bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isopycnal Averaging at Constant Height. Part II: Relating to the Residual Streamfunction in Eulerian Space
Authors: Nurser A. J. George , Lee Mei-Man 
Published: January 2005

Abstract
In Part I, the “vertical” transport streamfunction was defined as resulting from isopycnic averaging at constant height in the same way that the meridional streamfunction results from averaging at constant latitude. Part II here discusses the relationship between these two isopycnic streamfunctions and the Eulerian residual streamfunction that arises from the transformed Eulerian mean (TEM). It is known that the meridional isopycnic streamfunction can be approximated by a Taylor expansion to give an Eulerian residual streamfunction involving the horizontal eddy flux. This Taylor expansion approximation works well in the interior, removing the spurious mixing associated with the simple Eulerian-averaged streamfunction. However, it fails near the surface where isopycnals outcrop to the surface. It can be shown in a similar way that the vertical isopycnic streamfunction can formally be approximated by a residual streamfunction involving the vertical eddy flux. However, if horizontal isopycnal displacements are large, this approximation fails even in the ocean interior. Inspired by the two different residual streamfunctions, a more general form of TEM formulation is explored. It is shown that the different TEM residual streamfunctions arise from decomposing the eddy flux into a component along isopycnals, which leads to advective flow, and a remaining diffusive component, which is oriented either vertically or horizontally. In theory the diffusive flux can be oriented in any direction, although in practice the orientation should be such that neither the advective flow nor the diffusive flux cross any boundary (surface, sidewalls, and bottom). However, it is not clear how to merge the continuously changing orientation in a physically meaningful way. A variety of approaches are discussed.
Simulation of the Transformation of Internal Solitary Waves on Oceanic Shelves
Authors: Grimshaw Roger , Pelinovsky Efim , Talipova Tatiana , Kurkin Audrey 
Published: January 2005

AbstractInternal solitary waves transform as they propagate shoreward over the continental shelf into the coastal zone, from a combination of the horizontal variability of the oceanic hydrology (density and current stratification) and the variable depth. If this background environment varies sufficiently slowly in comparison with an individual solitary wave, then that wave possesses a soliton-like form with varying amplitude and phase. This stage is studied in detail in the framework of the variable-coefficient extended Korteweg–de Vries equation where the variation of the solitary wave parameters can be described analytically through an asymptotic description as a slowly varying solitary wave. Direct numerical simulation of the variable-coefficient extended Korteweg–de Vries equation is performed for several oceanic shelves (North West shelf of Australia, Malin shelf edge, and Arctic shelf) to demonstrate the applicability of the asymptotic theory. It is shown that the solitary wave may maintain its soliton-like form for large distances (up to 100 km), and this fact helps to explain why internal solitons are widely observed in the world's oceans. In some cases the background stratification contains critical points (where the coefficients of the nonlinear terms in the extended Korteweg–de Vries equation change sign), or does not vary sufficiently slowly; in such cases the solitary wave deforms into a group of secondary waves. This stage is studied numerically.
Dependence of Sea Ice Yield-Curve Shape on Ice Thickness
Authors: Wilchinsky Alexander V. , Feltham Daniel L. 
Published: January 2005

Abstract
In this note, the authors discuss the contribution that frictional sliding of ice floes (or floe aggregates) past each other and pressure ridging make to the plastic yield curve of sea ice. Using results from a previous study that explicitly modeled the amount of sliding and ridging that occurs for a given global strain rate, it is noted that the relative contribution of sliding and ridging to ice stress depends upon ice thickness. The implication is that the shape and size of the plastic yield curve is dependent upon ice thickness. The yield-curve shape dependence is in addition to plastic hardening/weakening that relates the size of the yield curve to ice thickness. In most sea ice dynamics models the yield-curve shape is taken to be independent of ice thickness. The authors show that the change of the yield curve due to a change in the ice thickness can be taken into account by a weighted sum of two thickness-independent rheologies describing ridging and sliding effects separately. It would be straightforward to implement the thickness-dependent yield-curve shape described here into sea ice models used for global or regional ice prediction.
Inhibition of c-Jun NH2-terminal kinase or extracellular signal-regulated kinase improves lung injury
Authors: Lee Hui Su , Kim Hee Jae , Moon Chang Sook , Chong Young Hae , Kang Jihee Lee 
Published: January 2005

Abstract
Background
Although in vitro studies have determined that the activation of mitogen-activated protein (MAP) kinases is crucial to the activation of transcription factors and regulation of the production of proinflammatory mediators, the roles of c-Jun NH2-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) in acute lung injury have not been elucidated.

Methods
Saline or lipopolysaccharide (LPS, 6 mg/kg of body weight) was administered intratracheally with a 1-hour pretreatment with SP600125 (a JNK inhibitor; 30 mg/kg, IO), or PD98059 (an MEK/ERK inhibitor; 30 mg/kg, IO). Rats were sacrificed 4 hours after LPS treatment.

Results
SP600125 or PD98059 inhibited LPS-induced phosphorylation of JNK and ERK, total protein and LDH activity in BAL fluid, and neutrophil influx into the lungs. In addition, these MAP kinase inhibitors substantially reduced LPS-induced production of inflammatory mediators, such as CINC, MMP-9, and nitric oxide. Inhibition of JNK correlated with suppression of NF-κB activation through downregulation of phosphorylation and degradation of IκB-α, while ERK inhibition only slightly influenced the NF-κB pathway.

Conclusion
JNK and ERK play pivotal roles in LPS-induced acute lung injury. Therefore, inhibition of JNK or ERK activity has potential as an effective therapeutic strategy in interventions of inflammatory cascade-associated lung injury.
Value of supplemental interventions to enhance the effectiveness of physical exercise during respiratory rehabilitation in COPD patients. A Systematic Review
Authors: Puhan Milo A , Schünemann Holger J , Frey Martin , Bachmann Lucas M 
Published: January 2005

Abstract
Background
There is a controversy about the additional benefit of various supplemental interventions used in clinical practice to further enhance the effectiveness of respiratory rehabilitation in patients with Chronic obstructive pulmonary disease (COPD). The aim of this research was to assess randomised controlled trials (RCTs) testing the additional benefit of supplemental interventions during respiratory rehabilitation in COPD patients.

Methods
Systematic review with literature searches in six electronic databases, extensive hand-searching and contacting of authors. Two reviewers selected independently eligible RCTs, rated the methodological quality and extracted the data, which were analyzed considering the minimal important difference of patient-important outcomes where possible.

Findings
We identified 20 RCTs whereof 18 provided sufficient data for analysis. The methodological quality was low and sample sizes were too small for most trials to produce meaningful results (median total sample size = 28). Data from five trials showed that supplemental oxygen during exercise did not have clinically meaningful effects on health-related quality of life while improvements of exercise capacity may be even larger for patients exercising on room air. RCTs of adding assisted ventilation, nutritional supplements or a number of anabolically acting drugs do not provide sufficient evidence for or against the use any of these supplemental interventions.

Interpretation
There is insufficient evidence for most supplemental interventions during respiratory rehabilitation to estimate their additional value, partly due to methodological shortcomings of included RCTs. Current data do not suggest benefit from supplemental oxygen during exercise, although the methodological quality of included trials limits conclusions. To appropriately assess any of the various supplemental interventions used in clinical practice, pragmatic trials on respiratory rehabilitation of COPD patients need to consider methodological aspects as well as appropriate sample sizes.
Application of microarray technology in pulmonary diseases
Authors: Tzouvelekis Argyris , Patlakas George , Bouros Demosthenes 
Published: January 2005

AbstractMicroarrays are a powerful tool that have multiple applications both in clinical and cell biology arenas of common lung diseases. To exemplify how this tool can be useful, in this review, we will provide an overview of the application of microarray technology in research relevant to common lung diseases and present some of the future perspectives.
Nicotine signals through muscle-type and neuronal nicotinic acetylcholine receptors in both human bronchial epithelial cells and airway fibroblasts
Authors: Carlisle Diane L , Hopkins Toni M , Gaither-Davis Autumn , Silhanek Michele J , Luketich James D , Christie Neil A , Siegfried Jill M 
Published: January 2005

Abstract
Background
Non-neuronal cells, including those derived from lung, are reported to express nicotinic acetylcholine receptors (nAChR). We examined nAChR subunit expression in short-term cultures of human airway cells derived from a series of never smokers, ex-smokers, and active smokers.

Methods and Results
At the mRNA level, human bronchial epithelial (HBE) cells and airway fibroblasts expressed a range of nAChR subunits. In multiple cultures of both cell types, mRNA was detected for subunits that constitute functional muscle-type and neuronal-type pentomeric receptors. Two immortalized cell lines derived from HBE cells also expressed muscle-type and neuronal-type nAChR subunits. Airway fibroblasts expressed mRNA for three muscle-type subunits (α1, δ, and ε) significantly more often than HBE cells. Immunoblotting of HBE cell and airway fibroblast extracts confirmed that mRNA for many nAChR subunits is translated into detectable levels of protein, and evidence of glycosylation of nAChRs was observed. Some minor differences in nAChR expression were found based on smoking status in fibroblasts or HBE cells. Nicotine triggered calcium influx in the immortalized HBE cell line BEAS2B, which was blocked by α-bungarotoxin and to a lesser extent by hexamethonium. Activation of PKC and MAPK p38, but not MAPK p42/44, was observed in BEAS2B cells exposed to nicotine. In contrast, nicotine could activate p42/44 in airway fibroblasts within five minutes of exposure.

Conclusions
These results suggest that muscle-type and neuronal-type nAChRs are functional in airway fibroblasts and HBE cells, that prior tobacco exposure does not appear to be an important variable in nAChR expression, and that distinct signaling pathways are observed in response to nicotine.
Rhodobacter capsulatus porphobilinogen synthase, a high activity metal ion independent hexamer
Authors: Bollivar David W , Clauson Cheryl , Lighthall Rachel , Forbes Siiri , Kokona Bashkim , Fairman Robert , Kundrat Lenka , Jaffe Eileen K 
Published: January 2005

Abstract
Background
The enzyme porphobilinogen synthase (PBGS), which is central to the biosynthesis of heme, chlorophyll and cobalamins, has long been known to use a variety of metal ions and has recently been shown able to exist in two very different quaternary forms that are related to metal ion usage. This paper reports new information on the metal ion independence and quaternary structure of PBGS from the photosynthetic bacterium Rhodobacter capsulatus.

Results
The gene for R. capsulatus PBGS was amplified from genomic DNA and sequencing revealed errors in the sequence database. R. capsulatus PBGS was heterologously expressed in E. coli and purified to homogeneity. Analysis of an unusual phylogenetic variation in metal ion usage by PBGS enzymes predicts that R. capsulatus PBGS does not utilize metal ions such as Zn2+, or Mg2+, which have been shown to act in other PBGS at either catalytic or allosteric sites. Studies with these ions and chelators confirm the predictions. A broad pH optimum was determined to be independent of monovalent cations, approximately 8.5, and the Km value shows an acidic pKa of ~6. Because the metal ions of other PBGS affect the quaternary structure, gel permeation chromatography and analytical ultracentrifugation experiments were performed to examine the quaternary structure of metal ion independent R. capsulatus PBGS. The enzyme was found to be predominantly hexameric, in contrast with most other PBGS, which are octameric. A protein concentration dependence to the specific activity suggests that the hexameric R. capsulatus PBGS is very active and can dissociate to smaller, less active, species. A homology model of hexameric R. capsulatus PBGS is presented and discussed.

Conclusion
The evidence presented in this paper supports the unusual position of the R. capsulatus PBGS as not requiring any metal ions for function. Unlike other wild-type PBGS, the R. capsulatus protein is a hexamer with an unusually high specific activity when compared to other octameric PBGS proteins.
Discriminative topological features reveal biological network mechanisms
Authors: Middendorf Manuel , Ziv Etay , Adams Carter , Hom Jen , Koytcheff Robin , Levovitz Chaya , Woods Gregory , Chen Linda , Wiggins Chris 
Published: January 2005

Abstract
Background
Recent genomic and bioinformatic advances have motivated the development of numerous network models intending to describe graphs of biological, technological, and sociological origin. In most cases the success of a model has been evaluated by how well it reproduces a few key features of the real-world data, such as degree distributions, mean geodesic lengths, and clustering coefficients. Often pairs of models can reproduce these features with indistinguishable fidelity despite being generated by vastly different mechanisms. In such cases, these few target features are insufficient to distinguish which of the different models best describes real world networks of interest; moreover, it is not clear a priori that any of the presently-existing algorithms for network generation offers a predictive description of the networks inspiring them.

Results
We present a method to assess systematically which of a set of proposed network generation algorithms gives the most accurate description of a given biological network. To derive discriminative classifiers, we construct a mapping from the set of all graphs to a high-dimensional (in principle infinite-dimensional) "word space". This map defines an input space for classification schemes which allow us to state unambiguously which models are most descriptive of a given network of interest. Our training sets include networks generated from 17 models either drawn from the literature or introduced in this work. We show that different duplication-mutation schemes best describe the E. coli genetic network, the S. cerevisiae protein interaction network, and the C. elegans neuronal network, out of a set of network models including a linear preferential attachment model and a small-world model.

Conclusions
Our method is a first step towards systematizing network models and assessing their predictability, and we anticipate its usefulness for a number of communities.
Protein family comparison using statistical models and predicted structural information
Authors: Chung Richard , Yona Golan 
Published: January 2005

Abstract
Background
This paper presents a simple method to increase the sensitivity of protein family comparisons by incorporating secondary structure (SS) information. We build upon the effective information theory approach towards profile-profile comparison described in [Yona & Levitt 2002]. Our method augments profile columns using PSIPRED secondary structure predictions and assesses statistical similarity using information theoretical principles.

Results
Our tests show that this tool detects more similarities between protein families of distant homology than the previous primary sequence-based method. A very significant improvement in performance is observed when the real secondary structure is used.

Conclusions
Integration of primary and secondary structure information can substantially improve detection of relationships between remotely related protein families.
Integrating partonomic hierarchies in anatomy ontologies
Authors: Burger Albert , Davidson Duncan , Yang Yiya , Baldock Richard 
Published: January 2005

Abstract
Background
Anatomy ontologies play an increasingly important role in developing integrated bioinformatics applications. One of the primary relationships between anatomical tissues represented in such ontologies is part-of. As there are a number of ways to divide up the anatomical structure of an organism, each may be represented by more than one valid partonomic (part-of) hierarchy. This raises the issue of how to represent and integrate multiple such hierarchies.

Results
In this paper we describe a solution that is based on our work on an anatomy ontology for mouse embryo development, which is part of the Edinburgh Mouse Atlas Project (EMAP). The paper describes the basic conceptual aspects of our approach and discusses strengths and limitations of the proposed solution. A prototype was implemented in Prolog for evaluation purposes.

Conclusion
With the proposed name set approach, rather than having to standardise hierarchies, it is sufficient to agree on a suitable set of basic tissue terms and their meaning in order to facilitate the integration of multiple partonomic hierarchies.
Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer
Authors: Aris Virginie M , Cody Michael J , Cheng Jeff , Dermody James J , Soteropoulos Patricia , Recce Michael , Tolias Peter P 
Published: January 2005

Abstract
Background
A major goal of cancer research is to identify discrete biomarkers that specifically characterize a given malignancy. These markers are useful in diagnosis, may identify potential targets for drug development, and can aid in evaluating treatment efficacy and predicting patient outcome. Microarray technology has enabled marker discovery from human cells by permitting measurement of steady-state mRNA levels derived from thousands of genes. However many challenging and unresolved issues regarding the acquisition and analysis of microarray data remain, such as accounting for both experimental and biological noise, transcripts whose expression profiles are not normally distributed, guidelines for statistical assessment of false positive/negative rates and comparing data derived from different research groups. This study addresses these issues using Affymetrix HG-U95A and HG-U133 GeneChip data derived from different research groups.

Results
We present here a simple non parametric approach coupled with noise filtering to identify sets of genes differentially expressed between the normal and cancer states in oral, breast, lung, prostate and ovarian tumors. An important feature of this study is the ability to integrate data from different laboratories, improving the analytical power of the individual results. One of the most interesting findings is the down regulation of genes involved in tissue differentiation.

Conclusions
This study presents the development and application of a noise model that suppresses noise, limits false positives in the results, and allows integration of results from individual studies derived from different research groups.
Haplotype frequency estimation error analysis in the presence of missing genotype data
Authors: Kelly Enda D , Sievers Fabian , McManus Ross 
Published: January 2005

Abstract
Background
Increasingly researchers are turning to the use of haplotype analysis as a tool in population studies, the investigation of linkage disequilibrium, and candidate gene analysis. When the phase of the data is unknown, computational methods, in particular those employing the Expectation-Maximisation (EM) algorithm, are frequently used for estimating the phase and frequency of the underlying haplotypes. These methods have proved very successful, predicting the phase-known frequencies from data for which the phase is unknown with a high degree of accuracy. Recently there has been much speculation as to the effect of unknown, or missing allelic data – a common phenomenon even with modern automated DNA analysis techniques – on the performance of EM-based methods. To this end an EM-based program, modified to accommodate missing data, has been developed, incorporating non-parametric bootstrapping for the calculation of accurate confidence intervals.

Results
Here we present the results of the analyses of various data sets in which randomly selected known alleles have been relabelled as missing. Remarkably, we find that the absence of up to 30% of the data in both biallelic and multiallelic data sets with moderate to strong levels of linkage disequilibrium can be tolerated. Additionally, the frequencies of haplotypes which predominate in the complete data analysis remain essentially the same after the addition of the random noise caused by missing data.

Conclusions
These findings have important implications for the area of data gathering. It may be concluded that small levels of drop out in the data do not affect the overall accuracy of haplotype analysis perceptibly, and that, given recent findings on the effect of inaccurate data, ambiguous data points are best treated as unknown.
DEDB: a database of Drosophila melanogaster exons in splicing graph form
Authors: Lee Bernett TK , Tan Tin Wee , Ranganathan Shoba 
Published: January 2005

Abstract
Background
A wealth of quality genomic and mRNA/EST sequences in recent years has provided the data required for large-scale genome-wide analysis of alternative splicing. We have capitalized on this by constructing a database that contains alternative splicing information organized as splicing graphs, where all transcripts arising from a single gene are collected, organized and classified. The splicing graph then serves as the basis for the classification of the various types of alternative splicing events.

Description
DEDB http://proline.bic.nus.edu.sg/dedb/index.html is a database of Drosophila melanogaster exons obtained from FlyBase arranged in a splicing graph form that permits the creation of simple rules allowing for the classification of alternative splicing events. Pfam domains were also mapped onto the protein sequences allowing users to access the impact of alternative splicing events on domain organization.

Conclusions
DEDB's catalogue of splicing graphs facilitates genome-wide classification of alternative splicing events for genome analysis. The splicing graph viewer brings together genome, transcript, protein and domain information to facilitate biologists in understanding the implications of alternative splicing.