bluuebunny/crossref_metadata_2025_split huggingface dataset:
Severe Aphasia: Possible Contributions of Using the ICF in Assessment
Authors: Threats Travis T. 
Published: April 2009

Abstract
Purpose: This article discusses the use of the World Health Organization's International Classification of Functioning, Disability, and Health (ICF) in the evaluation of persons with severe aphasia.
Method: Patterson and Chapey's (2008) descriptions of the hallmarks of the assessment in aphasia are presented. The ICF is described and examined in terms of whether it could be beneficial in meeting these hallmarks.
Results and Conclusions: The ICF is demonstrated to be able to contribute towards meeting the goals of this evaluation framework. It is concluded that use of the ICF by clinicians could assist in meeting the special challenges of conducting quality assessments of persons with severe aphasia.
KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways
Authors: Spasić Irena , Simeonidis Evangelos , Messiha Hanan L. , Paton Norman W. , Kell Douglas B. 
Published: April 2009

Abstract
Motivation: Most experimental evidence on kinetic parameters is buried in the literature, whose manual searching is complex, time consuming and partial. These shortcomings become particularly acute in systems biology, where these parameters need to be integrated into detailed, genome-scale, metabolic models. These problems are addressed by KiPar, a dedicated information retrieval system designed to facilitate access to the literature relevant for kinetic modelling of a given metabolic pathway in yeast. Searching for kinetic data in the context of an individual pathway offers modularity as a way of tackling the complexity of developing a full metabolic model. It is also suitable for large-scale mining, since multiple reactions and their kinetic parameters can be specified in a single search request, rather than one reaction at a time, which is unsuitable given the size of genome-scale models.
Results: We developed an integrative approach, combining public data and software resources for the rapid development of large-scale text mining tools targeting complex biological information. The user supplies input in the form of identifiers used in relevant data resources to refer to the concepts of interest, e.g. EC numbers, GO and SBO identifiers. By doing so, the user is freed from providing any other knowledge or terminology concerned with these concepts and their relations, since they are retrieved from these and cross-referenced resources automatically. The terminology acquired is used to index the literature by mapping concepts to their synonyms, and then to textual documents mentioning them. The indexing results and the previously acquired knowledge about relations between concepts are used to formulate complex search queries aiming at documents relevant to the user's information needs. The conceptual approach is demonstrated in the implementation of KiPar. Evaluation reveals that KiPar performs better than a Boolean search. The precision achieved for abstracts (60%) and full-text articles (48%) is considerably better than the baseline precision (44% and 24%, respectively). The baseline recall is improved by 36% for abstracts and by 100% for full text. It appears that full-text articles are a much richer source of information on kinetic data than are their abstracts. Finally, the combined results for abstracts and full text compared with the curated literature provide high values for relative recall (88%) and novelty ratio (92%), suggesting that the system is able to retrieve a high proportion of new documents.
Availability: Source code and documentation are available at: http://www.mcisb.org/resources/kipar/
Contact: i.spasic@manchester.ac.uk; dbk@manchester.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum
Authors: Jurgelenaite Rasa , Dijkstra Tjeerd M. H. , Kocken Clemens H. M. , Heskes Tom 
Published: April 2009

Abstract
Motivation: To date, there is little knowledge about one of the processes fundamental to the biology of Plasmodium falciparum, gene regulation including transcriptional control. We use noisy threshold models to identify regulatory sequence elements explaining membership to a gene expression cluster where each cluster consists of genes active during the part of the developmental cycle inside a red blood cell. Our approach is both able to capture the combinatorial nature of gene regulation and to incorporate uncertainty about the functionality of putative regulatory sequence elements.
Results: We find a characteristic pattern where the most common motifs tend to be absent upstream of genes active in the first half of the cycle and present upstream of genes active in the second half. We find no evidence that motif's score, orientation, location and multiplicity improves prediction of gene expression. Through comparative genome analysis, we find a list of potential transcription factors and their associated motifs.
Contact: r.jurgelenaite@cmbi.ru.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Hooke: an open software platform for force spectroscopy
Authors: Sandal Massimo , Benedetti Fabrizio , Brucale Marco , Gomez-Casado Alberto , Samorì Bruno 
Published: April 2009

Abstract
Summary: Hooke is an open source, extensible software intended for analysis of atomic force microscope (AFM)-based single molecule force spectroscopy (SMFS) data. We propose it as a platform on which published and new algorithms for SMFS analysis can be integrated in a standard, open fashion, as a general solution to the current lack of a standard software for SMFS data analysis. Specific features and support for file formats are coded as independent plugins. Any user can code new plugins, extending the software capabilities. Basic automated dataset filtering and semi-automatic analysis facilities are included.
Availability: Software and documentation are available at http://code.google.com/p/hooke. Hooke is a free software under the GNU Lesser General Public License.
Contact: massimo.sandal@unibo.it
Purification of Recombinant Drosophila ACF
Authors: Peterson Craig L. 
Published: April 2009

INTRODUCTIONThe goal of chromatin assembly procedures is to prepare extended nucleosomal arrays from cloned DNA templates and purified core and linker histones. The assembled chromatin should be highly defined in its protein content and resemble bulk chromatin isolated from living cell nuclei in terms of periodicity and nucleosome positioning. This protocol describes the preparation of Drosophila ACF (ATP-utilizing chromatin assembly and remodeling factor) for use in chromatin assembly reactions. In this method, ACF is prepared by the coexpression of the carboxyl-terminally FLAG-tagged Acf1 subunit with the untagged ISWI subunit in baculovirus. The complex is then purified in one step by FLAG immunoaffinity chromatography. This procedure typically results in a stoichiometric complex of Acf1 and ISWI.
Obtaining Ilyanassa Snail Embryos
Authors: Gharbiah Maey , Cooley James , Leise Esther M. , Nakamoto Ayaki , Rabinowitz Jeremy S. , Lambert J. David , Nagy Lisa M. 
Published: April 2009

INTRODUCTIONThe marine gastropod Ilyanassa obsoleta is a long-standing and very useful model for studies of embryonic development. It is an especially important model for spiralian development, and for studies of asymmetric cell division. The embryos are amenable to classic embryological manipulation techniques as well as a growing number of molecular approaches. Ilyanassa is also an important model for studies of metamorphosis, the ecology of parasitism, the effects of environmental contaminants on morphology and sexual function, and comparative neurobiology. Ilyanassa adults are readily obtainable and easy to keep in the laboratory. Although the normal spawning season for Ilyanassa is during early summer, they can produce high-quality embryos nearly year-round in the laboratory. Snails collected in the late fall, winter, or spring can be induced to deposit zygotes before the natural spawning season by warming them to room temperature, and snails collected before the natural spawning season can be made to postpone zygote deposition until needed (up to at least 6 mo) by maintaining them in tanks in a cold room at 4°C-8°C. This protocol describes how to induce embryo production in Ilyanassa snails, collect the embryos, and rear them to the stage required for study.
Microinjection of Helobdella (Leech) Embryos: Figure 1.
Authors: Weisblat David A. , Kuo Dian-Han 
Published: April 2009

INTRODUCTIONOne advantage of using Helobdella (leech) embryos as an experimental system is their amenability for microinjection. Blastomeres ranging in size from the zygote (400 μm diameter) down to micromeres and primary blast cells (~20 μm diameter) can be injected by pressure under a dissecting microscope. Smaller cells can be injected by iontophoresis under a compound microscope. Microinjection is useful for studying embryonic development. For example, developmental fates of a cell can be followed by injecting a lineage tracer. A specific cell can be killed by injecting a toxic substance. Furthermore, cells can be killed at a given developmental stage by directing intense fluorescence illumination or a blue laser beam on fluorescein-labeled cells. Finally, gene expression can be manipulated in leech embryos by injecting zygotes or selected blastomeres with synthetic mRNA, morpholino antisense oligo, or a plasmid construct. Molecules <1500 Da can diffuse freely among early blastomeres via gap junctions. When intercellular diffusion of an injected substance is undesirable, small molecules should be conjugated to larger molecules such as dextran (10 kDa). Different commercial microinjection setups can be adopted for Helobdella embryos. This article describes how to microinject embryos using a versatile homemade pressure injection system. Under a dissecting microscope, embryos are immobilized by suction in a custom-fabricated chamber with the target cell facing upward. Cells are visualized using transillumination via a long-working-distance, dark-field condenser. The tip of a micropipette is brought into the target cell with a micromanipulator, and the injectant is delivered into the cell by pressure.
Devitellinization of Living Helobdella (Leech) Embryos
Authors: Weisblat David A. , Kuo Dian-Han 
Published: April 2009

INTRODUCTIONEmbryos of glossiphoniid leeches are enclosed in a thin vitelline envelope until “hatching” (stage 10). This protocol describes the procedure for removing the vitelline envelope from Helobdella robusta and H. sp. (Austin) embryos. This protocol is applicable to embryos of stages 1-9 but is probably more useful for early stages. With careful culturing, the devitellinized embryos can develop normally.
Arnolds’ Silver Staining of Helbodella (Leech) Embryos
Authors: Weisblat David A. , Kuo Dian-Han 
Published: April 2009

INTRODUCTIONArnolds’ silver staining is used to visualize the boundaries of epidermal cells at the surface of embryos. As described in this article, silver staining can be performed on either living or fixed Helbodella (leech) embryos. To preserve the cell junction in fixed embryos, a special fixation procedure is used.
tDNA-PCR Followed by Automated Fluorescent Capillary Electrophoresis for Identification of Bacterial Species
Authors: Baele Margo , Stakenborg Tim , Lopes dos Santos Santiago Guido , Haesebrouck Freddy , Vaneechoutte Mario 
Published: April 2009

INTRODUCTIONTransfer RNA intergenic spacer length polymorphism analysis (tDNA-PCR) is a simple and reproducible polymerase chain reaction (PCR) technique for identification of bacteria at the species or even subspecies level. The primers used in the PCR are based on conserved sequences located at the edges of the tRNA genes. Because the selected consensus primers are directed outwardly, the intergenic spacers are amplified rather than the genes themselves. With each PCR, several amplicons of different lengths are obtained, because several intergenic spacers are present in each bacterial genome. The patterns thus obtained are identical within species, but differ between distinct species, and as a result, can be used for identification of bacterial species. The amplicons are separated using high-resolution (1 bp) electrophoresis (e.g., fluorescent capillary electrophoresis) and immediately digitized as tables composed of numerical lengths (expressed in base pairs) and peak intensities. For identification, the resulting peak pattern can be compared with a large database of patterns of well-identified bacterial strains, using an in-house-developed software package that is available online. New patterns (linked to the correct species name, which can be obtained, e.g., after 16S rRNA gene sequence determination) can be added to expand the database further. This protocol describes tDNA-PCR, followed by automated fluorescent capillary electrophoresis to identify bacterial species.
The glutamic acid decarboxylase 65 immunoglobulin G subclass profile differs between adult-onset type 1 diabetes and latent autoimmune diabetes in adults (LADA) up to 3 years after clinical onset
Authors: Hillman M , Törn C , Landin-Olsson M 
Published: April 2009

SummaryAutoantibodies against glutamic acid decarboxylase 65 (GADA) are found frequently in patients with autoimmune diabetes. Immunoglobulin (Ig)G1 is the most frequent subclass among the GADA IgG subclasses. IgG4 is a more common subclass in latent autoimmune diabetes in adults (LADA) at clinical onset compared to type 1 diabetes. The aim of this work was to study the different GADA-IgG subclass profiles during a 3-year follow-up in these groups of autoimmune diabetes. Adult-onset subjects, classified as either type 1 (n = 40) or LADA (n = 43), were included in the study. New samples were collected every year from these patients. In addition to conventional GADA analyses, GADA-IgG subclasses were also analysed with a radioimmunoprecipitation assay using biotin-conjugated antibodies (directed against human IgG subclasses and IgM) and streptavidin Sepharose. During 3 years' follow-up, all the IgG subclass levels decreased in type 1 diabetes – IgG1: P &lt; 0·001; IgG2: P &lt; 0·001; IgG3: P &lt; 0·001; IgG4: P &lt; 0·05 (Friedman's’ test) – while levels remained stable for all four subclasses in LADA. GADA IgM, however, decreased in both groups (P &lt; 0·001). Patients with LADA have higher GADA IgG3 and IgG4 at clinical onset and seem to maintain the levels and profile of their IgG subclasses up to 3 years after clinical onset, while all the GADA IgG subclass levels decrease in type 1 diabetic patients. This indicates a persistent different immune response in LADA compared to type 1 diabetes and further indicates the difference in pathogenesis.
Improving clinical outcome in patients with intestinal failure using individualised nutritional advice
Authors: Culkin A. , Gabe S. M. , Madden A. M. 
Published: April 2009

AbstractBackground: Patients with intestinal failure are required to adhere to a complex regimen. Written information may increase knowledge leading to improvements in clinical outcomes. The present study aimed to evaluate the effectiveness of nutrition advice incorporating the use of a booklet.Methods: Each patient completed a questionnaire evaluating their knowledge of the regime and quality of life and kept a diet and gastrointestinal output diary. The diary was assessed and they were given the booklet with a verbal explanation tailored to individual requirements. The booklet explained the causes of intestinal failure, diet and fluid recommendations in relation to intestinal anatomy, information on medications and long‐term monitoring. Patients were reassessed at their next appointment using the same tools. The primary endpoint was an improvement in knowledge. Secondary endpoints were an improvement in oral nutritional intake, nutritional status, quality of life and the content of home parenteral nutrition.Results: Forty‐eight patients completed the study. Knowledge improved significantly after dietetic intervention in association with the provision of the booklet (P < 0.001). Oral energy (P = 0.04) and fat (P = 0.003) intake increased with an improvement in body mass index (P = 0.02). Patients on home parenteral nutrition showed a reduction in parenteral energy (P = 0.02), nitrogen (P = 0.003), volume (P = 0.02) and frequency (P = 0.003).Conclusions: A booklet for patients with intestinal failure in conjunction with personalised dietary counselling improves knowledge and clinical outcomes.
Modelling evolutionary processes in small populations: not as ideal as you think
Authors: WAPLES ROBIN S. , FAULKNER JAMES R. 
Published: March 2009

AbstractEvolutionary processes are routinely modelled using ‘ideal’ Wright–Fisher populations of constant size N in which each individual has an equal expectation of reproductive success. In a hypothetical ideal population, variance in reproductive success (Vk) is binomial and effective population size (Ne) = N. However, in any actual implementation of the Wright–Fisher model (e.g., in a computer), Vk is a random variable and its realized value in any given replicate generation () only rarely equals the binomial variance. Realized effective size () thus also varies randomly in modelled ideal populations, and the consequences of this have not been adequately explored in the literature. Analytical and numerical results show that random variation in and can seriously distort analyses that evaluate precision or otherwise depend on the assumption that is constant. We derive analytical expressions for Var(Vk) [4(2N – 1)(N – 1)/N3] and Var(Ne) [N(N – 1)/(2N – 1) ≈ N/2] in modelled ideal populations and show that, for a genetic metric G = f(Ne), Var(Ĝ) has two components: VarGene (due to variance across replicate samples of genes, given a specific ) and VarDemo (due to variance in ). Var(Ĝ) is higher than it would be with constant Ne = N, as implicitly assumed by many standard models. We illustrate this with empirical examples based on F (standardized variance of allele frequency) and r2 (a measure of linkage disequilibrium). Results demonstrate that in computer models that track multilocus genotypes, methods of replication and data analysis can strongly affect consequences of variation in . These effects are more important when sampling error is small (large numbers of individuals, loci and alleles) and with relatively small populations (frequently modelled by those interested in conservation).
Sputum eosinophilia: an early marker of bronchial response to occupational agents
Authors: Vandenplas O. , D’Alpaos V. , Heymans J. , Jamart J. , Thimpont J. , Huaux F. , Lison D. , Renauld J‐C. 
Published: April 2009

Background:  False‐negative responses to specific inhalation challenge (SIC) with occupational agents may occur. We explored whether assessing changes in sputum cell counts would help improve the identification of bronchial reactivity to occupational agents during SICs.Methods:  The predictive value of the changes in sputum cell counts after a negative FEV1 response to a first challenge exposure to an occupational agent was determined using the changes in airway calibre observed during repeated challenges as the ‘gold standard’. The study included 68 subjects investigated for work‐related asthma in a tertiary centre. After a control day, the subjects were challenged with the suspected occupational agent(s) for up to 2 h. All subjects who did not show an asthmatic reaction were re‐challenged on the following day. Additional challenges were proposed to those who demonstrated a ≥ 2% increase in sputum eosinophils or an increase in nonspecific bronchial hyperresponsiveness to histamine after the second challenge day.Results:  Six of the 35 subjects without changes in FEV1 on the first challenge developed an asthmatic reaction on subsequent challenges. ROC analysis revealed that a >3% increase in sputum eosinophils at the end of the first challenge day was the most accurate parameter for predicting the development of an asthmatic response on subsequent challenges with a sensitivity of 67% and a specificity of 97%.Conclusions:  An increase in sputum eosinophils is an early marker of specific bronchial reactivity to occupational agents, which may help to identify subjects who will develop an asthmatic reaction only after repeated exposure.
Lower urinary tract symptoms in relation to lifestyle and medical conditions in Japanese workers
Authors: Tomita Kentaro , Mizoue Tetsuya , Matsumoto Tetsuro 
Published: April 2009

Objectives:  To examine the association of medical conditions and lifestyle with lower urinary tract symptoms (LUTS) in a population of Japanese male workers.Methods:  A questionnaire survey on LUTS was conducted at the time of a periodic health examination among workers of a group of engineering and shipbuilding companies in Southern Kanto, Japan. A total of 1278 (85%) men responded. LUTS were assessed by using a modified International Prostate Symptom Score questionnaire. Men having at least one point of the score were regarded as positive. Logistic regression analysis was used to examine the relation of the LUTS to age, smoking, drinking, body mass index, and medical treatment of diabetes mellitus, hypertension, and dyslipidemia.Results:  Age was a strong determinant of LUTS. Men undergoing medical treatment for diabetes mellitus were significantly more likely to have LUTS than men without treatment (multivariate‐adjusted odds ratio, 1.8; 95% confidence interval, 1.0–3.2). Increased odds of LUTS were also observed in men undergoing medical treatment for hypertension or dyslipidemia. Smoking, drinking alcohol, and obesity were not related to LUTS.Conclusions:  Our present findings, together with previous epidemiological and experimental evidence, suggest that LUTS might share common etiological factors with diabetes mellitus, hypertension, and dyslipidemia.
Style timing with the value spread in Australia
Authors: Hyde Charles E. , Beggs David 
Published: April 2009

AbstractThe value spread is shown to be positively related to the value premium in the Australian market. The relationship is especially strong for small cap portfolios and typically stronger when using the book‐to‐price ratio than other value metrics. In small cap portfolios, the positive value premium–spread relationship is primarily driven by the short side. Our results are consistent with previous findings in US and Asian markets. We also show that the small cap–large cap value spread differential is positively related to the corresponding value premium differential, suggesting the value spread can also be used for timing the large/small cap tilt.
SPATIAL EFFECTS ON PROVINCIAL CONVERGENCE AND INCOME DISTRIBUTION IN SPAIN: 1985–2003
Authors: MAZA ADOLFO , VILLAVERDE JOSÉ 
Published: April 2009

ABSTRACTThis paper examines the role of space (geographical location) in provincial income convergence and income distribution in Spain. To do that, and after showing the presence of spatial dependence in our income data, the paper compares two sample series: actual versus filtered (spaceless) data. The comparison of these two series comes out to two important differences: first, the speed of convergence is higher and, second, the income distribution is more concentrated (less biased) around the national average with filtered data. Besides this, the paper also shows that geographical location particularly explains relative income improvement in provinces with per capita income slightly above average. These results confirm that, as for Spain, space does indeed matter.