bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double-Loop Suture Repair for Acute Acromioclavicular Joint Disruption
Authors: Dimakopoulos Panayotis , Panagopoulos Andreas , Syggelos Spyros A. , Panagiotopoulos Elias , Lambiris Elias 
Published: February 2006

Background Although it has been established that surgical treatment for acromioclavicular joint disruption (types IV-VI and type III in overhead throwing athletes and heavy laborers) is preferred, the literature is inconclusive about the best type of surgery. Purpose With the goal of avoiding the potential complications of hardware use, the authors present a coracoclavicular functional stabilization technique with the intention to restore the anteroposterior and superior displacement of the clavicle. Study Design Case series; Level of evidence, 4. Methods From 1999 to 2003, 38 patients with an acute, complete acromioclavicular joint separation (34 men, 4 women; mean age, 33.5 years) underwent surgical reconstruction with the described coracoclavicular loop stabilization technique. With this technique, the superior and anteroposterior displacement of the clavicle can be easily controlled using 2 pairs of Ethibond No. 5 nonabsorbable sutures—one passed in front and the other behind the clavicle, through a central drill hole, 2 cm from its lateral end, directly above the base of the coracoid process (at the corresponded attachment of coracoclavicular ligaments). Passive shoulder motion was encouraged by the second postoperative day. Results Thirty-four patients were available for the last clinical and radiologic evaluation. At a mean follow-up of 33.2 months (range, 18-59 months), the mean Constant-Murley score was 93.5 points (range, 73-100 points), and 2 cases with slight loss of reduction (less than half of the width of the clavicle) were detected. Complications included 1 case with superficial infection and 1 patient (basketball player) with persistent tenderness in the acromioclavicular joint without signs of secondary arthritis. The incidence of periarticular ossification was 17.6% and did not affect the final outcome. Secondary degenerative changes were not detected. Conclusion Considering the nearly anatomical reconstruction, the avoidance of hardware complications, and the low rate of recurrence, this technique may be an attractive alternative to the management of acute acromioclavicular joint separations.
Functional analysis of zebrafish microfibril-associated glycoprotein-1 (Magp1) in vivo reveals roles for microfibrils in vascular development and function
Authors: Chen Eleanor , Larson Jon D. , Ekker Stephen C. 
Published: February 2006

AbstractMutations in fibrillin-1 (FBN1) result in Marfan syndrome, demonstrating a critical requirement for microfibrils in vessel structure and function. However, the identity and function of many microfibril-associated molecules essential for vascular development and function have yet to be characterized. In our morpholino-based screen for members of the secretome required for vascular development, we identified a key player in microfibril formation in zebrafish embryogenesis. Microfibril-associated glycoprotein-1 (MAGP1) is a conserved protein found in mammalian and zebrafish microfibrils. Expression of magp1 mRNA is detected in microfibril-producing cells. Analysis of a functional Magp1-mRFP fusion protein reveals localization along the midline and in the vasculature during embryogenesis. Underexpression and overexpression analyses demonstrate that specific Magp1 protein levels are critical for vascular development. Integrin function is compromised in magp1 morphant embryos, suggesting that reduced integrin–matrix interaction is the main mechanism for the vascular defects in magp1 morphants. We further show that Magp1 and fibrillin-1 interact in vivo. This study implicates MAGP1 as a key player in microfibril formation and integrity during development. The essential role for MAGP1 in vascular morphogenesis and function also supports a wide range of clinical applications, including therapeutic targets in vascular disease and cardiovascular tissue engineering.
Relation between air pollution and allergic rhinitis in Taiwanese schoolchildren
Authors: Hwang Bing-Fang , Jaakkola Jouni JK , Lee Yung-Ling , Lin Ying-Chu , Leon Guo Yue-liang 
Published: February 2006

AbstractBackgroundRecent findings suggest that exposure to outdoor air pollutants may increase the risk of allergic rhinitis. The results of these studies are inconsistent, but warrant further attention. The objective of the study was to assess the effect of relation between exposure to urban air pollution and the prevalence allergic rhinitis among school children.MethodsWe conducted a nationwide cross-sectional study of 32,143 Taiwanese school children. We obtained routine air-pollution monitoring data for sulphur dioxide (SO2), nitrogen oxides (NOx), ozone (O3), carbon monoxide (CO), and particles with an aerodynamic diameter of 10 μm or less (PM10). A parent-administered questionnaire provided information on individual characteristics and indoor environments (response rate 92%). Municipal-level exposure was calculated using the mean of the 2000 monthly averages. The effect estimates were presented as odds ratios (ORs) per 10 ppb change for SO2, NOx, and O3, 100 ppb change for CO, and 10 μg/m3change for PM10.ResultsIn two-stage hierarchical model adjusting for confounding, the prevalence of allergic rhinitis was significantly associated with SO2(adjusted odds ratio (OR) = 1.43, 95% confidence interval (CI): 1.25, 1.64), CO (aOR = 1.05, 95% CI: 1.04, 1.07), and NOx (aOR = 1.11, 95% CI: 1.08, 1.15). Contrary to our hypothesis, the prevalence of allergic rhinitis was weakly or not related to O3(aOR = 1.05, 95% CI: 0.98, 1.12) and PM10(aOR = 1.00, 95% CI: 0.99, 1.02).ConclusionPersistent exposure to NOx, CO, and SO2may increase the prevalence of allergic rhinitis in children.
Release of Ca2+ and Mg2+ from yeast mitochondria is stimulated by increased ionic strength
Authors: Bradshaw Patrick C , Pfeiffer Douglas R 
Published: February 2006

AbstractBackgroundDivalent cations are required for many essential functions of mitochondrial metabolism. Yet the transporters that mediate the flux of these molecules into and out of the mitochondrion remain largely unknown. Previous studies in yeast have led to the molecular identification of a component of the major mitochondrial electrophoretic Mg2+uptake system in this organism as well as a functional mammalian homolog. Other yeast mitochondrial studies have led to the characterization of an equilibrative fatty acid-stimulated Ca2+transport activity. To gain a deeper understanding of the regulation of mitochondrial divalent cation levels we further characterized the efflux of Ca2+and Mg2+from yeast mitochondria.ResultsWhen isolated mitochondria from the yeastSaccharomyces cerevisiaewere suspended in a salt-based suspension medium, Ca2+and Mg2+were released from the matrix space. Release did not spontaneously occur in a non-ionic mannitol media. When energized mitochondria were suspended in a mannitol medium in the presence of Ca2+they were able to accumulate Ca2+by the addition of the electrogenic Ca2+ionophore ETH-129. However, in a KCl or choline Cl medium under the same conditions, they were unable to retain the Ca2+that was taken up due to the activation of the Ca2+efflux pathway, although a substantial membrane potential driving Ca2+uptake was maintained. This Ca2+efflux was independent of fatty acids, which have previously been shown to activate Ca2+transport. Endogenous mitochondrial Mg2+was also released when mitochondria were suspended in an ionic medium, but was retained in mitochondria upon fatty acid addition. When suspended in a mannitol medium, metal chelators released mitochondrial Mg2+, supporting the existence of an external divalent cation-binding site regulating release. Matrix space Mg2+was also slowly released from mitochondria by the addition of Ca2+, respiratory substrates, increasing pH, or the nucleotides ATP, ADP, GTP, and ATP-gamma-S.ConclusionIn isolated yeast mitochondria Ca2+and Mg2+release was activated by increased ionic strength. Free nucleotides, metal ion chelators, and increased pH also stimulated release. In yeast cells this release is likely an important mechanism in the regulation of mitochondrial matrix space divalent cation concentrations.
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics
Authors: von Grotthuss Marcin , Plewczynski Dariusz , Ginalski Krzysztof , Rychlewski Leszek , Shakhnovich Eugene I 
Published: February 2006

Abstract

Background
The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity.

Results
Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0), for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes.

Conclusion
We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file.

Availability

http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF
A methodology for the structural and functional analysis of signaling and regulatory networks
Authors: Klamt Steffen , Saez-Rodriguez Julio , Lindquist Jonathan A , Simeoni Luca , Gilles Ernst D 
Published: February 2006

Abstract

Background
Structural analysis of cellular interaction networks contributes to a deeper understanding of network-wide interdependencies, causal relationships, and basic functional capabilities. While the structural analysis of metabolic networks is a well-established field, similar methodologies have been scarcely developed and applied to signaling and regulatory networks.

Results
We propose formalisms and methods, relying on adapted and partially newly introduced approaches, which facilitate a structural analysis of signaling and regulatory networks with focus on functional aspects. We use two different formalisms to represent and analyze interaction networks: interaction graphs and (logical) interaction hypergraphs. We show that, in interaction graphs, the determination of feedback cycles and of all the signaling paths between any pair of species is equivalent to the computation of elementary modes known from metabolic networks. Knowledge on the set of signaling paths and feedback loops facilitates the computation of intervention strategies and the classification of compounds into activators, inhibitors, ambivalent factors, and non-affecting factors with respect to a certain species. In some cases, qualitative effects induced by perturbations can be unambiguously predicted from the network scheme. Interaction graphs however, are not able to capture AND relationships which do frequently occur in interaction networks. The consequent logical concatenation of all the arcs pointing into a species leads to Boolean networks. For a Boolean representation of cellular interaction networks we propose a formalism based on logical (or signed) interaction hypergraphs, which facilitates in particular a logical steady state analysis (LSSA). LSSA enables studies on the logical processing of signals and the identification of optimal intervention points (targets) in cellular networks. LSSA also reveals network regions whose parametrization and initial states are crucial for the dynamic behavior.
We have implemented these methods in our software tool CellNetAnalyzer (successor of FluxAnalyzer) and illustrate their applicability using a logical model of T-Cell receptor signaling providing non-intuitive results regarding feedback loops, essential elements, and (logical) signal processing upon different stimuli.

Conclusion
The methods and formalisms we propose herein are another step towards the comprehensive functional analysis of cellular interaction networks. Their potential, shown on a realistic T-cell signaling model, makes them a promising tool.
FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
Authors: Yu Yanan , Breitbart Mya , McNairnie Pat , Rohwer Forest 
Published: February 2006

Abstract

Background
High-throughput sequencing makes it possible to rapidly obtain thousands of 16S rDNA sequences from environmental samples. Bioinformatic tools for the analyses of large 16S rDNA sequence databases are needed to comprehensively describe and compare these datasets.

Results
FastGroupII is a web-based bioinformatics platform to dereplicate large 16S rDNA libraries. FastGroupII provides users with the option of four different dereplication methods, performs rarefaction analysis, and automatically calculates the Shannon-Wiener Index and Chao1. FastGroupII was tested on a set of 16S rDNA sequences from coral-associated Bacteria. The different grouping algorithms produced similar, but not identical, results. This suggests that 16S rDNA datasets need to be analyzed in multiple ways when being used for community ecology studies.

Conclusion
FastGroupII is an effective bioinformatics tool for the trimming and dereplication of 16S rDNA sequences. Several standard diversity indices are calculated, and the raw sequences are prepared for downstream analyses.
Comparative analysis of haplotype association mapping algorithms
Authors: McClurg Phillip , Pletcher Mathew T , Wiltshire Tim , Su Andrew I 
Published: February 2006

Abstract

Background
Finding the genetic causes of quantitative traits is a complex and difficult task. Classical methods for mapping quantitative trail loci (QTL) in miceuse an F2 cross between two strains with substantially different phenotype and an interval mapping method to compute confidence intervals at each position in the genome. This process requires significant resources for breeding and genotyping, and the data generated are usually only applicable to one phenotype of interest. Recently, we reported the application of a haplotype association mapping method which utilizes dense genotyping data across a diverse panel of inbred mouse strains and a marker association algorithm that is independent of any specific phenotype. As the availability of genotyping data grows in size and density, analysis of these haplotype association mapping methods should be of increasing value to the statistical genetics community.

Results
We describe a detailed comparative analysis of variations on our marker association method. In particular, we describe the use of inferred haplotypes from adjacent SNPs, parametric and nonparametric statistics, and control of multiple testing error. These results show that nonparametric methods are slightly better in the test cases we study, although the choice of test statistic may often be dependent on the specific phenotype and haplotype structure being studied. The use of multi-SNP windows to infer local haplotype structure is critical to the use of a diverse panel of inbred strains for QTL mapping. Finally, because the marginal effect of any single gene in a complex disease is often relatively small, these methods require the use of sensitive methods for controlling family-wise error. We also report our initial application of this method to phenotypes cataloged in the Mouse Phenome Database.

Conclusion
The use of inbred strains of mice for QTL mapping has many advantages over traditional methods. However, there are also limitations in comparison to the traditional linkage analysis from F2 and RI lines. Application of these methods requires careful consideration of algorithmic choices based on both theoretical and practical factors. Our findings suggest general guidelines, though a complete evaluation of these methods can only be performed as more genetic data in complex diseases becomes available.
Bayesian detection of periodic mRNA time profiles without use of training examples
Authors: Andersson Claes R , Isaksson Anders , Gustafsson Mats G 
Published: February 2006

AbstractBackgroundDetection of periodically expressed genes from microarray data without use of known periodic and non-periodic training examples is an important problem, e.g. for identifying genes regulated by the cell-cycle in poorly characterised organisms. Commonly the investigator is only interested in genes expressed at a particular frequency that characterizes the process under study but this frequency is seldom exactly known. Previously proposed detector designs require access to labelled training examples and do not allow systematic incorporation of diffuse prior knowledge available about the period time.ResultsA learning-free Bayesian detector that does not rely on labelled training examples and allows incorporation of prior knowledge about the period time is introduced. It is shown to outperform two recently proposed alternative learning-free detectors on simulated data generated with models that are different from the one used for detector design. Results from applying the detector to mRNA expression time profiles fromS. cerevisiaeshowsthat the genes detected as periodically expressed only contain a small fraction of the cell-cycle genes inferred from mutant phenotype. For example, when the probability of false alarm was equal to 7%, only 12% of the cell-cycle genes were detected. The genes detected as periodically expressed were found to have a statistically significant overrepresentation of known cell-cycle regulated sequence motifs. One known sequence motif and 18 putative motifs, previously not associated with periodic expression, were also over represented.ConclusionIn comparison with recently proposed alternative learning-free detectors for periodic gene expression, Bayesian inference allows systematic incorporation of diffusea prioriknowledge about, e.g. the period time. This results in relative performance improvements due to increased robustness against errors in the underlying assumptions. Results from applying the detector to mRNA expression time profiles fromS. cerevisiaeinclude several new findings that deserve further experimental studies.
The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA
Authors: Parham James F , Feldman Chris R , Boore Jeffrey L 
Published: February 2006

AbstractBackgroundThe big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics.Platysternonwas traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis.ResultsWe sequenced the complete mt genome ofPlatysternonand the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement ofPlatysternonwith Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered thatPlatysternonmtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles.ConclusionOur study robustly determines the phylogenetic placement ofPlatysternonand provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placingPlatysternonwith chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of thePlatysternonmtDNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded, examples of this are rare. So far, duplicated control regions have been reported for mt genomes from just 12 clades of metazoans, includingPlatysternon.
Complete association between a retroviral insertion in the tyrosinase gene and the recessive white mutation in chickens
Authors: Chang Chung-Ming , Coville Jean-Luc , Coquerelle Gérard , Gourichon David , Oulmouden Ahmad , Tixier-Boichard Michèle 
Published: February 2006

Abstract

Background
In chickens, three mutant alleles have been reported at the C locus, including the albino mutation, and the recessive white mutation, which is characterized by white plumage and pigmented eyes. The albino mutation was found to be a 6 bp deletion in the tyrosinase (TYR) gene. The present work describes an approach to identify the structural rearrangement in the TYR gene associated with the recessive white mutation.

Results
Molecular analysis of the chicken TYR gene has revealed a major structural difference (Restriction Fragment Length Polymorphism, RFLP) in the genomic DNA of the recessive white chicken. A major size difference of 7.7 kb was found in intron 4 of the TYR gene by long-range PCR. Molecular cloning and sequencing results showed the insertion of a complete avian retroviral sequence of the Avian Leukosis Virus (ALV) family. Several aberrant transcripts of the tyrosinase gene were found in 10 week old recessive white chickens but not in the homozygous wild type colored chicken. We established a rapid genotyping diagnostic test based on the discovery of this retroviral insertion. It shows that all homozygous carriers of this insertion had a white plumage in various chicken strains. Furthermore, it was possible to distinguish heterozygous carriers from homozygous normal chickens in a segregating line.

Conclusion
In this study, we conclude that the insertion of a complete avian retroviral sequence in intron 4 of the tyrosinase gene is diagnostic of the recessive white mutation in chickens. This insertion causes aberrant transcripts lacking exon 5, and we propose that this insertion is the causal mutation for the recessive white allele in the chicken.