synchrony between interacting species. Recent studies have documented disrupted synchrony in plant–herbivore and predator–prey interactions. However, studies investigating climate‐related asynchrony in host–parasitoid interactions and exploring the relative responses of interacting hosts and parasitoids to climate change are lacking. This is an important gap in knowledge given the ubiquity of insect parasitoids and their importance in influencing the abundance and dynamics of their hosts. In the threatened marsh fritillary butterflyEuphydryas aurinia(Lepidoptera: Nymphalidae) and its specialized parasitoid,Cotesia bignellii(Hymenoptera: Braconidae) phenological synchrony (and consequently population fluctuations) are thought to be weather‐dependent. To assess the likely influence of climate and microenvironment change on synchrony betweenE. auriniaandC. bignellii, we experimentally manipulated the exposure of sensitive‐stage host larvae and parasitoid pupae to temperature (ambient or elevated) and shading (shaded or unshaded) regimes. We also analysed a 20‐year population dynamic dataset from the United Kingdom forE. auriniato investigate whether population variations could be explained by interannual variations in the thermal and sunshine environment. Development times were affected significantly by the experimental temperature and shading treatments forE. auriniabut not forC. bignellii. However, the contrasting responses were insufficient to significantly affect host availability for parasitoids. In the field, thermal and sunshine conditions did not influence population fluctuations, and population variations across a large (UK‐wide) scale were uncorrelated. Changes to the thermal and sunshine environment of the magnitude investigated in our experiment and within the range experienced by wildE. auriniapopulations over the last 20‐years thus seem unlikely to cause breakdown in host–parasitoid synchrony. We suggest that experiments investigating the mechanistic responses of interacting species to environmental change are needed to support the analysis and interpretation of observational data on species' phenology.