bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of the time required for appropriate chemical de‐epithelialization of an ileal segment for cystoplasty: an animal model
Authors: Bakhtiari Jalal , Fattahian Hamid Reza , Gharagozlou Mohammad Javad , Kajbafzadeh Abdolmohammad , Jafarzadeh Seyed Reza 
Published: March 2005

Another group of authors from Iran attempted experimentally to determine the required time for the appropriate enzymatic treatment of the ideal segment to complete de‐epithelialization, thus reducing its absorptive function. They found that 25 min of enzymatic treatment of the ideal segment was adequate for this, and that it was recommended from their experimental study for cystoplasty.OBJECTIVESTo determine the time required for the appropriate enzymatic treatment of an ileal segment to de‐epithelialize its mucosa and to reduce its absorptive function for cystoplasty in dogs.MATERIALS AND METHODSTwenty‐one adult female Persian mixed‐breed dogs were divided into seven equal groups: group 1 (negative control group) had no ileocystoplasty; group 2 (positive control group) had a routine ileocystoplasty with no enzymatic treatment of the ileal segment; and groups 3–7 had an ileocystoplasty with 5, 10, 15, 20 or 25 min, respectively, of enzymatic treatment of the ileal segment with collagenase and trypsin. The seven groups were then compared for haematological, biochemical and histological changes, and glucose reabsorption assessed using a glucose‐absorption test.RESULTSNo dogs showed any signs of metabolic disturbances, biochemical and haematological changes. There were significant differences in blood glucose level (BGL) for the groups at different times after the glucose‐absorption test, but a pair‐wise comparison showed significant differences in BGL between group 1 and the other groups, except group 7. The degree of histopathological change was associated with the duration of enzymatic treatment, in that changes were more prominent in group 7. There was no shrinkage or collagen deposition.CONCLUSIONSIn these conditions, 25 min of enzymatic treatment of the ileal segment is sufficient to remove the absorptive function of the augmented bladder, and is recommended for cystoplasty in dogs.
Expectancy effects on omission evoked potentials in musicians and non‐musicians
Authors: Jongsma Marijtje L.A. , Eichele Tom , Quiroga Rodrigo Quian , Jenks Kathleen M. , Desain Peter , Honing Henkjan , Van Rijn Clementina M. 
Published: March 2005

AbstractAn expanded omitted stimulus paradigm was investigated to determine whether expectancy would modulate the amplitude of the omission evoked potentials (OEPs). In addition, we examined the effects of musical expertise on OEPs. Trials started with 3–7 beats randomly and contained 5 omitted beats. Three types of trials (n=90) were presented with 1, 2, or 3 beats occurring between omissions. A tap response at the end of each trial was used to determine timing accuracy. Clear OEPs were observed over midline sites. We found main omission effects with respect to an N150 and a P400 OEPs component, such that peak amplitudes diminished whenever the occurrence of an omitted stimulus could be expected. In addition, an N600 OEPs component emerged in response to expectedly omitted stimuli toward the end of each trial within the group of musicians. Thus, musical training seems to lead to more efficient and more refined processing of auditory temporal patterns.
Genomic instability in radial growth phase melanoma cell lines after ultraviolet irradiation
Authors: Hussein M R , Haemel A K , Sudilovsky O , Wood G S 
Published: March 2005

Background/Aims:Although ultraviolet (UV) irradiation, apoptosis, and genomic instability are all potentially involved in the pathogenesis of melanoma, in vitro studies investigating these changes in the radial growth phase of this neoplasm are still lacking; therefore, this study was designed to investigate these changes.Method:An in vitro system consisting of three radial growth phase Wistar melanoma cell lines (WM35, WM3211, and WM1650) was established. Cells were UV irradiated (10 mJ/cm2for UVB and 6 J/cm2for UVA), harvested after UV exposure, and evaluated for viability and apoptosis using Trypan blue and terminal deoxynucleotidyl transferase mediated dUTP digoxigenin nick end labelling assays, respectively. Polymerase chain reaction based microsatellite assays were used to examine the cell lines for the presence of microsatellite instability (MSI) using 21 markers at the 1p, 2p, 3p, 4q, 9p, and 17p regions.Results:Exposure to UV initiated progressive cell death associated with pronounced apoptosis, with UVA having a greater effect than UVB. MSI was found in UVB (WM35 and WM3211) and UVA (WM35) irradiated cell lines at 1p, 9p, and 17p, but not in non-irradiated cells. The prevalence of MSI was higher after UVB irradiation (14%) than UVA irradiation (4.7%), and was most frequently found at D1S233.Conclusions:The ability of erythemogenic UV irradiation to induce both apoptosis and MSI in radial growth phase melanoma cells is suggestive of its role in melanoma pathogenesis. This instability may reflect a hypermutability state, oxidative stress induced DNA damage, replication infidelity, or a combination of these factors.
Transformed Eulerian-Mean Theory. Part II: Potential Vorticity Homogenization and the Equilibrium of a Wind- and Buoyancy-Driven Zonal Flow
Authors: Kuo Allen , Plumb R. Alan , Marshall John 
Published: March 2005

Abstract
The equilibrium of a modeled wind- and buoyancy-driven, baroclinically unstable, flow is analyzed using the transformed Eulerian-mean (TEM) approach described in Part I. Within the near-adiabatic interior of the flow, Ertel potential vorticity is homogenized along mean isopycnals—a finding readily explained using TEM theory, given the geometry of the domain. The equilibrium, zonal-mean buoyancy structure at the surface is determined entirely by a balance between imposed surface fluxes and residual mean and eddy buoyancy transport within a “surface diabatic layer.” Balance between these same processes and the wind stress determines the stratification, and hence potential vorticity, immediately below this layer. Ertel potential vorticity homogenization below then determines the mean buoyancy structure everywhere. Accordingly, the equilibrium structure of this flow can be described—and quantitatively reproduced—from knowledge of the eddy mixing rates within the surface diabatic zone and the depth of this zone, together with potential vorticity homogenization beneath. These results emphasize the need to include near-surface buoyancy transport, as well as interior PV transport, in eddy parameterization schemes. They also imply that, in more realistic models, the surface buoyancy balances may be impacted by processes in remote locations that allow diapycnal flow.
The Ventilated Pool: A Model of Subtropical Mode Water
Authors: Dewar W. K. , Samelson R. M. , Vallis G. K. 
Published: March 2005

Abstract
An analytical model of subtropical mode water is presented, based on ventilated thermocline theory and on numerical solutions of a planetary geostrophic basin model. In ventilated thermocline theory, the western pool is a region bounded on the east by subsurface streamlines that outcrop at the western edge of the interior, and in which additional dynamical assumptions are necessary to complete the solution. Solutions for the western pool were originally obtained under the assumption that the potential vorticity of the subsurface layer was homogenized. In the present theory, it is instead assumed that all of the water in the pool region is ventilated and, therefore, that all the Sverdrup transport is carried in the uppermost, outcropping layer. The result is the formation of a deep, vertically homogeneous, fluid layer in the northwest corner of the subtropical gyre that extends from the surface to the base of the ventilated thermocline. This ventilated pool is an analog of the observed subtropical mode waters. The pool also has the interesting properties that it determines its own boundaries and affects the global potential vorticity–pressure relationship. When there are multiple outcropping layers, ventilated pool fluid is subducted to form a set of nested annuli in ventilated, subsurface layers, which are the deepest subducted layers in the ventilated thermocline.
An Unsuspected Boundary-Induced Temporal Computational Mode in a Two-Time-Level Discretization
Authors: Staniforth Andrew , Wood Nigel 
Published: March 2005

Abstract
Normal-mode analyses are applied to various discrete forms of the one-dimensional, linearized, vertical acoustic equations in a height-based coordinate. First, the temporally discrete, spatially continuous equations are considered and the normal modes for a bounded system are compared to those of an unbounded system. Despite the use of a two-time-level discretization, a computational mode is found in the bounded case that is absent in the unbounded case. Second, the complete temporally and spatially discrete bounded system is considered and the normal modes and associated dispersion relation are derived. No computational modes are found. However, under certain limiting conditions, the temporal discretization leads to a distortion of the physical modes so that they resemble the computational mode of the spatially continuous bounded system. Implications for analyses based on spatially continuous equation sets are discussed.
Acatholic and Ecumenical Response to the Left Behind Series
Authors: Anderson C. 
Published: March 2005

AbstractThis article seeks to explore why Roman Catholics have responded so negatively to the Left Behind Series. The article critically evaluates the charges that Pentecostal and Evangelical expectations of the rapture are necessarily ‘fundamentalist’ or inherently ‘anti-Catholic’. By presenting the Catholic Church's history of its own apocalyptic movements and its experience in America, the author suggests ways that Roman Catholics and Pentecostals can strengthen each by sharing elements of each other's understanding of the Book of Revelation.
Type 3 repeat/C-terminal domain of thrombospondin-1 triggers caspase-independent cell death through CD47/αvβ3 in promyelocytic leukemia NB4 cells
Authors: Saumet Anne , Slimane Mouna Ben , Lanotte Michel , Lawler Jack , Dubernard Véronique 
Published: March 2005

AbstractBy means of its antiangiogenic activity, thrombospondin-1 (TSP-1) exerts indirect antitumoral action on solid tumors. Here, we investigated potential antitumor action in an in vitro cell model for promyelocytic leukemia (NB4-LR1), resistant to retinoid maturation. Purified soluble TSP-1 added to cultures induced a strong dose-dependent growth inhibition and a slowly developing maturation-independent cell death. Recombinant fragments of TSP-1 allowed mapping of these activities to its type 3 repeat/C-terminal domain, features that are distinct from those of TSP-1 action on solid tumors, previously ascribed to the type 1 repeat domain. Cell death in leukemia was characterized as a caspase-independent mechanism, without DNA fragmentation, but phosphatidylserine externalization followed by membrane permeabilization. Mitochondria membrane depolarization was inherent to TSP-1 action but did not produce release of death-promoting proteins (eg, noncaspase apoptosis regulators, apoptosis-induced factor [AIF], endonuclease G, or Omi/HtrA2 or the caspase regulators, cytochrome c or second mitochondrial activator of caspase/direct inhibitor of apoptosis protein-binding protein with low isoelectric point [Smac/DIABLO]). Although detected, reactive oxygen species (ROS) production was likely not involved in the death process. Finally, receptor agonist RFYVVM and RGD peptides indicated that TSP-1 death effects are mediated by membrane receptors CD47 and αvβ3. These results demonstrated a new domain-specific antitumoral activity of TSP-1 on a leukemia cell line, which extends TSP-1 therapeutic potential outside the area of vascularized solid tumors. (Blood. 2005;106:658-667)
Feature selection and nearest centroid classification for protein mass spectrometry
Authors: Levner Ilya 
Published: March 2005

Abstract
Background
The use of mass spectrometry as a proteomics tool is poised to revolutionize early disease diagnosis and biomarker identification. Unfortunately, before standard supervised classification algorithms can be employed, the "curse of dimensionality" needs to be solved. Due to the sheer amount of information contained within the mass spectra, most standard machine learning techniques cannot be directly applied. Instead, feature selection techniques are used to first reduce the dimensionality of the input space and thus enable the subsequent use of classification algorithms. This paper examines feature selection techniques for proteomic mass spectrometry.

Results
This study examines the performance of the nearest centroid classifier coupled with the following feature selection algorithms. Student-t test, Kolmogorov-Smirnov test, and the P-test are univariate statistics used for filter-based feature ranking. From the wrapper approaches we tested sequential forward selection and a modified version of sequential backward selection. Embedded approaches included shrunken nearest centroid and a novel version of boosting based feature selection we developed. In addition, we tested several dimensionality reduction approaches, namely principal component analysis and principal component analysis coupled with linear discriminant analysis. To fairly assess each algorithm, evaluation was done using stratified cross validation with an internal leave-one-out cross-validation loop for automated feature selection. Comprehensive experiments, conducted on five popular cancer data sets, revealed that the less advocated sequential forward selection and boosted feature selection algorithms produce the most consistent results across all data sets. In contrast, the state-of-the-art performance reported on isolated data sets for several of the studied algorithms, does not hold across all data sets.

Conclusion
This study tested a number of popular feature selection methods using the nearest centroid classifier and found that several reportedly state-of-the-art algorithms in fact perform rather poorly when tested via stratified cross-validation. The revealed inconsistencies provide clear evidence that algorithm evaluation should be performed on several data sets using a consistent (i.e., non-randomized, stratified) cross-validation procedure in order for the conclusions to be statistically sound.
Evolutionary cores of domain co-occurrence networks
Authors: Wuchty Stefan , Almaas Eivind 
Published: March 2005

Abstract
Background
The modeling of complex systems, as disparate as the World Wide Web and the cellular metabolism, as networks has recently uncovered a set of generic organizing principles: Most of these systems are scale-free while at the same time modular, resulting in a hierarchical architecture. The structure of the protein domain network, where individual domains correspond to nodes and their co-occurrences in a protein are interpreted as links, also falls into this category, suggesting that domains involved in the maintenance of increasingly developed, multicellular organisms accumulate links. Here, we take the next step by studying link based properties of the protein domain co-occurrence networks of the eukaryotes S. cerevisiae, C. elegans, D. melanogaster, M. musculus and H. sapiens.

Results
We construct the protein domain co-occurrence networks from the PFAM database and analyze them by applying a k-core decomposition method that isolates the globally central (highly connected domains in the central cores) from the locally central (highly connected domains in the peripheral cores) protein domains through an iterative peeling process. Furthermore, we compare the subnetworks thus obtained to the physical domain interaction network of S. cerevisiae. We find that the innermost cores of the domain co-occurrence networks gradually grow with increasing degree of evolutionary development in going from single cellular to multicellular eukaryotes. The comparison of the cores across all the organisms under consideration uncovers patterns of domain combinations that are predominately involved in protein functions such as cell-cell contacts and signal transduction. Analyzing a weighted interaction network of PFAM domains of Yeast, we find that domains having only a few partners frequently interact with these, while the converse is true for domains with a multitude of partners. Combining domain co-occurrence and interaction information, we observe that the co-occurrence of domains in the innermost cores (globally central domains) strongly coincides with physical interaction. The comparison of the multicellular eukaryotic domain co-occurrence networks with the single celled of S. cerevisiae (the overlap network) uncovers small, connected network patterns.

Conclusion
We hypothesize that these patterns, consisting of the domains and links preserved through evolution, may constitute nucleation kernels for the evolutionary increase in proteome complexity. Combining co-occurrence and physical interaction data we argue that the driving force behind domain fusions is a collective effect caused by the number of interactions and not the individual interaction frequency.
Exogenous glycosaminoglycans coat damaged bladder surfaces in experimentally damaged mouse bladder
Authors: Kyker Kimberly D , Coffman Jean , Hurst Robert E 
Published: March 2005

Abstract
Background
Interstital cystitis is often treated with exogenous glycosaminoglycans such as heparin, chondroitin sulphate (Uracyst), hyaluronate (Cystistat) or the semi-synthetic pentosan polysulphate (Elmiron). The mechanism of action is presumed to be due to a coating of the bladder surface to replace the normally present chondroitin sulphate and heparan sulphate lost as a result of the disease. This study used fluorescent labelled chondroitin sulphate to track the distribution of glycosaminoglycans administered intravesically to mouse bladder that had been damaged on the surface.

Methods
The surfaces of mouse bladders were damaged by 3 mechanisms – trypsin, 10 mM HCl, and protamine sulphate. Texas Red-labeled chondroitin sulphate was instilled into the bladders of animals with damaged bladders and controls instilled only with saline. Bladders were harvested, frozen, and sectioned for examination by fluorescence.

Results
The normal mouse bladder bound a very thin layer of the labelled chondroitin sulphate on the luminal surface. Trypsin- and HCl-damaged bladders bound the labelled chondroitin sulphate extensively on the surface with little penetration into the bladder muscle. Protamine produced less overt damage, and much less labelling was seen, presumably due to loss of the label as it complexed with the protamine intercalated into the bladder surface.

Conclusion
Glycosaminoglycan administered intravesically does bind to damaged bladder. Given that the changes seen following bladder damage resemble those seen naturally in interstitial cystitis, the mechanisms proposed for the action of these agents is consistent with a coating of damaged bladder.
Systems for grading the quality of evidence and the strength of recommendations II: Pilot study of a new system
Authors: Atkins David , Briss Peter A , Eccles Martin , Flottorp Signe , Guyatt Gordon H , Harbour Robin T , Hill Suzanne , Jaeschke Roman , Liberati Alessandro , Magrini Nicola , Mason James , O'Connell Dianne , Oxman Andrew D , Phillips Bob , Schünemann Holger , Edejer Tessa Tan-Torres , Vist Gunn E , Williams John W ,   The GRADE Working Group
Published: March 2005

Abstract
Background
Systems that are used by different organisations to grade the quality of evidence and the strength of recommendations vary. They have different strengths and weaknesses. The GRADE Working Group has developed an approach that addresses key shortcomings in these systems. The aim of this study was to pilot test and further develop the GRADE approach to grading evidence and recommendations.

Methods
A GRADE evidence profile consists of two tables: a quality assessment and a summary of findings. Twelve evidence profiles were used in this pilot study. Each evidence profile was made based on information available in a systematic review. Seventeen people were given instructions and independently graded the level of evidence and strength of recommendation for each of the 12 evidence profiles. For each example judgements were collected, summarised and discussed in the group with the aim of improving the proposed grading system. Kappas were calculated as a measure of chance-corrected agreement for the quality of evidence for each outcome for each of the twelve evidence profiles. The seventeen judges were also asked about the ease of understanding and the sensibility of the approach. All of the judgements were recorded and disagreements discussed.

Results
There was a varied amount of agreement on the quality of evidence for the outcomes relating to each of the twelve questions (kappa coefficients for agreement beyond chance ranged from 0 to 0.82). However, there was fair agreement about the relative importance of each outcome. There was poor agreement about the balance of benefits and harms and recommendations. Most of the disagreements were easily resolved through discussion. In general we found the GRADE approach to be clear, understandable and sensible. Some modifications were made in the approach and it was agreed that more information was needed in the evidence profiles.

Conclusion
Judgements about evidence and recommendations are complex. Some subjectivity, especially regarding recommendations, is unavoidable. We believe our system for guiding these complex judgements appropriately balances the need for simplicity with the need for full and transparent consideration of all important issues.
Actinomycetes as host cells for production of recombinant proteins
Authors: Nakashima Nobutaka , Mitani Yasuo , Tamura Tomohiro 
Published: March 2005

Abstract
Actinomycetes (Actinobacteria) are highly attractive as cell factories or bioreactors for applications in industrial, agricultural, environmental, and pharmaceutical fields. Genome sequencing of several species of actinomycetes has paved the way for biochemical and structural analysis of important proteins and the production of such proteins as recombinants on a commercial scale. In this regard, there is a need for improved expression vectors that will be applicable to actinomycetes. Recent advancements in gene expression systems, knowledge regarding the intracellular environment, and identification and characterization of plasmids has made it possible to develop practicable recombinant expression systems in actinomycetes as described in this review.