bluuebunny/crossref_metadata_2025_split huggingface dataset:
Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways
Authors: Hardy Simon , Robillard Pierre N. 
Published: November 2007

Abstract
Motivation: Cellular signaling networks are dynamic systems that propagate and process information, and, ultimately, cause phenotypical responses. Understanding the circuitry of the information flow in cells is one of the keys to understanding complex cellular processes. The development of computational quantitative models is a promising avenue for attaining this goal. Not only does the analysis of the simulation data based on the concentration variations of biological compounds yields information about systemic state changes, but it is also very helpful for obtaining information about the dynamics of signal propagation.
Results: This article introduces a new method for analyzing the dynamics of signal propagation in signaling pathways using Petri net theory. The method is demonstrated with the Ca2+/calmodulin-dependent protein kinase II (CaMKII) regulation network. The results constitute temporal information about signal propagation in the network, a simplified graphical representation of the network and of the signal propagation dynamics and a characterization of some signaling routes as regulation motifs.
Contact: simon.hardy@polymtl.ca
Supplementary information: Complete data of the Petri net model of the CaMKII regulation pathway available at http://www.polymtl.ca/rgl/Downloads.php
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models
Authors: Qian Yuntao , Murphy Robert F. 
Published: November 2007

Abstract
Motivation: There is extensive interest in automating the collection, organization and analysis of biological data. Data in the form of images in online literature present special challenges for such efforts. The first steps in understanding the contents of a figure are decomposing it into panels and determining the type of each panel. In biological literature, panel types include many kinds of images collected by different techniques, such as photographs of gels or images from microscopes. We have previously described the SLIF system (http://slif.cbi.cmu.edu) that identifies panels containing fluorescence microscope images among figures in online journal articles as a prelude to further analysis of the subcellular patterns in such images. This system contains a pretrained classifier that uses image features to assign a type (class) to each separate panel. However, the types of panels in a figure are often correlated, so that we can consider the class of a panel to be dependent not only on its own features but also on the types of the other panels in a figure.
Results: In this article, we introduce the use of a type of probabilistic graphical model, a factor graph, to represent the structured information about the images in a figure, and permit more robust and accurate inference about their types. We obtain significant improvement over results for considering panels separately.
Availability: The code and data used for the experiments described here are available from http://murphylab.web.cmu.edu/software
Contact: murphy@cmu.edu
Analysis of a Gibbs sampler method for model-based clustering of gene expression data
Authors: Joshi Anagha , Van de Peer Yves , Michoel Tom 
Published: November 2007

Motivation: Over the last decade, a large variety of clustering algorithms have been developed to detect coregulatory relationships among genes from microarray gene expression data. Model-based clustering approaches have emerged as statistically well-grounded methods, but the properties of these algorithms when applied to large-scale data sets are not always well understood. An in-depth analysis can reveal important insights about the performance of the algorithm, the expected quality of the output clusters, and the possibilities for extracting more relevant information out of a particular data set.
Results: We have extended an existing algorithm for model-based clustering of genes to simultaneously cluster genes and conditions, and used three large compendia of gene expression data for Saccharomyces cerevisiae to analyze its properties. The algorithm uses a Bayesian approach and a Gibbs sampling procedure to iteratively update the cluster assignment of each gene and condition. For large-scale data sets, the posterior distribution is strongly peaked on a limited number of equiprobable clusterings. A GO annotation analysis shows that these local maxima are all biologically equally significant, and that simultaneously clustering genes and conditions performs better than only clustering genes and assuming independent conditions. A collection of distinct equivalent clusterings can be summarized as a weighted graph on the set of genes, from which we extract fuzzy, overlapping clusters using a graph spectral method. The cores of these fuzzy clusters contain tight sets of strongly coexpressed genes, while the overlaps exhibit relations between genes showing only partial coexpression.
Availability: GaneSh, a Java package for coclustering, is available under the terms of the GNU General Public License from our website at http://bioinformatics.psb.ugent.be/software
Contact: yves.vandepeer@psb.ugent.be
Supplementary information: Supplementary data are available on our website at http://bioinformatics.psb.ugent.be/supplementary_data/anjos/gibbs
NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks
Authors: Kachalo Sema , Zhang Ranran , Sontag Eduardo , Albert Réka , DasGupta Bhaskar 
Published: November 2007

Abstract
Summary: We present a software for combined synthesis, inference and simplification of signal transduction networks. The main idea of our method lies in representing observed indirect causal relationships as network paths and using techniques from combinatorial optimization to find the sparsest graph consistent with all experimental observations. We illustrate the biological usability of our software by applying it to a previously published signal transduction network and by using it to synthesize and simplify a novel network corresponding to activation-induced cell death in large granular lymphocyte leukemia.
Availability: NET-SYNTHESIS is freely downloadable from http://www.cs.uic.edu/~dasgupta/network-synthesis/
Contact: dasgupta@cs.uic.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees
Authors: Fuchsberger Christian , Falchi Mario , Forer Lukas , Pramstaller Peter P. 
Published: November 2007

Abstract
Summary: PedVizApi is a Java API (application program interface) for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. While available packages are mostly focused on a static representation or cannot be added to an existing application, PedVizApi is a highly flexible open source library for the efficient construction of visual-based applications for the analysis of family data. An extensive demo application and a R interface is provided.
Availability: http://www.pedvizapi.org
Contact: christian.fuchsberger@eurac.edu
Reflective process in action: the uncovering of the ritual of washing in clinical nursing practice
Authors: JONES ADRIAN 
Published: November 2007

Summary

Reflection can be utilized to reveal aspects of clinical practice which remain shrouded in ritualistic origin.
The underlying themes surrounding the action of washing patients can be traced to Victorian legacies and the nurse education process.
The nurse‐patient relationship serves as a template for the deliverance of nursing interventions.
An incomplete awareness of the nurse‐patient relationship persists as to its initiation, continuation and usefulness in clinical nursing.
Following reflection, there has been an increased awareness of feelings and attitudes surrounding the activity of washing a patient.
Nurse involvement in cardiac rehabilitation prior to hospital discharge
Authors: NEWENS ANDREW J. , BOND SENGA , PRIEST JONATHAN , McCOLL ELAINE 
Published: November 2007

Summary

Interviews were undertaken with 202 men admitted to five hospitals in northeast England following an uncomplicated first myocardial infarction. The likelihood of patients speaking to a nurse about recovery or seeing a physiotherapist, dietician or specialist rehabilitation nurse, varied considerably between hospitals.
Whilst virtually all patients received written information concerning some aspect of life‐style change or cardiac rehabilitation, the quality and range of information, particularly with regard to information about stress or anxiety, was frequently limited.
Instructions about seeing a general practitioner following discharge were often vague; formal rehabilitation programmes, where they existed, excluded some patients.
The study suggests that much patient education is dependent on the provision of written information alone, and that further evaluation of the effectiveness of self‐help material supported by nursing input is desirable.
Immediate Functional Loading of Single‐Tooth TiO2 Grit‐Blasted Implant Restoration. A Controlled Prospective Study in a Porcine Model. Part II: Histology and Histomorphometry
Authors: Bousdras Vasilios A. , Walboomers Frank , Jansen John A. , Cunningham James L. , Blunn Gordon , Petrie Aviva , Jaecques Siegfried , Naert Ignace E. , Sindet‐Pedersen Steen , Goodship Allen E. 
Published: November 2007

ABSTRACTBackground:  Evidently, there is a fast‐moving shift from delayed to immediate implant loading. The hypothesis to be tested was that bone reactions adjacent to single TiO2‐microthreaded implants exposed to immediate masticatory loading for 10 weeks after placement would modulate osseointegration.Materials and Methods:  Cylindrical‐ and tapered‐designed implants (Astra Tech AB, Mölndal, Sweden) replaced first and third mandibular premolars respectively in 12 pigs. The animals were allocated into two groups based on soft and hard diet feeding. Each animal received, at random positions, four different masticatory loading conditions: implant with either (1) a cover screw only, (2) a healing abutment, (3) an implant with a crown without occlusal contact, or (4) an implant with a crown in contact with the antagonistic teeth.Results:  Histomorphometry showed that there were no statistically significant differences in bone‐implant contact (BIC), bone mass inside/outside of the threads and soft tissue ingrowth ratio for all the implants at 10 weeks after placement irrespective of masticatory loading condition. Bone loss showed a trend of progressive increase for implants with a healing abutment toward implants with occlusal contact.Conclusions:  The results of this study rejected the hypothesis and could be explained by the fact that grit‐blasted acid‐etched implants were already placed in dense bone.
DETECTION OF MULTIDRUG‐RESISTANT SALMONELLA TYPHIMURIUM DT104 IN POULTRY BY SELECTIVE ENRICHMENT AND CLOTH‐BASED HYBRIDIZATION ARRAY SYSTEM
Authors: BLAIS BURTON W. , MARTINEZ‐PEREZ AMALIA , LEGGATE JOHANNA , GAUTHIER MARTINE 
Published: November 2007

ABSTRACT A rapid method was devised for the selective enrichment and detection of multi‐antibiotic‐resistant Salmonella enterica subsp. enterica serotype Typhimurium (S. Typhimurium) DT104 in poultry. The target organism was pre‐enriched in trypticase soy broth supplemented with chloramphenicol, followed by plating on modified semisolid Rappaport Vassiliadis medium and sampling a portion of the swarming growth. The presence of S. Typhimurium DT104 was determined by testing the growth using a cloth‐based hybridization array system (CHAS) targeting antibiotic resistance and other marker genes associated with this organism. In this CHAS, a multiplex polymerase chain reaction incorporating digoxigenin–dUTP was used to simultaneously amplify seven target gene sequences, with subsequent rapid detection of the amplicons by hybridization with an array of probes immobilized on polyester cloth and immunoenzymatic assay of the bound label. This procedure permitted the rapid determination of S. Typhimurium DT104 in chicken carcass rinse, powdered egg and feed samples inoculated with different levels of the target organism.PRACTICAL APPLICATIONSThe combined selective enrichment and CHAS procedure will enable the rapid screening of poultry and related products for the presence of multidrug resistant Salmonella Typhimurium DT104. The convenience of this approach lies in the fact that samples containing salmonellae requiring more comprehensive analysis can be rapidly identified on the basis of a simple preliminary enrichment procedure involving examination of MSRV plating media for characteristic swarming growth. The swarming growth is readily sampled and analyzed by the DT104 CHAS to determine the presence of key marker genes associated with the multidrug resistant pathogen, obviating the need for time‐ and labor‐consuming conventional purification and antimicrobial susceptibility testing procedures.
AUTOMATIC AND RAPID MEASUREMENT OF MICROBIAL SUSPENSION GROWTH PARAMETERS: APPLICATION TO THE EVALUATION OF EFFECTOR AGENTS
Authors: ELLISON W.J. , PEDARROS‐CAUBET F. , CAUBET R. 
Published: November 2007

ABSTRACT Traditional methods of assessing antimicrobial agents give little information about the quantitative effect of an inhibitor or stimulator (effector) upon the growth parameters of microbial suspension. Current methods using conductance and light absorption data have lightened the workload, but they do not go beyond determining the exponential growth rate. We have developed mathematical models which, when combined with data provided by these rapid methods, measure the quantitative effect of an antimicrobial agent upon five characteristic growth parameters of a suspension: adaptation time, specific reduction rate during the adaptation phase, exponential growth rate, maximum cell concentration and specific reduction rate during the stationary phase. In addition, our methods can measure the instantaneous growth rate. This allows real‐time studies of the effect of chemical or physical stresses upon subsequent microbial growth. We illustrate some of the applications with examples taken from studies of the antimicrobial effects of certain essential oils and spices upon bacterial suspensions.
MEASUREMENT OF MECHANICAL PROPERTIES OF COEXTRUDED DUAL‐PHASE PRODUCTS
Authors: SAMUEL LALITHA , DOGAN HULYA , MCGRANE SCOTT , KOKINI JOZEF L. 
Published: November 2007

ABSTRACT This study focused on developing and validating a comprehensive, objective and robust methodology for the textural characterization of coextruded dual‐phase products. Uniaxial compression and penetration tests were done to measure the mechanical properties of the different phases, the shell and the filler on whole dual‐phase products. The resulting force deformation curves were used to derive quantitative measures for the textural properties of the shell and the filler phases of the products. Among the techniques used for textural characterization, penetration tests with a punch probe gave the most reliable, reproducible and comprehensive mechanical characterization of the dual‐phase products. Textural parameters corresponding to the shell and filler were hardness, energy required to shear through the individual phases (toughness) and the elasticity of the shell. The developed methodology was first tested with model materials, whose mechanical properties are well known, and then validated using dual‐phase products available commercially for human and pet consumption. PRACTICAL APPLICATIONSDual‐texture products utilizing extrusion are commercially available with a crunchy exterior shell and a soft viscous filler inside the shell. A method was developed in this study using a penetration probe to assess the quality of dual‐texture extruded products. The developed method works on model systems and commercially available samples.
Effects of neuromuscular electrical stimulation of the knee extensor muscles on muscle soreness and different serum parameters in young male athletes: preliminary data
Authors: Zorn Carina , Szekeres Thomas , Keilani Mohammad , Fialka-Moser Veronika , Crevenna Richard 
Published: November 2007

Aim:To evaluate the effects of neuromuscular electrical stimulation (NMES) on muscle soreness and on a variety of serum parameters during and after NMES of knee extensor muscles of young, well trained subjects over a study period of 96 h.Methods:Five male cyclists were included in this clinical observation. NMES (biphasic, asymmetric impulses) was applied through surface electrodes to both knee extensor muscles of each subject for 30 min. To determine changes in serum concentration of muscle proteins, blood samples were drawn at defined measure points before and after NMES. Muscle soreness was evaluated using a visual analogue scale at all measure points.Results:There was a maximum (p<0.05) for “muscle pain” during stimulation but no significant changes could be detected after the stimulation period. Serum creatine kinase showed a peak with a significant increase (p<0.05) 24 h after NMES. Serum lactate levels only increased slightly (p = 0.08) during NMES.Conclusions:Although the changes of blood parameters measured in the present work correspond to those reported in the literature on eccentric strength training, no delayed onset muscle pain could be detected. Further studies should be carried out, also investigating different stimulation protocols in non-trained healthy subjects and in patients with less muscle mass.
Gene array identification of Ipf1/Pdx1-/-regulated genes in pancreatic progenitor cells
Authors: Svensson Per , Williams Cecilia , Lundeberg Joakim , Rydén Patrik , Bergqvist Ingela , Edlund Helena 
Published: November 2007

Abstract

Background
The homeodomain transcription factor IPF1/PDX1 exerts a dual role in the pancreas; Ipf1/Pdx1 global null mutants fail to develop a pancreas whereas conditional inactivation of Ipf1/Pdx1 in β-cells leads to impaired β-cell function and diabetes. Although several putative target genes have been linked to the β-cell function of Ipf1/Pdx1, relatively little is known with respect to genes regulated by IPF1/PDX1 in early pancreatic progenitor cells.

Results
Microarray analyses identified a total of 111 genes that were differentially expressed in e10.5 pancreatic buds of Ipf1/Pdx1
-/- embryos. The expression of one of these, Spondin 1, which encodes an extracellular matrix protein, has not previously been described in the pancreas. Quantitative real-time RT-PCR analyses and immunohistochemical analyses also revealed that the expression of FgfR2IIIb, that encodes the receptor for FGF10, was down-regulated in Ipf1/Pdx1
-/- pancreatic progenitor cells.

Conclusion
This microarray analysis has identified a number of candidate genes that are differentially expressed in Ipf1/Pdx1
-/- pancreatic buds. Several of the differentially expressed genes were known to be important for pancreatic progenitor cell proliferation and differentiation whereas others have not previously been associated with pancreatic development.
An accurate method for quantifying and analyzing copy number variation in porcine KIT by an oligonucleotide ligation assay
Authors: Seo Bo-Young , Park Eung-Woo , Ahn Sung-Jin , Lee Sang-Ho , Kim Jae-Hwan , Im Hyun-Tae , Lee Jun-Heon , Cho In-Cheol , Kong Il-Keun , Jeon Jin-Tae 
Published: November 2007

Abstract

Background
Aside from single nucleotide polymorphisms, copy number variations (CNVs) are the most important factors in susceptibility to genetic disorders because they affect expression levels of genes. In previous studies, pyrosequencing, mini-sequencing, real-time PCR, invader assays and other techniques have been used to detect CNVs. However, the higher the copy number in a genome, the more difficult it is to resolve the copies, so a more accurate method for measuring CNVs and assigning genotype is needed.

Results
PCR followed by a quantitative oligonucleotide ligation assay (qOLA) was developed for quantifying CNVs. The accuracy and precision of the assay were evaluated for porcine KIT, which was selected as a model locus. Overall, the root mean squares of bias and standard deviation of qOLA were 2.09 and 0.45, respectively. These values are less than half of those in the published pyrosequencing assay for analyzing CNV in porcine KIT. Using a combined method of qOLA and another pyrosequencing for quantitative analysis of KIT copies with spliced forms, we confirmed the segregation of KIT alleles in 145 F1 animals with pedigree information and verified the correct assignment of genotypes. In a diagnostic test on 100 randomly sampled commercial pigs, there was perfect agreement between the genotypes obtained by grouping observations on a scatter plot and by clustering using the nearest centroid sorting method implemented in PROC FASTCLUS of the SAS package. In a test on 159 Large White pigs, there were only two discrepancies between genotypes assigned by the two clustering methods (98.7% agreement), confirming that the quantitative ligation assay established here makes genotyping possible through the accurate measurement of high KIT copy numbers (>4 per diploid genome). Moreover, the assay is sensitive enough for use on DNA from hair follicles, indicating that DNA from various sources could be used.

Conclusion
We have established a high resolution quantification method using an oligonucleotide ligation assay to measure CNVs, and verified the reliability of genotype assignment for random animal samples using the nearest centroid sorting method. This new method will make it more practical to determine KIT CNV and to genotype the complicated Dominant White/KIT locus in pigs. This procedure could have wide applications for studying gene or segment CNVs in other species.