bluuebunny/crossref_metadata_2025_split huggingface dataset:
GENERATING MESSAGE-PASSING PROGRAMS FROM ABSTRACT SPECIFICATIONS BY PARTIAL EVALUATION
Authors: HERRMANN CHRISTOPH A. 
Published: September 2005

This paper demonstrates how parallel programs with message-passing can be generated from abstract specifications embedded in the functional language MetaOCaml. The functional style permits to design parallel programs with a high degree of parameterization, so-called skeletons. Programmers who are unexperienced in parallelism can take such skeletons for a simple and safe generation of parallel applications. Since MetaOCaml also has efficient imperative features and an MPI interface, the entire program can be written in one language, without the need to use a language interface restricting the set of data objects which could be exchanged. The semantics of abstract specifications is expressed by an interpreter written in MetaOCaml. A cost model is defined by abstract interpretation of the specification. Partial evaluation of the interpreter with a specification, a feature which MetaOCaml provides, yields a parallel program. The partial evaluation process takes time on each MPI process directly before the execution of the application program, exploiting knowledge of the number of processes, the current process identifier and the communication structure. Our example is the specification of a divide-and-conquer skeleton which is used to compute the multiplication of multi-digit numbers using Karatsuba's algorithm.
The Predictive Value of the Extensor Grip Test for the Effectiveness of Bracing for Tennis Elbow
Authors: Struijs Peter A. A. , Assendelft Willem J. J. , Kerkhoffs Gino M. M. J. , Souer Sebastiaan , van Dijk C. Niek 
Published: September 2005

Background Tennis elbow is a common complaint. Several treatment strategies, such as corticosteroid injections and physical therapy and braces, have been described. Hypothesis The extensor grip test has predictive value in assessing the effectiveness of bracing in tennis elbow. Study Design Cohort study (prognosis); Level of evidence, 1. Methods Patients with tennis elbow complaints were randomized into 3 groups: brace only, physical therapy, and combination brace and physical therapy. The extensor grip test was performed before randomization on all patients. Outcome measures at 6-week follow-up were success rate, severity of complaints, pain, disability, inconvenience during daily life, and satisfaction. Results In the brace-only group, significant differences were identified between patients with a positive test result and patients with a negative test result for 3 outcome measures. The success rate in the test-negative group was 23% (5/22) compared to 47% (21/45) in the test-positive group. Mean decrease in pain was 23 (95% confidence interval, -3 to 49) in the test-positive group compared to 11 (95% confidence interval, -6 to 28) in the test-negative group, and mean satisfaction in the test-positive group was 71 (95% confidence interval, 48 to 94) compared to 51 (95% confidence interval, 24 to 78) in the test-negative group. In the physical therapy and combination groups, no differences were identified between test-positive and test-negative patients. Conclusion The extensor grip test seems valuable as a predictive factor for the effectiveness of bracing as treatment for tennis elbow over the short term.
Contact Area, Contact Pressure, and Pressure Patterns of the Tendon-Bone Interface after Rotator Cuff Repair
Authors: Tuoheti Yilihamu , Itoi Eiji , Yamamoto Nobuyuki , Seki Nobutoshi , Abe Hidekazu , Minagawa Hiroshi , Okada Kyoji , Shimada Yoichi 
Published: September 2005

Background The contact pressure and contact area at the tendon-bone interface after the most commonly used rotator cuff repair methods have not been investigated. Hypothesis There are no significant differences among the transosseous, the single-row suture anchor, and the double-row suture anchor techniques in terms of contact pressure, contact area, and pressure patterns at the tendon-bone interface. Study Design Controlled laboratory study. Methods After creating a full-thickness supraspinatus tendon tear in 10 cadaveric shoulder specimens, we inserted pressure-sensitive film between the tendon stump and the bone, and we repaired the tear by (1) transosseous, (2) single-row suture anchor, and (3) double-row suture anchor techniques. Results The contact area of the double-row technique was 42% greater than that of the transosseous technique (P <. 0001) and 60% greater than that of the single-row technique. The contact area of the transosseous technique was 31% greater than that of the single-row technique (P =. 0015). The average pressures of the single-row and double-row techniques were 18% (P =. 014) and 16% (P =. 03) greater, respectively, than that of the transosseous technique, but there was no significant difference between the single-row and double-row techniques (P =. 915). Conclusions The double-row technique produced the greatest contact area and the second-highest contact pressure, whereas the single-row technique created the highest contact pressure and the least contact area. The transosseous technique produced the second-greatest contact area and the least contact pressure. Clinical Relevance The double-row suture anchor technique and the transosseous technique may provide a better environment for tendon healing.
Thermal Capsulorrhaphy for Isolated Posterior Instability of the Glenohumeral Joint without Labral Detachment
Authors: Bisson Leslie J. 
Published: September 2005

Background Posterior instability of the glenohumeral joint is uncommon, and a minimally invasive, technically easy method of treatment with consistent results has not been reported. Hypothesis Thermal capsulorrhaphy for posterior instability with a period of postoperative immobilization will satisfactorily reestablish shoulder stability. Study Design Case series; Level of evidence, 4. Methods A total of 15 shoulders (13 patients) with isolated posterior instability without labral detachment were treated with thermal capsulorrhaphy. Eleven shoulders were immobilized for 6 weeks after surgery; 14 shoulders were clinically evaluated at a mean of 36 months (range, 26-53 months) after surgery. Of these patients, 2 (3 shoulders) had declined postoperative immobilization. Results Eleven shoulders were rated as excellent or good, and 3 experienced recurrent instability and were considered failures. The 3 failures occurred in 1 of 11 shoulders that were immobilized and 2 of 3 (in the same patient) that were not immobilized postoperatively. Conclusion Thermal capsulorrhaphy for posterior instability of the glenohumeral joint, followed by 6 weeks of postoperative immobilization, restored glenohumeral stability in this group of patients.
Long-term Outcome for Large Meniscal Defects Treated with Small Intestinal Submucosa in a Dog Model
Authors: Cook James L. , Fox Derek B. , Malaviya Prasanna , Tomlinson James L. , Kuroki Keiichi , Cook Cristi Reeves , Kladakis Stephanie 
Published: September 2005

Background Large meniscal defects are a common problem for which current treatment options are limited. Hypothesis Treatment of posterior medial meniscal defects in dogs with small intestinal submucosa is superior to partial meniscectomy in terms of clinical limb function, chondroprotection, and amount and type of new tissue in the defect. Study Design Controlled laboratory study. Methods A total of 51 mongrel dogs underwent medial arthrotomy with creation of standardized meniscal defects. The dogs were divided into groups based on defect treatment: small intestinal submucosa meniscal implant (n = 29) or meniscectomy (n = 22). The dogs were assessed for lameness by subjective scoring after surgery and sacrificed at 3, 6, or 12 months and assessed for articular cartilage damage, gross and histologic appearance of the operated meniscus, amount of new tissue in the defect, equilibrium compressive modulus of meniscal tissue, and relative compressive stiffness of articular cartilage. Results Dogs in the meniscectomy groups were significantly (P <. 001) more lame than dogs treated with small intestinal submucosa. Joints treated with small intestinal submucosa had significantly (P <. 001) less articular cartilage damage, based on india ink staining, than did those treated with meniscectomy. Menisci receiving small intestinal submucosa had more tissue filling in the defects than did menisci receiving no implants, and this new tissue was more mature and meniscus-like and better integrated with remaining meniscus. Conclusion Small intestinal submucosa scaffolds placed in large meniscal defects resulted in production of meniscus-like replacement tissue, which was consistently superior to meniscectomy in amount, type, and integration of new tissue; chondroprotection; and limb function in the long term. Clinical Relevance Small intestinal submucosa implants might be useful for treatment of large posterior vascular meniscal defects in humans.
Pivotal role of PAI-1 in a murine model of hepatic vein thrombosis
Authors: Smith Layton H. , Dixon John D. , Stringham John R. , Eren Mesut , Elokdah Hassan , Crandall Dave L. , Washington Kay , Vaughan Douglas E. 
Published: September 2005

Abstract
Hepatic veno-occlusive disease (VOD) is a common complication of high-dose chemotherapy associated with bone marrow transplantation. While the pathogenesis of VOD is uncertain, plasminogen activator inhibitor-1 (PAI-1) has emerged as a diagnostic marker and predictor of VOD in humans. In this study, we investigated the role of PAI-1 in a murine model of VOD produced by long-term nitric oxide synthase inhibition using L-NAME. After 6 weeks, wild-type (WT) mice developed extensive fibrinoid hepatic venous thrombi and biochemical evidence of hepatic injury and dysfunction. In contrast, PAI-1–deficient mice were largely protected from the development of hepatic vein thrombosis. Furthermore, WT mice that received tiplaxtinin, an antagonist of PAI-1, were effectively protected from L-NAME–induced thrombosis. Taken together, these data indicate that NO and PAI-1 play pivotal and antagonistic roles in hepatic vein thrombosis and that PAI-1 is a potential target in the prevention and treatment of VOD in humans.
Interaction between human lung fibroblasts and T-lymphocytes prevents activation of CD4+ cells
Authors: Vancheri Carlo , Mastruzzo Claudio , Trovato-Salinaro Elisa , Gili Elisa , Lo Furno Debora , Pistorio Maria P , Caruso Massimo , La Rosa Cristina , Crimi Claudia , Failla Marco , Crimi Nunzio 
Published: September 2005

AbstractBackgroundT lymphocytes are demonstrated to play an important role in several chronic pulmonary inflammatory diseases. In this study we provide evidence that human lung fibroblasts are capable of mutually interacting with T-lymphocytes leading to functionally significant responses by T-cells and fibroblasts.MethodsHuman lung fibroblast were co-cultured with PMA-ionomycin activated T-CD4 lymphocytes for 36 hours. Surface as well as intracellular proteins expression, relevant to fibroblasts and lymphocytes activation, were evaluated by means of flow cytometry and RT-PCR. Proliferative responses of T lymphocytes to concanavalin A were evaluated by the MTT assay.ResultsIn lung fibroblasts, activated lymphocytes promote an increase of expression of cyclooxygenase-2 and ICAM-1, expressed as mean fluorescence intensity (MFI), from 5.4 ± 0.9 and 0.7 ± 0.15 to 9.1 ± 1.5 and 38.6 ± 7.8, respectively. Fibroblasts, in turn, induce a significant reduction of transcription and protein expression of CD69, LFA-1 and CD28 in activated lymphocytes and CD3 in resting lymphocytes. In activated T lymphocytes, LFA-1, CD28 and CD69 expression was 16.6 ± 0.7, 18.9 ± 1.9 and 6.6 ± 1.3, respectively, and was significantly reduced by fibroblasts to 9.4 ± 0.7, 9.4 ± 1.4 and 3.5 ± 1.0. CD3 expression in resting lymphocytes was 11.9 ± 1.4 and was significantly reduced by fibroblasts to 6.4 ± 1.1. Intracellular cytokines, TNF-alpha and IL-10, were evaluated in T lymphocytes. Co-incubation with fibroblasts reduced the number of TNF-alpha positive lymphocytes from 54,4% ± 6.12 to 30.8 ± 2.8, while IL-10 positive cells were unaffected. Finally, co-culture with fibroblasts significantly reduced Con A proliferative response of T lymphocytes, measured as MTT absorbance, from 0.24 ± 0.02 nm to 0.16 ± 0.02 nm. Interestingly, while the activation of fibroblasts is mediated by a soluble factor, a cognate interaction ICAM-1 mediated was demonstrated to be responsible for the modulation of LFA-1, CD28 and CD69.ConclusionFindings from this study suggest that fibroblasts play a role in the local regulation of the immune response, being able to modulate effector functions of cells recruited into sites of inflammation.
Pathway level analysis of gene expression using singular value decomposition
Authors: Tomfohr John , Lu Jun , Kepler Thomas B 
Published: September 2005

Abstract
Background
A promising direction in the analysis of gene expression focuses on the changes in expression of specific predefined sets of genes that are known in advance to be related (e.g., genes coding for proteins involved in cellular pathways or complexes). Such an analysis can reveal features that are not easily visible from the variations in the individual genes and can lead to a picture of expression that is more biologically transparent and accessible to interpretation. In this article, we present a new method of this kind that operates by quantifying the level of 'activity' of each pathway in different samples. The activity levels, which are derived from singular value decompositions, form the basis for statistical comparisons and other applications.

Results
We demonstrate our approach using expression data from a study of type 2 diabetes and another of the influence of cigarette smoke on gene expression in airway epithelia. A number of interesting pathways are identified in comparisons between smokers and non-smokers including ones related to nicotine metabolism, mucus production, and glutathione metabolism. A comparison with results from the related approach, 'gene-set enrichment analysis', is also provided.

Conclusion
Our method offers a flexible basis for identifying differentially expressed pathways from gene expression data. The results of a pathway-based analysis can be complementary to those obtained from one more focused on individual genes. A web program PLAGE (Pathway Level Analysis of Gene Expression) for performing the kinds of analyses described here is accessible at http://dulci.biostat.duke.edu/pathways.
Assessing local structural perturbations in proteins
Authors: Lema Martin A , Echave Julian 
Published: September 2005

Abstract
Background
Protein structure research often deals with the comparison of two or more structures of the same protein, for instance when handling alternative structure models for the same protein, point mutants, molecule movements, structure predictions, etc. Often the difference between structures is small, restricted to a local neighborhood, and buried in structural "noise" due to trivial differences resulting from experimental artifacts. In such cases, whole-structure comparisons by means of structure superposition may be unsatisfactory and researchers have to perform a tedious process of manually superposing different segments individually and/or use different frames of reference, chosen roughly by educated guessing.

Results
We have developed an algorithm to compare local structural differences between alternative structures of the same protein. We have implemented the algorithm through a computer program that performs the numerical evaluation and allows inspecting visually the results of the structure comparison. We have tested the algorithm on different kinds of model systems. Here we present the algorithm and some results to illustrate its characteristics.

Conclusion
This program may provide an insight into the local structural changes produced in a protein structure by different interactions or modifications. It is convenient for the general user and it can be applied to standard or specific tasks on protein structure research.
Association of the Hermansky-Pudlak syndrome type-3 protein with clathrin
Authors: Helip-Wooley Amanda , Westbroek Wendy , Dorward Heidi , Mommaas Mieke , Boissy Raymond E , Gahl William A , Huizing Marjan 
Published: September 2005

Abstract

Background
Hermansky-Pudlak syndrome (HPS) is a disorder of lysosome-related organelle biogenesis characterized by oculocutaneous albinism and prolonged bleeding. These clinical findings reflect defects in the formation of melanosomes in melanocytes and dense bodies in platelets. HPS type-3 (HPS-3) results from mutations in the HPS3 gene, which encodes a 1004 amino acid protein of unknown function that contains a predicted clathrin-binding motif (LLDFE) at residues 172–176.

Results
Clathrin was co-immunoprecipitated by HPS3 antibodies from normal but not HPS3 null melanocytes. Normal melanocytes expressing a GFP-HPS3 fusion protein demonstrated partial co-localization of GFP-HPS3 with clathrin following a 20°C temperature block. GFP-HPS3 in which the predicted clathrin-binding domain of HPS3 was mutated (GFP-HPS3-delCBD) did not co-localize with clathrin under the same conditions. Immunoelectron microscopy of normal melanocytes expressing GFP-HPS3 showed co-localization of GFP-HPS3 with clathrin, predominantly on small vesicles in the perinuclear region. In contrast, GFP-HPS3-delCBD did not co-localize with clathrin and exhibited a largely cytoplasmic distribution.

Conclusion
HPS3 associates with clathrin, predominantly on small clathrin-containing vesicles in the perinuclear region. This association most likely occurs directly via a functional clathrin-binding domain in HPS3. These results suggest a role for HPS3 and its protein complex, BLOC-2, in vesicle formation and trafficking.
A comparison of variation between a MHC pseudogene and microsatellite loci of the little greenbul (Andropadus virens)
Authors: Aguilar Andres , Smith Thomas B , Wayne Robert K 
Published: September 2005

Abstract

Background
We investigated genetic variation of a major histcompatibility complex (MHC) pseudogene (Anvi-DAB1) in the little greenbul (Andropadus virens) from four localities in Cameroon and one in Ivory Coast, West Africa. Previous microsatellite and mitochondrial DNA analyses had revealed little or no genetic differentiation among Cameroon localities but significant differentiation between localities in Cameroon and Ivory Coast.

Results
Levels of genetic variation, heterozygosity, and allelic diversity were high for the MHC pseudogene in Cameroon. Nucleotide diversity of the MHC pseudogene in Cameroon and Ivory Coast was comparable to levels observed in other avian species that have been studied for variation in nuclear genes. An excess of rare variants for the MHC pseudogene was found in the Cameroon population, but this excess was not statistically significant. Pairwise measures of population differentiation revealed high divergence between Cameroon and Ivory Coast for microsatellites and the MHC locus, although for the latter distance measures were much higher than the comparable microsatellite distances.

Conclusion
We provide the first ever comparison of variation in a putative MHC pseudogene to variation in neutral loci in a passerine bird. Our results are consistence with the action of neutral processes on the pseudogene and suggest they can provide an independent perspective on demographic history and population substructure.
Computational evidence for hundreds of non-conserved plant microRNAs
Authors: Lindow Morten , Krogh Anders 
Published: September 2005

Abstract

Background
MicroRNAs (miRNA) are small (20–25 nt) non-coding RNA molecules that regulate gene expression through interaction with mRNA in plants and metazoans. A few hundred miRNAs are known or predicted, and most of those are evolutionarily conserved. In general plant miRNA are different from their animal counterpart: most plant miRNAs show near perfect complementarity to their targets. Exploiting this complementarity we have developed a method for identification plant miRNAs that does not rely on phylogenetic conservation.

Results
Using the presumed targets for the known miRNA as positive controls, we list and filter all segments of the genome of length ~20 that are complementary to a target mRNA-transcript. From the positive control we recover 41 (of 92 possible) of the already known miRNA-genes (representing 14 of 16 families) with only four false positives.
Applying the procedure to find possible new miRNAs targeting any annotated mRNA, we predict of 592 new miRNA genes, many of which are not conserved in other plant genomes. A subset of our predicted miRNAs is additionally supported by having more than one target that are not homologues.

Conclusion
These results indicate that it is possible to reliably predict miRNA-genes without using genome comparisons. Furthermore it suggests that the number of plant miRNAs have been underestimated and points to the existence of recently evolved miRNAs in Arabidopsis.
Duplication and positive selection among hominin-specific PRAME genes
Authors: Birtle Zoë , Goodstadt Leo , Ponting Chris 
Published: September 2005

Abstract

Background
The physiological and phenotypic differences between human and chimpanzee are largely specified by our genomic differences. We have been particularly interested in recent duplications in the human genome as examples of relatively large-scale changes to our genome. We performed an in-depth evolutionary analysis of a region of chromosome 1, which is copy number polymorphic among humans, and that contains at least 32 PRAME (Preferentially expressed antigen of melanoma) genes and pseudogenes. PRAME-like genes are expressed in the testis and in a large number of tumours, and are thought to possess roles in spermatogenesis and oogenesis.

Results
Using nucleotide substitution rate estimates for exons and introns, we show that two large segmental duplications, of six and seven human PRAME genes respectively, occurred in the last 3 million years. These duplicated genes are thus hominin-specific, having arisen in our genome since the divergence from chimpanzee. This cluster of PRAME genes appears to have arisen initially from a translocation approximately 95–85 million years ago. We identified multiple sites within human or mouse PRAME sequences which exhibit strong evidence of positive selection. These form a pronounced cluster on one face of the predicted PRAME protein structure.

Conclusion
We predict that PRAME genes evolved adaptively due to strong competition between rapidly-dividing cells during spermatogenesis and oogenesis. We suggest that as PRAME gene copy number is polymorphic among individuals, positive selection of PRAME alleles may still prevail within the human population.