bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Zonal Momentum Balance on Density Layers for the Central and Eastern Equatorial Pacific
Authors: Brown Jaclyn N. , Godfrey J. Stuart , Fiedler Russell 
Published: August 2007

Abstract
Brown et al. analyzed the kinematics of flow in the equatorial Pacific Ocean, along time-varying isopycnals in a three-dimensional eddy-permitting model. Here the dynamics of these flows is explored in the same model via the zonal momentum equation (ZME). Previous work has shown that the dominant terms of the ZME, on and near the equator, are the pressure gradient, wind stress, and Coriolis term. In one model study, the nonlinear and friction terms were significant but negated each other. In this study, with a higher-resolution model and more realistic friction scheme it is shown that the nonlinear term is important along and north of the equator, while the explicit friction term is negligible. The part of the nonlinear term derived from high-frequency eddy flows acts like a friction on the Equatorial Undercurrent, while the remaining part of the nonlinear term from smooth flows enhances it. In density coordinates, meridional tropical cells lie on either side of the equator in the first half of the year (January–June) as expected. In July–December, a continuous southward surface flow appears from 4°N into the Southern Hemisphere and arises from variations in the geostrophic flow and the nonlinear term. Variations in the geostrophic flow are due to both seasonal variability in the thermocline and a surface bolus effect arising from baroclinic instability. The nonlinear term increases in the surface layers at the same time assisting the southward flow, most likely because of tropical instability waves.
Dissipative Losses in Nonlinear Internal Waves Propagating across the Continental Shelf
Authors: Moum J. N. , Farmer D. M. , Shroyer E. L. , Smyth W. D. , Armi L. 
Published: August 2007

Abstract
A single nonlinear internal wave tracked more than 100 wavelengths across Oregon’s continental shelf over a 12-h period exhibited nearly constant wave speed, c = 0.75 m s−1, and amplitude, a = 15 m. The wavelength L gradually decreased from 220 m in 170-m water depth to 60 m in 70-m water depth. As the water shallowed beyond 50 m, the wave became unrecognizable as such. The total energy decreased from 1.1 to 0.5 MJ m−1. The rate at which wave energy was lost, −dE/dt = 14 [7, 22] W m−1, was approximately equal to the energy lost to turbulence dissipation, ρɛ = 10 [7, 14] W m−1, as inferred from turbulence measurements in the wave cores plus estimates in the wave-induced bottom boundary layer. The approximate balance, dE/dt = −ρɛ, differs from the solibore model of Henyey and Hoering in which the potential energy across the wave balances ρɛ. However, other evidence suggests that the wave evolved from a solibore-like state to a dissipative solitary wavelike state over the observed propagation path.
Target proteins of C/EBPαp30 in AML: C/EBPαp30 enhances sumoylation of C/EBPαp42 via up-regulation of Ubc9
Authors: Geletu Mulu , Balkhi Mumtaz Y. , Peer Zada Abdul A. , Christopeit Maximilian , Pulikkan John A. , Trivedi Arun K. , Tenen Daniel G. , Behre Gerhard 
Published: August 2007

AbstractCCAAT/enhancer-binding protein α (C/EBPα) is a critical regulator for early myeloid differentiation. Mutations in C/EBPα occur in 10% of patients with acute myeloid leukemia (AML), leading to the expression of a 30-kDa dominant-negative isoform (C/EBPαp30). In the present study, using a global proteomics approach to identify the target proteins of C/EBPαp30, we show that Ubc9, an E2-conjugating enzyme essential for sumoylation, is increased in its expression when C/EBPαp30 is induced. We confirmed the increased expression of Ubc9 in patients with AML with C/EBPαp30 mutations compared with other subtypes. We further confirmed that the increase of Ubc9 expression was mediated through increased transcription. Furthermore, we show that Ubc9-mediated enhanced sumoylation of C/EBPαp42 decreases the transactivation capacity on a minimal C/EBPα promoter. Importantly, overexpression of C/EBPαp30 in granulocyte colony-stimulating factor (G-CSF)–stimulated human CD34+ cells leads to a differentiation block, which was overcome by the siRNA-mediated silencing of Ubc9. In summary, our data indicate that Ubc9 is an important C/EBPαp30 target through which C/EBPαp30 enhances the sumoylation of C/EBPαp42 to inhibit granulocytic differentiation.
A cis-regulatory logic simulator
Authors: Zeigler Robert D , Gertz Jason , Cohen Barak A 
Published: August 2007

AbstractBackgroundA major goal of computational studies of gene regulation is to accurately predict the expression of genes based on the cis-regulatory content of their promoters. The development of computational methods to decode the interactions among cis-regulatory elements has been slow, in part, because it is difficult to know, without extensive experimental validation, whether a particular method identifies the correct cis-regulatory interactions that underlie a given set of expression data. There is an urgent need for test expression data in which the interactions among cis-regulatory sites that produce the data are known. The ability to rapidly generate such data sets would facilitate the development and comparison of computational methods that predict gene expression patterns from promoter sequence.ResultsWe developed a gene expression simulator which generates expression data using user-defined interactions between cis-regulatory sites. The simulator can incorporate additive, cooperative, competitive, and synergistic interactions between regulatory elements. Constraints on the spacing, distance, and orientation of regulatory elements and their interactions may also be defined and Gaussian noise can be added to the expression values. The simulator allows for a data transformation that simulates the sigmoid shape of expression levels from real promoters. We found good agreement between sets of simulated promoters and predicted regulatory modules from real expression data. We present several data sets that may be useful for testing new methodologies for predicting gene expression from promoter sequence.ConclusionWe developed a flexible gene expression simulator that rapidly generates large numbers of simulated promoters and their corresponding transcriptional output based on specified interactions between cis-regulatory sites. When appropriate rule sets are used, the data generated by our simulator faithfully reproduces experimentally derived data sets. We anticipate that using simulated gene expression data sets will facilitate the direct comparison of computational strategies to predict gene expression from promoter sequence. The source code is available online and as additional material. The test sets are available as additional material.
Molecular evolution of the MAGUK family in metazoan genomes
Authors: te Velthuis Aartjan JW , Admiraal Jeroen F , Bagowski Christoph P 
Published: August 2007

Abstract

Background
Development, differentiation and physiology of metazoans all depend on cell to cell communication and subsequent intracellular signal transduction. Often, these processes are orchestrated via sites of specialized cell-cell contact and involve receptors, adhesion molecules and scaffolding proteins. Several of these scaffolding proteins important for synaptic and cellular junctions belong to the large family of membrane-associated guanylate kinases (MAGUK). In order to elucidate the origin and the evolutionary history of the MAGUKs we investigated full-length cDNA, EST and genomic sequences of species in major phyla.

Results
Our results indicate that at least four of the seven MAGUK subfamilies were present in early metazoan lineages, such as Porifera. We employed domain sequence and structure based methods to infer a model for the evolutionary history of the MAGUKs. Notably, the phylogenetic trees for the guanylate kinase (GK)-, the PDZ- and the SH3-domains all suggested a matching evolutionary model which was further supported by molecular modeling of the 3D structures of different GK domains. We found no MAGUK in plants, fungi or other unicellular organisms, which suggests that the MAGUK core structure originated early in metazoan history.

Conclusion
In summary, we have characterized here the molecular and structural evolution of the large MAGUK family. Using the MAGUKs as an example, our results show that it is possible to derive a highly supported evolutionary model for important multidomain families by analyzing encoded protein domains. It further suggests that larger superfamilies encoded in the different genomes can be analyzed in a similar manner.
A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly
Authors: Marques Elisa , de Givry Simon , Stothard Paul , Murdoch Brenda , Wang Zhiquan , Womack James , Moore Stephen S 
Published: August 2007

Abstract

Background
Radiation hybrid (RH) maps are considered to be a tool of choice for fine mapping closely linked loci, considering that the resolution of linkage maps is determined by the number of informative meiosis and recombination events which may require very large mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL), haplotype map construction and refinement of candidate gene searches.

Results
A 12 k Radiation hybrid map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting map was aligned with the latest version of the bovine assembly (Btau_3.1) as well as other previously published RH maps. The resulting map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH map presented here and the latest sequence assembly are in very good agreement.

Conclusion
The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.
cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome
Authors: Lu Fangli , Jiang Hongying , Ding Jinhui , Mu Jianbing , Valenzuela Jesus G , Ribeiro José MC , Su Xin-zhuan 
Published: August 2007

Abstract

Background
The completion of the Plasmodium falciparum genome represents a milestone in malaria research. The genome sequence allows for the development of genome-wide approaches such as microarray and proteomics that will greatly facilitate our understanding of the parasite biology and accelerate new drug and vaccine development. Designing and application of these genome-wide assays, however, requires accurate information on gene prediction and genome annotation. Unfortunately, the genes in the parasite genome databases were mostly identified using computer software that could make some erroneous predictions.

Results
We aimed to obtain cDNA sequences to examine the accuracy of gene prediction in silico. We constructed cDNA libraries from mixed blood stages of P. falciparum parasite using the SMART cDNA library construction technique and generated 17332 high-quality expressed sequence tags (EST), including 2198 from primer-walking experiments. Assembly of our sequence tags produced 2548 contigs and 2671 singletons versus 5220 contigs and 5910 singletons when our EST were assembled with EST in public databases. Comparison of all the assembled EST/contigs with predicted CDS and genomic sequences in the PlasmoDB database identified 356 genes with predicted coding sequences fully covered by EST, including 85 genes (23.6%) with introns incorrectly predicted. Careful automatic software and manual alignments found an additional 308 genes that have introns different from those predicted, with 152 new introns discovered and 182 introns with sizes or locations different from those predicted. Alternative spliced and antisense transcripts were also detected. Matching cDNA to predicted genes also revealed silent chromosomal regions, mostly at subtelomere regions.

Conclusion
Our data indicated that approximately 24% of the genes in the current databases were predicted incorrectly, although some of these inaccuracies could represent alternatively spliced transcripts, and that more genes than currently predicted have one or more additional introns. It is therefore necessary to annotate the parasite genome with experimental data, although obtaining complete cDNA sequences from this parasite will be a formidable task due to the high AT nature of the genome. This study provides valuable information for genome annotation that will be critical for functional analyses.
Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice
Authors: Gómez-Porras Judith L , Riaño-Pachón Diego Mauricio , Dreyer Ingo , Mayer Jorge E , Mueller-Roeber Bernd 
Published: August 2007

AbstractBackgroundIn plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used anin-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsivecis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa).ResultsOur results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters.ConclusionOur computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks.
Treatment of two postoperative endophthalmitis cases due to Aspergillus flavus and Scopulariopsis spp. with local and systemic antifungal therapy
Authors: Aydin Sayime , Ertugrul Bulent , Gultekin Berna , Uyar Guliz , Kir Erkin 
Published: August 2007

Abstract

Background
Endophthalmitis is the inflammatory response to invasion of the eye with bacteria or fungi. The incidence of endophthalmitis after cataract surgery varies between 0.072–0.13 percent. Treatment of endophthalmitis with fungal etiology is difficult.

Case Presentation

Case 1: A 71-year old male diabetic patient developed postoperative endophthalmitis due to Aspergillus flavus. The patient was treated with topical amphotericin B ophthalmic solution, intravenous (IV) liposomal amphotericin-B and caspofungin following vitrectomy.

Case 2: A 72-year old male cachectic patient developed postoperative endophthalmitis due to Scopulariopsis spp. The patient was treated with topical and IV voriconazole and caspofungin.

Conclusion

Aspergillus spp. are responsible of postoperative fungal endophthalmitis. Endophthalmitis caused by Scopulariopsis spp. is a very rare condition. The two cases were successfully treated with local and systemic antifungal therapy.
Inhibition of APN/CD13 leads to suppressed progressive potential in ovarian carcinoma cells
Authors: Terauchi Mikio , Kajiyama Hiroaki , Shibata Kiyosumi , Ino Kazuhiko , Nawa Akihiro , Mizutani Shigehiko , Kikkawa Fumitaka 
Published: August 2007

Abstract

Background
Aminopeptidase N (APN/CD13), a 150-kDa metalloprotease, is a multifunctional cell surface aminopeptidase with ubiquitous expression. Recent studies have suggested that APN/CD13 plays an important role in tumor progression of several human malignancies. In the current study, we investigated the role of APN/CD13 in ovarian carcinoma (OVCA) progression.

Methods
We first examined the expression of APN/CD13 at the protein level in a variety of OVCA cell lines and tissues. We subsequently investigated whether there was a correlation between APN/CD13 expression and invasive potential of various OVCA cell lines. Moreover, we investigated the function of APN/CD13 in OVCA cells using bestatin, an APN/CD13 inhibitor, or transfection of siRNA for APN/CD13.

Results
We confirmed that APN/CD13 was expressed in OVCA tissues and cell lines to various extents. There was a positive correlation between APN/CD13 expression and migratory potential in various OVCA cell lines with accordingly enhanced secretion of endogenous MMP-2. Subsequently, we found a significant decrease in the proliferative and migratory abilities of OVCA cells after the addition of bestatin or the inhibition of APN/CD13 expression by siRNA. Furthermore, in an animal model, daily intraperitoneal administration of bestatin after inoculation of OVCA cells resulted in a decrease of peritoneal dissemination and in prolonged survival of nude mice.

Conclusion
The current data indicate the possible involvement of APN/CD13 in the development of OVCA, and suggest that clinical use of bestatin may contribute to better prognosis for ovarian carcinoma patients.
Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins
Authors: Chen Yunjia , Qiu Shihong , Luan Chi-Hao , Luo Ming 
Published: August 2007

Abstract

Background
Expression of higher eukaryotic genes as soluble, stable recombinant proteins is still a bottleneck step in biochemical and structural studies of novel proteins today. Correct identification of stable domains/fragments within the open reading frame (ORF), combined with proper cloning strategies, can greatly enhance the success rate when higher eukaryotic proteins are expressed as these domains/fragments. Furthermore, a HTP cloning pipeline incorporated with bioinformatics domain/fragment selection methods will be beneficial to studies of structure and function genomics/proteomics.

Results
With bioinformatics tools, we developed a domain/domain boundary prediction (DDBP) method, which was trained by available experimental data. Combined with an improved cloning strategy, DDBP had been applied to 57 proteins from C. elegans. Expression and purification results showed there was a 10-fold increase in terms of obtaining purified proteins. Based on the DDBP method, the improved GATEWAY cloning strategy and a robotic platform, we constructed a high throughput (HTP) cloning pipeline, including PCR primer design, PCR, BP reaction, transformation, plating, colony picking and entry clones extraction, which have been successfully applied to 90 C. elegans genes, 88 Brucella genes, and 188 human genes. More than 97% of the targeted genes were obtained as entry clones. This pipeline has a modular design and can adopt different operations for a variety of cloning/expression strategies.

Conclusion
The DDBP method and improved cloning strategy were satisfactory. The cloning pipeline, combined with our recombinant protein HTP expression pipeline and the crystal screening robots, constitutes a complete platform for structure genomics/proteomics. This platform will increase the success rate of purification and crystallization dramatically and promote the further advancement of structure genomics/proteomics.
Construction of miniantibodies for the in vivo study of human autoimmune diseases in animal models
Authors: Di Niro Roberto , Ziller Federica , Florian Fiorella , Crovella Sergio , Stebel Marco , Bestagno Marco , Burrone Oscar , Bradbury Andrew RM , Secco Paola , Marzari Roberto , Sblattero Daniele 
Published: August 2007

AbstractBackgroundPhage display antibody libraries have been made from the lymphocytes of patients suffering from autoimmune diseases in which the antibodies are known to play a role in the pathogenesis or are important for the diagnosis of the disease. In the case of Celiac Disease, the immune response is directed against the autoantigen tissue transglutaminase. However, despite numerous studies, the role of these antibodies in the pathogenesis of this disease has not been elucidated.ResultsWe were able to engineer specific anti-transglutaminase antibody fragments in the form called "miniantibody". These are produced by genetic fusion of anti-tTG scFv to Human, Mouse or Rat Fc domains, making them suitable for in vivo expression. The results obtained here indicate that the miniantibody molecule is efficiently secreted, and that the reactivity to the antigen is retained even after fusion to heterologous Fc domains. Further analysis demonstrate that the molecule is secreted as homodimeric, mimicking original antibody structure. Finally, the in vivo expression in mice leads to detectable serum levels with no apparent gross immune response by the host.ConclusionIn this work we demonstrated the usefulness of a method for the in vivo expression of miniantibodies specific to transglutaminase, corresponding to the autoimmune specificity of Celiac Disease. This can be proposed as a general method to study the pathogenic role of autoimmune antibodies in autoimmune diseases.