bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soft Tissue Injections in the Athlete
Authors: Nepple Jeffrey J. , Matava Matthew J. 
Published: August 2009

Background:Injections into or adjacent to soft tissue structures, including muscle, tendon, bursa, and fascia, for pain relief and an earlier return to play have become common in the field of sports medicine.Study Design:Clinical review.Results:Corticosteroids, local anesthetics, and ketorolac tromethamine (Toradol) are the most commonly used injectable agents in athletes. The use of these injectable agents have proven efficacy in some disorders, whereas the clinical benefit for others remain questionable. All soft tissue injections performed for pain control and/or an anti-inflammatory effect have potentially serious side effects, which must be considered, especially in the pregame setting.Conclusions:The primary concern regarding corticosteroid and local anesthetic injections is an increased risk of tendon rupture associated with the direct injection into the tendon. Intramuscular Toradol injections provide significant analgesia, as well as an anti-inflammatory effect via its inhibitory effect on the cyclooxygenase pathway. The risk of bleeding associated with Toradol use is recognized but not accurately quantified.
Dynamic accumulation of plasmacytoid dendritic cells in lymph nodes is regulated by interferon-β
Authors: Gao Yunfei , Majchrzak-Kita Beata , Fish Eleanor N. , Gommerman Jennifer L. 
Published: August 2009

AbstractPlasmacytoid dendritic cells (pDCs) represent a major cellular component of our front-line defense against viruses because of their capacity to rapidly secrete type I interferon (IFN)–α and -β after infection. Constant immunosurveillance of the host requires that lymphocytes traffic through lymph nodes (LNs) to sample antigen, yet little is known about the dynamics of pDC accumulation within the secondary lymphoid organs. Here we show that pDCs readily accumulate within the secondary lymphoid organs of mice after virus infection. Interestingly, retention of pDC within LNs is enhanced in the presence of the sphingoshine-1-phosphate receptor agonist FTY720 in a manner similar to that observed for B and T lymphocytes. Ex vivo comparison of mouse pDCs with lymphocytes revealed that pDCs express sphingoshine-1-phosphate 4 and also constitutively express CD69, which is further up-regulated upon virus infection. In IFN-β−/− mice, accumulation of pDC and lymphocytes within LNs is reduced both during viral infection and under steady state conditions, and these defects can be reversed by adding recombinant IFN-β in vivo. These data suggest that pDC and lymphocytes use similar mechanisms for retention within LNs and that these processes are influenced by IFN-β even in the absence of viral infection.
MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation
Authors: Figueroa Maria E. , Skrabanek Lucy , Li Yushan , Jiemjit Anchalee , Fandy Tamer E. , Paietta Elisabeth , Fernandez Hugo , Tallman Martin S. , Greally John M. , Carraway Hetty , Licht Jonathan D. , Gore Steven D. , Melnick Ari 
Published: August 2009

Abstract
Increasing evidence shows aberrant hypermethylation of genes occurring in and potentially contributing to pathogenesis of myeloid malignancies. Several of these diseases, such as myelodysplastic syndromes (MDSs), are responsive to DNA methyltransferase inhibitors. To determine the extent of promoter hypermethylation in such tumors, we compared the distribution of DNA methylation of 14 000 promoters in MDS and secondary acute myeloid leukemia (AML) patients enrolled in a phase 1 trial of 5-azacytidine and the histone deacetylase inhibitor entinostat against de novo AML patients and normal CD34+ bone marrow cells. The MDS and secondary AML patients displayed more extensive aberrant DNA methylation involving thousands of genes than did the normal CD34+ bone marrow cells or de novo AML blasts. Aberrant methylation in MDS and secondary AML tended to affect particular chromosomal regions, occurred more frequently in Alu-poor genes, and included prominent involvement of genes involved in the WNT and MAPK signaling pathways. DNA methylation was also measured at days 15 and 29 after the first treatment cycle. DNA methylation was reversed at day 15 in a uniform manner throughout the genome, and this effect persisted through day 29, even without continuous administration of the study drugs. This trial was registered at www.clinicaltrials.gov as J0443.
Construction and use of gene expression covariation matrix
Authors: Hennetin Jérôme , Pehkonen Petri , Bellis Michel 
Published: August 2009

Abstract

Background
One essential step in the massive analysis of transcriptomic profiles is the calculation of the correlation coefficient, a value used to select pairs of genes with similar or inverse transcriptional profiles across a large fraction of the biological conditions examined. Until now, the choice between the two available methods for calculating the coefficient has been dictated mainly by technological considerations. Specifically, in analyses based on double-channel techniques, researchers have been required to use covariation correlation, i.e. the correlation between gene expression changes measured between several pairs of biological conditions, expressed for example as fold-change. In contrast, in analyses of single-channel techniques scientists have been restricted to the use of coexpression correlation, i.e. correlation between gene expression levels. To our knowledge, nobody has ever examined the possible benefits of using covariation instead of coexpression in massive analyses of single channel microarray results.

Results
We describe here how single-channel techniques can be treated like double-channel techniques and used to generate both gene expression changes and covariation measures. We also present a new method that allows the calculation of both positive and negative correlation coefficients between genes. First, we perform systematic comparisons between two given biological conditions and classify, for each comparison, genes as increased (I), decreased (D), or not changed (N). As a result, the original series of n gene expression level measures assigned to each gene is replaced by an ordered string of n(n-1)/2 symbols, e.g. IDDNNIDID....DNNNNNNID, with the length of the string corresponding to the number of comparisons. In a second step, positive and negative covariation matrices (CVM) are constructed by calculating statistically significant positive or negative correlation scores for any pair of genes by comparing their strings of symbols.

Conclusion
This new method, applied to four different large data sets, has allowed us to construct distinct covariation matrices with similar properties. We have also developed a technique to translate these covariation networks into graphical 3D representations and found that the local assignation of the probe sets was conserved across the four chip set models used which encompass three different species (humans, mice, and rats). The application of adapted clustering methods succeeded in delineating six conserved functional regions that we characterized using Gene Ontology information.
Piecewise multivariate modelling of sequential metabolic profiling data
Authors: Rantalainen Mattias , Cloarec Olivier , Ebbels Timothy MD , Lundstedt Torbjörn , Nicholson Jeremy K , Holmes Elaine , Trygg Johan 
Published: August 2009

AbstractBackgroundModelling the time-related behaviour of biological systems is essential for understanding their dynamic responses to perturbations. In metabolic profiling studies, the sampling rate and number of sampling points are often restricted due to experimental and biological constraints.ResultsA supervised multivariate modelling approach with the objective to model the time-related variation in the data for short and sparsely sampled time-series is described. A set of piecewise Orthogonal Projections to Latent Structures (OPLS) models are estimated, describing changes between successive time points. The individual OPLS models are linear, but the piecewise combination of several models accommodates modelling and prediction of changes which are non-linear with respect to the time course. We demonstrate the method on both simulated and metabolic profiling data, illustrating how time related changes are successfully modelled and predicted.ConclusionThe proposed method is effective for modelling and prediction of short and multivariate time series data. A key advantage of the method is model transparency, allowing easy interpretation of time-related variation in the data. The method provides a competitive complement to commonly applied multivariate methods such as OPLS and Principal Component Analysis (PCA) for modelling and analysis of short time-series data.
Universal seeds for cDNA-to-genome comparison
Authors: Zhou Leming , Stanton Jonathan , Florea Liliana 
Published: August 2009

AbstractBackgroundTo meet the needs of gene annotation for newly sequenced organisms, optimized spaced seeds can be implemented into cross-species sequence alignment programs to accurately align gene sequences to the genome of a related species. So far, seed performance has been tested for comparisons between closely related species, such as human and mouse, or on simulated data. As the number and variety of genomes increases, it becomes desirable to identify a small set ofuniversalseeds that perform optimally or near-optimally on a large range of comparisons.ResultsUsing statistical regression methods, we investigate the sensitivity of seeds, in particular good seeds, between four cDNA-to-genome comparisons at different evolutionary distances (human-dog, human-mouse, human-chicken and human-zebrafish), and identify classes of comparisons that show similar seed behavior and therefore can employ the same seed. In addition, we find that with high confidence good seeds for more distant comparisons perform well on closer comparisons, within 98–99% of the optimal seeds, and thus represent universal good seeds.ConclusionWe show for the first time that optimal and near-optimal seeds for distant species-to-species comparisons are more generally applicable to a wide range of comparisons. This finding will be instrumental in developing practical and user-friendly cDNA-to-genome alignment applications, to aid in the annotation of new model organisms.
O-GlcNAc modifications regulate cell survival and epiboly during zebrafish development
Authors: Webster Danielle M , Teo Chin Fen , Sun Yuhua , Wloga Dorota , Gay Steven , Klonowski Kimberly D , Wells Lance , Dougan Scott T 
Published: August 2009

Abstract

Background
The post-translational addition of the monosaccharide O-linked β-N-acetylglucosamine (O-GlcNAc) regulates the activity of a wide variety of nuclear and cytoplasmic proteins. The enzymes O-GlcNAc Transferase (Ogt) and O-GlcNAcase (Oga) catalyze, respectively, the attachment and removal of O-GlcNAc to target proteins. In adult mice, Ogt and Oga attenuate the response to insulin by modifying several components of the signal transduction pathway. Complete loss of ogt function, however, is lethal to mouse embryonic stem cells, suggesting that the enzyme has additional, unstudied roles in development. We have utilized zebrafish as a model to determine role of O-GlcNAc modifications in development. Zebrafish has two ogt genes, encoding six different enzymatic isoforms that are expressed maternally and zygotically.

Results
We manipulated O-GlcNAc levels in zebrafish embryos by overexpressing zebrafish ogt, human oga or by injecting morpholinos against ogt transcripts. Each of these treatments results in embryos with shortened body axes and reduced brains at 24 hpf. The embryos had 23% fewer cells than controls, and displayed increased rates of cell death as early as the mid-gastrula stages. An extensive marker analysis indicates that derivatives of three germ layers are reduced to variable extents, and the embryos are severely disorganized after gastrulation. Overexpression of Ogt and Oga delayed epiboly and caused a severe disorganization of the microtubule and actin based cytoskeleton in the extra-embryonic yolk syncytial layer (YSL). The cytoskeletal defects resemble those previously reported for embryos lacking function of the Pou5f1/Oct4 transcription factor spiel ohne grenzen. Consistent with this, Pou5f1/Oct4 is modified by O-GlcNAc in human embryonic stem cells.

Conclusion
We conclude that O-GlcNAc modifications control the activity of proteins that regulate apoptosis and epiboly movements, but do not seem to regulate germ layer specification. O-GlcNAc modifies the transcription factor Spiel ohne grenzen/Pou5f1 and may regulate its activity.
The evolution of protostome GATA factors: Molecular phylogenetics, synteny, and intron/exon structure reveal orthologous relationships
Authors: Gillis William Q , Bowerman Bruce A , Schneider Stephan Q 
Published: August 2009

Abstract

Background
Invertebrate and vertebrate GATA transcription factors play important roles in ectoderm and mesendoderm development, as well as in cardiovascular and blood cell fate specification. However, the assignment of evolutionarily conserved roles to GATA homologs requires a detailed framework of orthologous relationships. Although two distinct classes, GATA123 and GATA456, have been unambiguously recognized among deuterostome GATA genes, it has been difficult to resolve exact orthologous relationships among protostome homologs. Protostome GATA genes are often present in multiple copies within any one genome, and rapidly evolving gene sequences have obscured orthology among arthropod and nematode GATA homologs. In addition, a lack of taxonomic sampling has prevented a stepwise reconstruction of protostome GATA gene family evolution.

Results
We have identified the complete GATA complement (53 genes) from a diverse sampling of protostome genomes, including six arthropods, three lophotrochozoans, and two nematodes. Reciprocal best hit BLAST analysis suggested orthology of these GATA genes to either the ancestral bilaterian GATA123 or the GATA456 class. Using molecular phylogenetic analyses of gene sequences, together with conserved synteny and comparisons of intron/exon structure, we inferred the evolutionary relationships among these 53 protostome GATA homologs. In particular, we resolved the orthology and evolutionary birth order of all arthropod GATA homologs including the highly divergent Drosophila GATA genes.

Conclusion
Our combined analyses confirm that all protostome GATA transcription factor genes are members of either the GATA123 or GATA456 class, and indicate that there have been multiple protostome-specific duplications of GATA456 homologs. Three GATA456 genes exhibit linkage in multiple protostome species, suggesting that this gene cluster arose by tandem duplications from an ancestral GATA456 gene. Within arthropods this GATA456 cluster appears orthologous and widely conserved. Furthermore, the intron/exon structures of the arthropod GATA456 orthologs suggest a distinct order of gene duplication events. At present, however, the evolutionary relationship to similarly linked GATA456 paralogs in lophotrochozoans remains unclear. Our study shows how sampling of additional genomic data, especially from less derived and interspersed protostome taxa, can be used to resolve the orthologous relationships within more divergent gene families.
Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales
Authors: Xiong Ye , Brandley Matthew C , Xu Shixia , Zhou Kaiya , Yang Guang 
Published: August 2009

Abstract

Background
The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages.

Results
The "deep" phylogenetic relationships are well supported including the monophyly of Cetacea and Odontoceti. However, there is ambiguity in the phylogenetic affinities of two of the river dolphin clades Platanistidae (Indian River dolphins) and Lipotidae (Yangtze River dolphins). The phylogenetic analyses support a sister relationship between Delphinidae and Monodontidae + Phocoenidae. Additionally, there is statistically significant support for the paraphyly of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins).

Conclusion
Our phylogenetic analysis of complete mitochondrial genomes using recently developed models of rate autocorrelation resolved the phylogenetic relationships of the major Cetacean lineages with a high degree of confidence. Our results indicate that a rapid radiation of lineages explains the lack of support the placement of Platanistidae and Lipotidae. Moreover, our estimation of molecular divergence dates indicates that these radiations occurred in the Middle to Late Oligocene and Middle Miocene, respectively. Furthermore, by collecting and analyzing seven new mitochondrial genomes, we provide strong evidence that the delphinid genera Tursiops and Stenella are not monophyletic, and the current taxonomy masks potentially interesting patterns of morphological, physiological, behavioral, and ecological evolution.
A strong association of axillary osmidrosis with the wet earwax type determined by genotyping of the ABCC11 gene
Authors: Nakano Motoi , Miwa Nobutomo , Hirano Akiyoshi , Yoshiura Koh-ichiro , Niikawa Norio 
Published: August 2009

Abstract

Background
Two types of cerumen occur in humans: the wet type with brownish, sticky earwax, and the dry type with a lack of or reduced ceruminous secretion. The wet type is common in populations of European and African origin, while the dry type is frequently seen in Eastern Asian populations. An association between axillary odor and the wet-type earwax was first identified approximately 70 years ago. The data were based on a phenotypical analysis of the two phenotypes among the Japanese by a researcher or by self-declaration of the subjects examined, and were not obtained using definite diagnostic methods. Recently, we identified a single-nucleotide polymorphism (SNP; rs17822931) of the ABCC11 gene as the determinant of the earwax types. In the present study, to determine whether the SNP can serve as a diagnostic marker for axillary osmidrosis (AO), we examined genotypes at rs17822931 in 79 Japanese AO individuals. AO was defined here as a clinical condition of individuals with a deep anxiety regarding axillary odor and had undergone the removal of bilateral axillary apocrine glands.

Results
A comparison of the frequencies of genotypes at rs17822931 in the 79 AO individuals and in 161 Japanese from the general population showed that AO was strongly associated with the wet earwax genotype. A total of 78 (98.7%) of 79 AO patients had either the GG or GA genotype, while these genotypes were observed in 35.4% (57/161) of the subjects from the general population (p < 1.1 × 10-24, by Fisher's exact test).

Conclusion
The strong association between the wet-earwax associated ABCC11- genotypes (GG and GA) and AO identified in this study indicates that the genotypes are good markers for the diagnosis of AO. In addition, these results suggest that having the allele G is a prerequisite for the axillary odor expression. In other words, the ABCC11 protein may play a role in the excretory function of the axillary apocrine gland. Together, these results suggest that when an AO individual visiting a hospital is diagnosed with dry-type earwax by ABCC11-genotyping, surgical removal of their axillary glands may not be indicated.
Proteomic-based identification of maternal proteins in mature mouse oocytes
Authors: Zhang Ping , Ni Xiaojian , Guo Ying , Guo Xuejiang , Wang Yufeng , Zhou Zuomin , Huo Ran , Sha Jiahao 
Published: August 2009

Abstract

Background
The mature mouse oocyte contains the full complement of maternal proteins required for fertilization, reprogramming, zygotic gene activation (ZGA), and the early stages of embryogenesis. However, due to limitations of traditional proteomics strategies, only a few abundantly expressed proteins have yet been identified. Our laboratory applied a more effective strategy: one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D SDS-PAGE) and reverse-phase liquid chromatography tandem mass spectrometry (RP-LC-MS/MS) were employed to analyze the mature oocyte proteome in depth.

Results
Using this high-performance proteomic approach, we successfully identified 625 different proteins from 2700 mature mouse oocytes lacking zona pellucidae. This is the largest catalog of mature mouse oocyte proteins compiled to date. According to their pattern of expression, we screened 76 maternal proteins with high levels of mRNA expression both in oocytes and fertilized eggs. Many well-known maternal effect proteins were included in this subset, including MATER and NPM2. In addition, our mouse oocyte proteome was compared with a recently published mouse embryonic stem cell (ESC) proteome and 371 overlapping proteins were identified.

Conclusion
This proteomics analysis will be a valuable resource to aid in the characterization of important maternal proteins involved in oogenesis, fertilization, early embryonic development and in revealing their mechanisms of action.
Klebsiella pneumoniae triggers a cytotoxic effect on airway epithelial cells
Authors: Cano Victoria , Moranta David , Llobet-Brossa Enrique , Bengoechea José Antonio , Garmendia Junkal 
Published: August 2009

AbstractBackgroundKlebsiella pneumoniaeis a capsulated Gram negative bacterial pathogen and a frequent cause of nosocomial infections. Despite its clinical relevance, little is known about the features of the interaction betweenK. pneumoniaeand lung epithelial cells on a cellular level, neither about the role of capsule polysaccharide, one of its best characterised virulence factors, in this interaction.ResultsThe interaction betweenKlebsiella pneumoniaeand cultured airway epithelial cells was analysed.K. pneumoniaeinfection triggered cytotoxicity, evident by cell rounding and detachment from the substrate. This effect required the presence of live bacteria and of capsule polysaccharide, since it was observed with isolates expressing different amounts of capsule and/or different serotypes but not with non-capsulated bacteria. Cytotoxicity was analysed by lactate dehydrogenase and formazan measurements, ethidium bromide uptake and analysis of DNA integrity, obtaining consistent and complementary results. Moreover, cytotoxicity of non-capsulated strains was restored by addition of purified capsule during infection. While a non-capsulated strain was avirulent in a mouse infection model, capsulatedK. pneumoniaeisolates displayed different degrees of virulence.ConclusionOur observations allocate a novel role toK. pneumoniaecapsule in promotion of cytotoxicity. Although this effect is likely to be associated with virulence, strains expressing different capsule levels were not equally virulent. This fact suggests the existence of other bacterial requirements for virulence, together with capsule polysaccharide.