bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of locally stable RNA secondary structures for genome-wide surveys
Authors: Hofacker I. L. , Priwitzer B. , Stadler P. F.
Published: January 2004

Motivation: Recently novel classes of functional RNAs, most prominently the miRNAs have been discovered, strongly suggesting that further types of functional RNAs are still hidden in the recently completed genomic DNA sequences. Only few techniques are known, however, to survey genomes for such RNA genes. When sufficiently similar sequences are not available for comparative approaches the only known remedy is to search directly for structural features.

Results: We present here efficient algorithms for computing locally stable RNA structures at genome-wide scales. Both the minimum energy structure and the complete matrix of base pairing probabilities can be computed in 𝒪(N × L2) time and 𝒪(N + L2) memory in terms of the length N of the genome and the size L of the largest secondary structure motifs of interest. In practice, the 100 Mb of the complete genome of Caenorhabditis elegans can be folded within about half a day on a modern PC with a search depth of L = 100. This is sufficient example for a survey for miRNAs.

Availability: The software described in this contribution will be available for download at http://www.tbi.univie.ac.at/~ivo/RNA/ as part of the Vienna RNA Package.
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network
Authors: Wren Jonathan D. , Garner Harold R.
Published: January 2004

Motivation: There is a general scientific need to be able to identify and evaluate what any given set of ‘objects’ (e.g. genes, phenotypes, chemicals, diseases) has in common. Whether it is to classify, expand upon or identify commonalities and functional groupings, informational needs can be diverse and the best source to identify relationships among a potentially heterogeneous set of objects is the scientific literature.

Results: We first establish a network of related objects by their co-occurrence within MEDLINE records. A set of objects within this network can then be queried to identify shared relationships, and a method is presented to score their statistical relevance by comparing observed frequencies with what would be expected in a random network model. Using Gene Ontology (GO) categories, we demonstrate that this method enables a quantitative ranking of the ‘cohesiveness’ of a set of objects and, importantly, allows other objects related to this set to be identified and evaluated for their ‘cohesion’ to it.

Supplemental information: A list of ranked genes related to each GO category analyzed can be found at http://innovation.swmed.edu/IRIDESCENT/GO_relationships.htm
Comparative evaluation of word composition distances for the recognition of SCOP relationships
Authors: Vinga Susana , Gouveia-Oliveira Rodrigo , Almeida Jonas S.
Published: January 2004

Motivation: Alignment-free metrics were recently reviewed by the authors, but have not until now been object of a comparative study. This paper compares the classification accuracy of word composition metrics therein reviewed. It also presents a new distance definition between protein sequences, the W-metric, which bridges between alignment metrics, such as scores produced by the Smith–Waterman algorithm, and methods based solely in L-tuple composition, such as Euclidean distance and Information content.

Results: The comparative study reported here used the SCOP/ASTRAL protein structure hierarchical database and accessed the discriminant value of alternative sequence dissimilarity measures by calculating areas under the Receiver Operating Characteristic curves. Although alignment methods resulted in very good classification accuracy at family and superfamily levels, alignment-free distances, in particular Standard Euclidean Distance, are as good as alignment algorithms when sequence similarity is smaller, such as for recognition of fold or class relationships. This observation justifies its advantageous use to pre-filter homologous proteins since word statistics techniques are computed much faster than the alignment methods.

Availability: All MATLAB code used to generate the data is available upon request to the authors. Additional material available at http://bioinformatics.musc.edu/wmetric
GAPSCORE: finding gene and protein names one word at a time
Authors: Chang Jeffrey T. , Schütze Hinrich , Altman Russ B.
Published: January 2004

Motivation: New high-throughput technologies have accelerated the accumulation of knowledge about genes and proteins. However, much knowledge is still stored as written natural language text. Therefore, we have developed a new method, GAPSCORE, to identify gene and protein names in text. GAPSCORE scores words based on a statistical model of gene names that quantifies their appearance, morphology and context.

Results: We evaluated GAPSCORE against the Yapex data set and achieved an F-score of 82.5% (83.3% recall, 81.5% precision) for partial matches and 57.6% (58.5% recall, 56.7% precision) for exact matches. Since the method is statistical, users can choose score cutoffs that adjust the performance according to their needs.

Availability: GAPSCORE is available at http://bionlp.stanford.edu/gapscore/
An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments
Authors: Datta Susmita , Satten Glen A. , Benos Dale J. , Xia Jiazeng , Heslin Martin J. , Datta Somnath
Published: January 2004

Motivation: Detection of differentially expressed genes is one of the major goals of microarray experiments. Pairwise comparison for each gene is not appropriate without controlling the overall (experimentwise) type 1 error rate. Dudoit et al. have advocated use of permutation-based step-down P-value adjustments to correct the observed significance levels for the individual (i.e. for each gene) two sample t-tests.

Results: In this paper, we consider an ANOVA formulation of the gene expression levels corresponding to multiple tissue types. We provide resampling-based step-down adjustments to correct the observed significance levels for the individual ANOVA t-tests for each gene and for each pair of tissue type comparisons. More importantly, we introduce a novel empirical Bayes adjustment to the t-test statistics that can be incorporated into the step-down procedure. Using simulated data, we show that the empirical Bayes adjustment improved the sensitivity of detecting differentially expressed genes up to 16%, while maintaining a high level of specificity. This adjustment also reduces the false non-discovery rate to some degree at the cost of a modest increase in the false discovery rate. We illustrate our approach using a human colon cancer dataset consisting of oligonucleotide arrays of normal, adenoma and carcinoma cells. The number of genes with differential expression level declared statistically significant was about 50 when comparing normal to adenoma cells and about five when comparing adenoma to carcinoma cells. This list includes genes previously known to be associated with colon cancer as well as some novel genes.

Availability: R code for the empirical Bayes adjustment and step-down P-value calculation via resampling are available from the supplementary web-site.

Supplementary information:  http://www.mathstat.gsu.edu/~matsnd/EB/supp.htm
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
Authors: Crass T. , Antes I. , Basekow R. , Bork P. , Buning C. , Christensen M. , Claußen H. , Ebeling C. , Ernst P. , Gailus-Durner V. , Glatting K.-H. , Gohla R. , Gößling F. , Grote K. , Heidtke K. , Herrmann A. , O'Keeffe S. , Kießlich O. , Kolibal S. , Korbel J. O. , Lengauer T. , Liebich I. , van der Linden M. , Luz H. , Meissner K. , von Mering C. , Mevissen H.-T. , Mewes H.-W. , Michael H. , Mokrejs M. , Müller T. , Pospisil H. , Rarey M. , Reich J. G. , Schneider R. , Schomburg D. , Schulze-Kremer S. , Schwarzer K. , Sommer I. , Springstubbe S. , Suhai S. , Thoppae G. , Vingron M. , Warfsmann J. , Werner T. , Wetzler D. , Wingender E. , Zimmer R.
Published: January 2004

Summary: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The ‘Guided Solution Finder’ which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades (‘tasks’), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided.

Availability: The HNB portal is available at http://www.hnbioinfo.de
Is cross-validation better than resubstitution for ranking genes?
Authors: Braga-Neto Ulisses , Hashimoto Ronaldo , Dougherty Edward R. , Nguyen Danh V. , Carroll Raymond J.
Published: January 2004

Motivation: Ranking gene feature sets is a key issue for both phenotype classification, for instance, tumor classification in a DNA microarray experiment, and prediction in the context of genetic regulatory networks. Two broad methods are available to estimate the error (misclassification rate) of a classifier. Resubstitution fits a single classifier to the data, and applies this classifier in turn to each data observation. Cross-validation (in leave-one-out form) removes each observation in turn, constructs the classifier, and then computes whether this leave-one-out classifier correctly classifies the deleted observation. Resubstitution typically underestimates classifier error, severely so in many cases. Cross-validation has the advantage of producing an effectively unbiased error estimate, but the estimate is highly variable. In many applications it is not the misclassification rate per se that is of interest, but rather the construction of gene sets that have the potential to classify or predict. Hence, one needs to rank feature sets based on their performance.

Results: A model-based approach is used to compare the ranking performances of resubstitution and cross-validation for classification based on real-valued feature sets and for prediction in the context of probabilistic Boolean networks (PBNs). For classification, a Gaussian model is considered, along with classification via linear discriminant analysis and the 3-nearest-neighbor classification rule. Prediction is examined in the steady-distribution of a PBN. Three metrics are proposed to compare feature-set ranking based on error estimation with ranking based on the true error, which is known owing to the model-based approach. In all cases, resubstitution is competitive with cross-validation relative to ranking accuracy. This is in addition to the enormous savings in computation time afforded by resubstitution.
Formalization of mouse embryo anatomy
Authors: Burger Albert , Davidson Duncan , Baldock Richard
Published: January 2004

Motivation: The Edinburgh Mouse Atlas and Gene Expression Database project has developed a digital atlas of mouse development to provide a spatio-temporal framework for spatially mapped data such as in situ gene expression and cell lineage. As part of this database, a mouse embryo anatomy ontology has been created. A formalization of this anatomy is required to document its precise semantics and how it is used in the context of the Mouse Atlas.

Results: The paper describes the existing anatomy ontology and formalizes aspects of it using a predicate logic based approach. It therefore provides a guide for users of the current version of the ontology, as well as the basis for a description of the anatomy using an ontology language, such as OWL, thus enabling future work on reasoning about the Mouse Atlas in the context of an intelligent gene expression bioinformatics workflow system. The logic has been implemented in a Prolog prototype.

Availability: The Mouse Atlas is available on-line at http://genex.hgu.mrc.ac.uk
ROSO: optimizing oligonucleotide probes for microarrays
Authors: Reymond Nancie , Charles Hubert , Duret Laurent , Calevro Federica , Beslon Guillaume , Fayard Jean-Michel
Published: January 2004

Summary: ROSO is software to design optimal oligonucleotide probe sets for microarrays. Selected probes show no significant cross-hybridization, no stable secondary structures and their Tm are chosen to minimize the Tm variability of the probe set.

Availability: The program is available on the internet. Sources are freely available, for non-profit use, on request to the authors.

Supplementary information:  http://pbil.univ-lyon1.fr/roso
LVB: parsimony and simulated annealing in the search for phylogenetic trees
Authors: Barker D.
Published: January 2004

Summary: The program LVB seeks parsimonious phylogenies from nucleotide alignments, using the simulated annealing heuristic. LVB runs fast and gives high quality results.

Availability: The software is available at http://www.rubic.reading.ac.uk/lvb/

Supplementary information: Supplementary information may be downloaded from http://www.rubic.reading.ac.uk/~daniel/
JDotter: a Java interface to multiple dotplots generated by dotter
Authors: Brodie Ryan , Roper Rachel L. , Upton Chris
Published: January 2004

Summary: Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client–server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization.

Availability: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location.

Supplementary information: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.
EST-PAGE—managing and analyzing EST data
Authors: Matukumalli Lakshmi K. , Grefenstette John J. , Sonstegard Tad S. , Van Tassell Curtis P.
Published: January 2004

Summary: EST-PAGE provides a bioinformatics solution for expressed sequence tags (EST) data entry, database management, GenBank submission, process control and data retrieval from a unified web interface that can be easily customized and adapted by groups working on diverse EST sequencing projects.

Availability: The system and source code are available upon request from the authors.

Supplementary information:  http://EST-PAGE.binf.gmu.edu
APE: Analyses of Phylogenetics and Evolution in R language
Authors: Paradis Emmanuel , Claude Julien , Strimmer Korbinian
Published: January 2004

Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes.

Availability: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
AnaGram: protein function assignment
Authors: Pérez A. J. , Thode G. , Trelles O.
Published: January 2004

Summary: AnaGram is a web service for protein function assignment based on identity detection of small significant fragments (protomotifs) that can act as modular pieces in peptide construction. The system is able to assign function by finding correlations between protomotifs and functional annotations contained in SWISS-PROT and Medline databases. In addition, function ontologies are used for hierarchical organization of the predicted functions. Extensive tests have been carried out to evaluate the accuracy and performance of the system.

Availability:  http://jaguar.genetica.uma.es/anagram.htm
Transposable element annotation of the rice genome
Authors: Juretic Nikoleta , Bureau Thomas E. , Bruskiewich Richard M.
Published: January 2004

Motivation: The high content of repetitive sequences in the genomes of many higher eukaryotes renders the task of annotating them computationally intensive. Presently, the only widely accepted method of searching and annotating transposable elements (TEs) in large genomic sequences is the use of the RepeatMasker program, which identifies new copies of TEs by pairwise sequence comparisons with a library of known TEs. Profile hidden Markov models (HMMs) have been used successfully in discovering distant homologs of known proteins in large protein databases, but this approach has only rarely been applied to known model TE families in genomic DNA.

Results: We used a combination of computational approaches to annotate the TEs in the finished genome of Oryza sativa ssp. japonica. In this paper, we discuss the strengths and the weaknesses of the annotation methods used. These approaches included: the default configuration of RepeatMasker using cross_match, an implementation of the Smith–Waterman–Gotoh algorithm; RepeatMasker using WU-BLAST for similarity searching; and the HMMER package, used to search for TEs with profile HMMs. All the results were converted into GFF format and post-processed using a set of Perl scripts.

RepeatMasker was used in the case of most TE families. The WU-BLAST implementation of RepeatMasker was found to be manifold faster than cross_match with only a slight loss in sensitivity and was thus used to obtain the final set of data. HMMER was used in the annotation of the Mutator-like element (MULE) superfamily and the miniature inverted-repeat transposable element (MITE) polyphyletic group of families, for which large libraries of elements were available and which could be divided into well-defined families. The HMMER search algorithm was extremely slow for models over 1000 bp in length, so MULE families with members over 1000 bp long were processed with RepeatMasker instead. The main disadvantage of HMMER in this application is that, since it was developed with protein sequences in mind, it does not search the negative DNA strand. With the exception of TE families with essentially palindromic sequences, reverse complement models had to be created and run to compensate for this shortcoming. We conclude that a modification of RepeatMasker to incorporate libraries of profile HMMs in searches could improve the ability to detect degenerated copies of TEs.

Availability: The Perl scripts and TE sequences used in construction of the RepeatMasker library and the profile HMMs are available upon request.
Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome
Authors: Zhu Qingsong , Deng Youping , Vanka Phaneendra , Brown Susan J. , Muthukrishnan Subbaratnam , Kramer Karl J.
Published: January 2004

Motivation: Multiple chitinases as well as lectins closely related to them have been characterized previously from many insect species and the corresponding genes/cDNAs have been cloned. However, the identification of the entire assortment of genes for chitinase family proteins and their differences in biochemical properties have not been carried out in any individual insect species. The completion of the entire DNA sequence of Drosophila melanogaster (fruit fly) genome and identification of open reading frames presents an opportunity to study the structures and functions of chitinase-like proteins, and also to identify new members of this family in Drosophila. We are, therefore, interested in studying the functional genomics of chitinase-like gene families in insects.

Methods: We searched the Drosophila protein sequences database using fully characterized insect chitinase sequences and BLASTP software, identified all the putative chitinase-like proteins encoded in Drosophila genome, and predicted their structures using domain analysis tools. A phylogenetic analysis of the chitinase-like proteins from Drosophila and several other insect species was carried out. The structures of these chitinases were modeled using homology modeling software.

Results: Our analysis revealed the presence of 18 chitinase-like proteins in the Drosophila protein database. Among these are seven novel chitinase-like proteins that contain four signature amino acid sequences of chitinases belonging to family 18 glycosylhydrolases, including both acidic and hydrophobic amino acid residues critical for enzyme activity. All the proteins contain at least one catalytic domain with one having four catalytic domains. Phylogenetic analysis of chitinase-like proteins from Drosophila and other insects revealed an evolutionary relationship among all these proteins, which indicated gene duplication and domain shuffling to generate the observed diversity in the encoded proteins. Homology modeling showed that all the Drosophila chitinase-like proteins contain one or more catalytic domains with a (α/β)8 barrel-like structure. Our results suggest that insects utilize multiple family 18 chitinolytic enzymes and also non-enzymatic chitinase-like proteins for degrading/remodeling/binding to chitin in different insect anatomical extracellular structures, such as the cuticle, peritrophic membrane, trachea and mouth parts during insect development, and possibly for other roles including chitin synthesis.

Availability: Perl program and supplementary material are available at http://www.ksu.edu/bioinformatics/supplementary.htm
Phylogenomic inference of protein molecular function: advances and challenges
Authors: Sjölander Kimmen
Published: January 2004

Motivation: Protein families evolve a multiplicity of functions through gene duplication, speciation and other processes. As a number of studies have shown, standard methods of protein function prediction produce systematic errors on these data. Phylogenomic analysis—combining phylogenetic tree construction, integration of experimental data and differentiation of orthologs and paralogs—has been proposed to address these errors and improve the accuracy of functional classification. The explicit integration of structure prediction and analysis in this framework, which we call structural phylogenomics, provides additional insights into protein superfamily evolution.

Results: Results of protein functional classification using phylogenomic analysis show fewer expected false positives overall than when pairwise methods of functional classification are employed. We present an overview of the motivations and fundamental principles of phylogenomic analysis, new methods developed for the key tasks, benchmark datasets for these tasks (when available) and suggest procedures to increase accuracy. We also discuss some of the methods used in the Celera Genomics high-throughput phylogenomic classification of the human genome.

Availability: Software tools from the Berkeley Phylogenomics Group are available at http://phylogenomics.berkeley.edu
Burns as a Complication of the Use of Diathermy
Authors: Vedovato J. W. , Pólvora V. P. , Leonardi D. F.
Published: January 2004

Surgical diathermy is an invaluable aid in modern surgery, and most contemporary diathermy machines are considered safe. The literature has proven to be very sparse in terms of reference to complications, although prolonged courses of treatment are required in individual cases. We report a case of burns that occurred during a saphenous vein coronary bypass graft caused by the inadequate use of the electrosurgical materials. Care should be taken in the use of these resources to avoid complications of this kind.
The Circle of Safety: A Campfire Burn Prevention Campaign Expanding Nationwide
Authors: Maguiña Pirko , Palmieri Tina L. , Curri Terese , Nelson Kate , Greenhalgh David G.
Published: January 2004

Camping is a popular family activity, especially during the spring and summer months. Campfires are a common activity among campers. They offer a source of recreation but also pose a risk for severe burns. The rising number of children with campfire burns seen at our institution triggered a quest for a campaign for the prevention of these injuries. A chart review was performed to study the characteristics and the circumstances of burn injuries of all children treated for campfire-related injuries over a 4-year period between 1997 and 2001. Thirty-two children sustained campfire-related burn injuries, with 88% being under the age of 7. The children had either fallen into the campfire or walked into simmering coals. All accidents would have been prevented if the children had kept a safe distance from the campfire. Normal growth charts were used to determine the average height of 7-year-old children as being 48 inches. A campaign was started to encourage families to keep a safe distance of 4 feet from their campfires by drawing a “circle of safety” with a stick on the ground 4 feet away from the fire.
Management of Postburn Recalcitrant Knee Ulcers in Pediatric Patients
Authors: Dhanraj Prema , Asuku Malachy , Oh Seunghee , McCauley Robert L.
Published: January 2004

The sequelae of severe lower-extremity burn injuries in children include ulcerations and unstable scars of the anterior knee. Although the weight-bearing and ambulatory demands on this joint predispose the ulcers to chronicity, recalcitrance to treatment in the absence of systemic factors may be indicative of the presence of less-than-optimal local factors mitigating against healing. In our experience, excessive skin tightness around the knee joint has played a key role in this respect. This retrospective study on 10 patients with 16 recalcitrant knee ulcers demonstrated the inadequacy of the traditional treatment approach of ulcer excision and grafting. However, incisional release of tight skin above the knee joint and resurfacing the defect with split-thickness skin graft (mean size, 118.26 ± 35.32 cm2) eliminated excessive tension and allowed the ulcers to heal spontaneously and permanently. We found this approach useful in select patients, and we are favorably disposed to additional releasing incision and grafting if the need arises in the growing child.
Shedding the Layers: Exploring the Impact of the Burn Camp Experience on Adolescent Campers' Body Image
Authors: Cox Ellen R. , Call Serena B. , Williams Nancy R. , Reeves Patricia M.
Published: January 2004

The purpose of this qualitative study was to explore the impact of the burn camp experience, as it relates to body image, on participating burn-injured adolescents. Focus groups were conducted with 52 burn-injured adolescents at three burn camps in geographically diverse regions of the United States. Data revealed that burn camp is a place where these adolescents feel a sense of belonging and acceptance, a place where they don't have to hide their bodies, and a place where they can learn to integrate their scars into their overall body image in a positive way. Implications of this study include highlighting the contributions that burn camps may provide in helping burn-injured adolescents learn to cope with the devastating disfigurements that often accompany their injuries.
Burn Pain and Anxiety: The Use of Music Relaxation During Rehabilitation
Authors: Ferguson S. L. , Voll K. V.
Published: January 2004

Pain and anxiety are well-documented problems during the rehabilitation of patients with burns. This study examined the effect of music on anxiety and pain during range of motion. Eleven subjects with partial-thickness or deeper burns were randomly assigned to a control group (without music intervention) or experimental group (with music intervention). Vital signs, pain, and anxiety were recorded before and after treatments. There was no difference in pretest and posttest anxiety across the groups; however, there was a difference in anxiety between the groups. Conversely, there was a difference in pretest and posttest pain across the groups but no difference in pain between the groups. Results showed no significant reduction in anxiety and pain during therapy with music relaxation. Limitations included nonhomogenous groups, small sample size, potentially unrepresentative sample, variation in exercise protocol, and small musical selection. Further research is recommended.
THE 2003 CLINICAL RESEARCH AWARD
Authors: Lawrence John W. , Fauerbach James A. , Heinberg Leslie , Doctor Marion
Published: January 2004

This study examined the relationship among burn scarring, severity and visibility, and body esteem. Previous work addressing this question has relied on case studies and small samples. We mailed a survey to 2500 members of a national burn survivor support group. Survivors were asked to complete and return the mailed survey or complete the survey on line at our Web site. Three hundred sixty-one survivors completed all questionnaires in the survey relevant to this study, which included measures of burn characteristics, social stigmatization, social support, depression, and body esteem. The sample characteristics were as follows: 52% were women, the mean age was 44.1 years, the mean age burned was 26 years, 88% were European American, 5% were African American, 4% were multiracial, 3% were other, the average TBSA was 48%, and the mean educational level was high school graduate. We measured scar visibility by asking survivors to rate “how often are your burn scars visible to others” on a six-point scale. We also asked them to rate the presence or absence of scars on 15 body parts, total TBSA, and number of surgeries. The correlation between visible scarring and different aspects of body esteem, that is, self-satisfaction with appearance (−.19) and perception of others reaction to your appearance (−.27), was statistically significant but low. Visible scarring was unrelated to self-satisfaction with weight (.01). Visible scarring had a low but significant correlation with perceived stigmatization (.23) and was not correlated with depression (0.01). Other measures of scarring also had low correlations with social and emotional outcome variables. Because scar severity and visibility are hypothesized to be particularly relevant to body esteem, we performed a multiple regression predicting body esteem. We entered the variables in three blocks: burn characteristics, demographic characteristics, and social and emotional characteristics. Burn characteristics accounted for less than 20% of the variance. R square for the final equation equaled .62, with social adjustment and depression accounting for the largest portion of the variance. In this sample, burn scar visibility and severity did not have a strong relationship with social and emotional adjustment variables. More effort must be placed into developing psychosocial interventions that help survivors accept scars, reduce depression, and build a strong loving support system.
Contact Palm Burns in Toddlers from Glass Enclosed Fireplaces
Authors: Dunst C. M. , Scott E. C. , Kraatz J. J. , Anderson P. M. , Twomey J. A. , Peltier G. L.
Published: January 2004

We have seen an alarming increase in the incidence of pediatric palm burns associated with gas fireplaces. The increasing popularity of these units places more children at risk. Medical records of patients under the age of 5 years who sustained hand burns from contact with the glass enclosure of gas fireplaces from 1996 through 2002 were reviewed. Thirty-nine patients were identified, with a mean age of 12.8 months. A 15-fold increase in incidence was observed. Thirty-three patients suffered superficial second-degree burns that were treated conservatively. Twenty-one percent of children developed significant wound complications requiring intensive therapy including extension splinting or surgery. Pediatric burns resulting from palmar contact with the glass enclosures of gas fireplaces have emerged as an avoidable new danger within the home. Although most of these injuries heal with conservative treatment alone, many require surgery or other intensive management to regain acceptable function.
Combination of Surgery and Intralesional Verapamil Injection in the Treatment of the Keloid
Authors: Copcu Eray , Sivrioglu Nazan , Oztan Yucel
Published: January 2004

Keloid scars are one of the most challenging problems for physicians and surgeons. These scars have been treated in many ways, with varying success. Verapamil is a widely used calcium channel antagonist, and it has been shown that calcium channel blockers inhibit the synthesis/secretion of extracellular matrix molecules, including collagen, glycosaminoglycans, and fibronectin, and increase collagenase. In this study, we performed total keloid excision in combination with reconstruction with W-plasty or skin grafting and injection of verapamil hydrochloride into the lesions of 21 patients with keloids. Patients were followed for minimum of 2 years, and the treatment outcome was evaluated based on the cosmetic appearances, symptomatic improvements, and the results of microscopic examinations. Also, patient satisfaction was scored with a visual analog scale. Two years after the operations, two patients had keloid in lesser diameter than the original lesions, two patients had lesions that were hypertrophic scars in appearance, and four patients had pruritus. One patient had keloid on the donor site. The rate of patient satisfaction was 6.4 on a scale of 1 to 10. We reviewed the treatment of keloid in this study and obtained one of the lower rates of complication in the literature. We believe that surgical excision with W-plasty or skin grafting and intralesional verapamil injection may be a good alternative in the treatment of keloid.
Digital Photography: Enhancing Communication Between Burn Therapists and Nurses
Authors: Van Lan B. , Sicotte K. M. , Lassiter R. R. , Jablonski K. A. , Crean D. A. , Jeng J. C. , Jordan M. H.
Published: January 2004

Burn rehabilitation therapists rely on nursing staff to follow through with the positioning and splinting programs. To communicate more effectively, a communication tool that consisted of digital photos and written instructions was created. Microsoft Word® and Nikon View® software were used to design the communication tool. The purpose of the study was to assess the perceived effectiveness of a communication tool between burn therapists and burn nurses for splinting and positioning. Thirty-two surveys were distributed to burn nursing staff to assess their perception of the communication tool (digital photographs with written instructions) compared with previous methods of instructions (without digital photographs). Seventy-three percent of nurses felt the communication tool with verbal instructions were the best methods of communicating splinting and positioning needs. All respondents felt that the rehabilitation staff should continue to use the communication tool.
THE 2003 CARL A. MOYER AWARD
Authors: Light T. D. , Jeng James C. , Jain A. K. , Jablonski K. A. , Kim D. E. , Phillips T. M. , Rizzo A. G. , Jordan M. H.
Published: January 2004

Real-time metabolic monitoring of varied vascular beds provides the raw data necessary to conduct ultraprecise burn shock resuscitation based on second-by-second assessment of regional tissue perfusion. It also illustrates shortcomings of current clinical practices. Arterial base deficit was continuously monitored during 11 clinical resuscitations of patients suffering burn shock using a Paratrend monitor. Separately, in a 30% TBSA rat burn model (N = 70), three Paratrend monitors simultaneously recorded arterial blood gas and tissue pCO2 of the burn wound and colonic mucosa during resuscitation at 0, 2, 4, 6, and 8 ml/kg/%TBSA. Paratrend data were analyzed in conjunction with previously reported laser Doppler images of actual burn wound capillary perfusion. With current clinical therapy, continuous monitoring of arterial base deficit revealed repetitive cycles of resolution/worsening/resolution during burn shock resuscitation. In the rat model, tissue pCO2 in both burn wounds and splanchnic circulation differed depending on the rate of fluid resuscitation (P < .01 between sham and 0 ml/kg/%TBSA and between 2 ml/kg/%TBSA and 4 ml/kg/%TBSA). Burn wound pCO2 values correlated well with laser Doppler determination of actual capillary perfusion (ρ = −.48, P < .01). The following conclusions were reached: 1) Gratuitous and repetitive ischemia-reperfusion-ischemia cycles plague current clinical therapy as demonstrated by numerous “false starts” in the resolution of arterial base deficit; 2) in a rat model, real-time monitoring of burn wound and splanchnic pCO2 demonstrate a dose-response relationship with rate of fluid administration; and 3) burn wound and splanchnic pCO2 are highly correlated with direct measurement of burn wound capillary perfusion by laser Doppler imager. Either technique can serve as a resuscitation endpoint for real-time feedback-controlled ultraprecise resuscitation.
Psychological Problems Reported by Young Adults Who Were Burned as Children
Authors: Meyer W. J. , Blakeney P. , Russell W. , Thomas C. , Robert R. , Berniger F. , Holzer C.
Published: January 2004

This study assessed long-term psychosocial sequelae of young adult pediatric burn survivors. Subjects were 101 young adults (43 females and 58 males) between the ages of 18 and 28 years who were at least 2 years (average, 14 years) postburn at least 30% TBSA (mean = 54 ± 20%). Educational status was 25% high school dropouts, 28% high school graduation only, 32% some college, and 5% completed college. Seventy-seven percent either worked or attended school; 28% had had a long-term partner. When assessed by Achenbach's Young Adult Self-Report (YASR) scale and compared with its published reference group, the males reported differences only in the somatic complaints, but the females endorsed significantly more externalizing and total problems, specifically withdrawn behaviors, somatic complaints, thought problems, aggressive behavior, and delinquent behavior. Despite these problems suffered by some female pediatric burn survivors, the overall outcome revealed that most pediatric burn survivors are making the transition into adulthood with minimal unexpected difficulty.
A methylation-mediator complex in hormone signaling
Authors: Xu Wei , Cho Helen , Kadam Shilpa , Banayo Ester M. , Anderson Scott , Yates John R. , Emerson Beverly M. , Evans Ronald M.
Published: January 2004

The recruitment of coactivators by nuclear hormone receptors (NRs) promotes transcription by subverting chromatin-mediated repression. Although the histone methylation enzyme CARM1 and an ATP-remodeling complex have been individually implicated in nuclear receptor-dependent transcription, neither a functional nor mechanistic linkage between these systems has been identified. In the process of purifying endogenous CARM1-interacting proteins, we identified an associated complex, nucleosomal methylation activator complex (NUMAC), which includes at least eight components of SWI/SNF, including the ATPase BRG1. In the NUMAC complex, the methylase, CARM1, acquires the ability to covalently modify nucleosomal histones, and the directed nucleosome versus free core histone methylation-specificity change is increased dramatically. Reciprocally, CARM1 stimulates the ATPase activity of BRG1, a key component in nucleosome remodeling. In vivo, CARM1 and BRG1 coassemble on an estrogen receptor (ER)-target gene to cooperatively activate ER-dependent transcription. This association of ATP-remodeling factors with HMT CARM1 defines a new component of regulation in the nuclear hormone-signaling pathway.
A pre-ribosome-associated HEAT-repeat protein is required for export of both ribosomal subunits
Authors: Oeffinger Marlene , Dlakić Mensur , Tollervey David
Published: January 2004

Rrp12p (Ypl012w) is unusual among characterized ribosome synthesis factors in being associated with late precursors to both the 40S and 60S subunits. Rrp12p is predominately nuclear with nucleolar enrichment at steady state, but shuttled between the nucleus and cytoplasm in a heterokaryon assay. Strains depleted of Rrp12p are impaired in the nuclear export of both ribosomal subunits. Sequence analysis combined with fold recognition and modeling showed that Rrp12p is a member of a family of pre-ribosome-associated HEAT-repeat proteins. Like other HEAT-repeat transport factors, Rrp12p binds in vitro to nucleoporin FG-repeats of both the GLFG and FXFG families and to the GTPase Gsp1p (yeast RAN). Rrp12p also showed robust in vitro binding to a pre-rRNA transcript, in addition to poly(A) and poly(U). We propose that Rrp12p binds to the RNA components of the pre-ribosomes and promotes export of both subunits via its interactions with the nucleoporins and Gsp1p.
On the space-group dispute of stibnite
Authors: Sørensen Henning Osholm , Lundegaard Lars Fahl
Published: January 2004

Violations of the systematically absent reflections in a data set of stibnite in the space groupPnmahave been shown to originate from multiple diffraction, and for a few reflections additional intensity from λ/2 radiation was found. The study was performed by measurements of the Ψ profiles for a number of reflections and comparison with the theoretical Ψ profiles.
Simultaneous refinement of structure and microstructure of layered materials
Authors: Leoni Matteo , Gualtieri Alessandro F. , Roveri Norberto
Published: January 2004

The recursive description of stacking in layered crystals, originally developed by Treacyet al.[Proc. R. Soc. London Ser. A(1991),433, 499–520] and implemented in theDIFFaXcode, is enclosed in a non-linear least-squares minimization routine and combined with additional models (of specimen-related broadening and instrumental broadening) to allow the simultaneous refinement of both structural and microstructural parameters of a layered crystal. This implementation is namedDIFFaX+. As examples, the refinements both of a simulated pattern of diamond, showing fault clustering, and of the observed powder pattern of a synthetic stoichiometric nanocrystalline chrysotile are reported.
Maximum-entropy method as a routine tool for determination of particle size distributions by small-angle scattering
Authors: Tatchev Dragomir , Kranold Rainer
Published: January 2004

Several aspects of the application of the maximum-entropy method (MEM) to the determination of particle size distributions by small-angle scattering (SAS) are discussed. The `historic' version of the MEM produces completely satisfying results. Limiting the data error from below (i.e.imposing a minimal relative error) is proposed as a solution of some convergence problems. The MEM is tested against the Fourier transform technique. The size distribution of Pb particles in an Al–Pb alloy is determined by the MEM and the Fourier transform technique. The size distributions obtained by transmission electron microscopy (TEM) and SAXS show partial agreement.
Analysis of the mutual coherence function of X-rays using dynamical diffraction
Authors: Yamazaki Hiroshi , Ishikawa Tetsuya
Published: January 2004

X-ray rocking-curve profiles for a perfect crystal are calculated using the mutual coherence function of the incident wave. The derived result is that the rocking curve to be measured should be a convolution of the intrinsic profile of the crystal reflection with the Fourier transform of the complex degree of coherence of the incident wave. This allows experimental evaluation of the complex degree of coherence from measured rocking-curve profiles with the help of the calculated intrinsic profile. The mutual coherence function of synchrotron X-rays prepared with a conventional Si double-crystal monochromator was mapped as a function of both spatial separation and time delay.
Fine-rotation attachment to standard goniometers
Authors: Suortti P. , Keyriläinen J. , Fernández M.
Published: January 2004

A new type of fine-rotation stage has been constructed and tested. It can be attached to standard goniometers used in X-ray and neutron crystallography. The device consists of a shaft and a bar that is fitted tightly to a hole traversing the shaft. The diameter of the shaft is 5 to 10 times larger than the diameter of the bar and the length of the bar is about 5 times larger than the height of the shaft. The bottom of the shaft is attached to the top plate of the goniometer and a goniometer head can be fitted to the other end of the shaft. The free end of the bar is pushed tangentially by a linear actuator to produce a torsion moment at the shaft. The dimensions and materials of the prototype were chosen such that a 1 mm bend of the bar corresponded to a torsion angle of the shaft of about 20 µrad. The rotation angle was measured using a double-crystal diffractometer in the non-dispersive setting, with MoKα1radiation from a fine-focus X-ray tube. Accurately known angular deviations were produced by refraction in a prism and the shifts in the rocking-curve position were measured. The measured torsion angle agreed within 4% with the value calculated from the elastic constants and dimensions of the device. The repeatability of the angle was ±20 nrad (0.004 arcsec).
Characterization of dislocations in protein crystals by means of synchrotron double-crystal topography
Authors: Capelle B. , Epelboin Y. , Härtwig J. , Moraleda A. B. , Otálora F. , Stojanoff V.
Published: January 2004

Hen egg-white lysozyme (HEWL) crystals have been studied by means of double-crystal synchrotron topography. The crystals reveal a number of features that are quite well known in hydrothermally grown inorganic crystals: dislocations, growth bands and growth sector boundaries. Dislocations in the 〈110〉 sectors have been characterized as edge dislocations with Burgers vector parallel to thecaxis. They are distinguishable only under weak beam conditions. The presence of edge dislocations shown in this paper is consistent with the spiral growth steps previously reported. This spiral growth on protein crystals has been observed many times by surface techniques.
Quantitative microstructural and texture characterization by X-ray diffraction of polycrystalline ferroelectric thin films
Authors: Ricote Jesús , Chateigner Daniel
Published: January 2004

Texture becomes an important issue in ferroelectric materials as it greatly influences the physical properties of polycrystalline films. The use of advanced methods of analysis of the X-ray diffraction profiles, namely quantitative texture analysis or the recently developed combined approach, allows access to quantitative information on the different components of the global texture and to more accurate values of structural and microstructural parameters of both the ferroelectric film and the substrate, not available by more conventional methods of analysis. The results obtained allow important conclusions to be drawn regarding the mechanisms that lead to the development of preferred orientations in thin films and, also, the correlation between them and the ferroelectric behaviour. For example, it is observed that the inducement of a strong 〈111〉 texture component does not mean the complete disappearance of the so-called `natural' 〈100〉, 〈001〉 components, and that the ratio between the contributions to the global texture of these two components can be changed by the presence of tensile or compressive stress during crystallization of the films. The relative contributions of these texture components are also related to the final properties of the ferroelectric films.