bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observations of Transient Linear Organization and Nonlinear Scale Interactions in Lake-Effect Clouds. Part II: Nonlinear Scale Interactions
Authors: Miles Natasha L. , Verlinde Johannes 
Published: March 2005

Abstract
Linearly organized convection and associated horizontal roll vortices occasionally occur in atmospheric conditions in which theory predicts only cellular organization. One possible contributor to the occurrence of rolls in such conditions is nonlinear interactions between different scales of motion. In the winter of 1997/98, the Lake-Induced Convection Experiment (Lake-ICE) was conducted in part to investigate scale interactions in linearly organized convection. As discussed in Part I of this series, transient linear organization was observed during a wintertime lake-effect event during Lake-ICE. In Part II two-part nonlinear scale interactions and their possible role in the occurrence of linear organization in an unfavorable environment are investigated. Turbulence-scale vertical velocity variance peaks were consistently observed during roll strengthening and decay, suggesting a link between the scales. Composites of the nonlinear interaction terms in the roll-scale vertical turbulent kinetic energy (TKE) budget revealed that nonlinear interactions between the roll and turbulence scales were large compared to the observed change in roll-scale TKE, but do not coincide in time.
Wildfire: distributed, Grid-enabled workflow construction and execution
Authors: Tang Francis , Chua Ching Lian , Ho Liang-Yoong , Lim Yun Ping , Issac Praveen , Krishnan Arun 
Published: March 2005

Abstract
Background
We observe two trends in bioinformatics: (i) analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii) multiple CPU clusters and Grids are available to more scientists. The traditional solution to the problem of running workflows across multiple CPUs required programming, often in a scripting language such as perl. Programming places such solutions beyond the reach of many bioinformatics consumers.

Results
We present Wildfire, a graphical user interface for constructing and running workflows. Wildfire borrows user interface features from Jemboss and adds a drag-and-drop interface allowing the user to compose EMBOSS (and other) programs into workflows. For execution, Wildfire uses GEL, the underlying workflow execution engine, which can exploit available parallelism on multiple CPU machines including Beowulf-class clusters and Grids.

Conclusion
Wildfire simplifies the tasks of constructing and executing bioinformatics workflows.
Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains
Authors: Chen Liang , Zhao Hongyu 
Published: March 2005

Abstract
Background
It has been a long-term puzzle whether chromatin can be further divided into distinct gene expression domains. Because histone deacetylation affects chromatin structure, that in turn may affect the expression of nearby genes, histone deacetylation sites may act to partition chromatin into different gene expression domains. In this article, we explore the relationship between histone deacetylation sites and gene expression patterns on the genome scale using different data sources, including microarray data measuring gene expression levels, microarray data measuring histone deacetylation sites, and information on regulatory targets of transcription factors.

Results
Using 269 Saccharomyces cerevisiae microarray datasets, histone deacetylation datasets, and regulatory targets of transcription factors assembled from the Yeast Proteome Database and ChIP-chip data, we found that histone deacetylation sites can reduce the level of co-expression of neighboring genes.

Conclusion
Histone deacetylation sites may serve as possible partition sites for chromatin domains and affect gene expression.
Identification to the species level of Lactobacillus isolated in probiotic prospecting studies of human, animal or food origin by 16S-23S rRNA restriction profiling
Authors: Moreira João Luiz S , Mota Rodrigo M , Horta Maria F , Teixeira Santuza MR , Neumann Elisabeth , Nicoli Jacques R , Nunes Álvaro C 
Published: March 2005

Abstract
Background
The accurate identification of Lactobacillus and other co-isolated bacteria during microbial ecological studies of ecosystems such as the human or animal intestinal tracts and food products is a hard task by phenotypic methods requiring additional tests such as protein and/or lipids profiling.

Results
Bacteria isolated in different probiotic prospecting studies, using de Man, Rogosa and Sharpe medium (MRS), were typed at species level by PCR amplification of 16S-23S rRNA intergenic spacers using universal primers that anneal within 16S and 23S genes, followed by restriction digestion analyses of PCR products. The set of enzymes chosen differentiates most species of Lactobacillus genus and also co-isolated bacteria such as Enterococcus, Streptococcus, Weissella, Staphylococcus, and Escherichia species. The in silico predictions of restriction patterns generated by the Lactobacillus shorter spacers digested with 11 restriction enzymes with 6 bp specificities allowed us to distinguish almost all isolates at the species level but not at the subspecies one. Simultaneous theoretical digestions of the three spacers (long, medium and short) with the same set of enzymes provided more complex patterns and allowed us to distinguish the species without purifying and cloning of PCR products.

Conclusion
Lactobacillus isolates and several other strains of bacteria co-isolated on MRS medium from gastrointestinal ecosystem and fermented food products could be identified using DNA fingerprints generated by restriction endonucleases. The methodology based on amplified ribosomal DNA restriction analysis (ARDRA) is easier, faster and more accurate than the current methodologies based on fermentation profiles, used in most laboratories for the purpose of identification of these bacteria in different prospecting studies.
Frequent detection of worm movements in onchocercal nodules by ultrasonography
Authors: Mand Sabine , Marfo-Debrekyei Yeboah , Debrah Alex , Buettner Marcelle , Batsa Linda , Pfarr Kenneth , Adjei Ohene , Hoerauf Achim 
Published: March 2005

Abstract
Background
Ultrasonography (USG) is known to be a suitable tool for diagnosis in lymphatic filariasis as the adult filarial nematode Wuchereria bancrofti in scrotal lymphatic vessels of infected men can be detected by the characteristic pattern of movement, the Filaria Dance Sign. In onchocerciasis, moving adult worms have not yet been demonstrated by USG. In addition the verification of drug effects on living adult Onchocerca volvulus filariae in trials is hampered by the lack of tools for longitudinal observation of alterations induced by potentially macrofilaricidal drugs in vivo. The present study was carried out to determine the frequency of detection of moving adult filariae of O. volvulus by USG.

Methods
In an endemic region for onchocerciasis in Ghana, 61 patients infected with onchocerciasis were recruited by palpation and onchocercomas examined by USG using an ultrasound system equipped with a 7.5 – 10 MHz linear transducer. Onchocercomas were recorded on videotape and evaluated with regard to location, number and size, as well as to movements of adult filariae.

Results
In the 61 patients 303 onchocercomas were found by palpation and 401 onchocercomas were detected by USG. In 18 out of 61 patients (29.5%), altogether 22 nodules with moving adult O. volvulus filariae were detected and are presented in animated ultrasound images as mp-4 videos.

Conclusion
Ultrasonographical examinations of onchocercomas where living adult filariae can be displayed may serve as a new tool for the longitudinal observation in vivo of patients with onchocerciasis undergoing treatment and as an adjunct to histological evaluation.
On geography and medical journalology: a study of the geographical distribution of articles published in a leading medical informatics journal between 1999 and 2004
Authors: Boulos Maged N Kamel 
Published: March 2005

Abstract

Background
Studying the contribution of individual countries to leading journals in a given discipline can highlight which countries have the most impact on that discipline, and also give some idea about the geographical outreach of those journals. This paper examines the number of countries that contributed articles to one leading medical informatics journal, Medical Informatics & the Internet in Medicine, and the amount of their contributions between 1999 and the first half of 2004.

Methods
The PubMed citations of all indexed articles from the chosen journal (n = 128) were retrieved online (up to Volume 29, Number 2/June 2004 issue, the latest indexed issue as at 28 January 2005). The country of corresponding author's affiliation for each retrieved citation was recorded. The five-year-and-half corpus of abstracts retrieved from PubMed was further explored using MetaCarta Geographic Text Search http://www.metacarta.com/.

Results
The examined journal has an international outreach, with authors from 24 countries, spanning four continents, contributing to the journal during the studied period. The journal is dominated by a very large number of articles from Europe (81.25% of all articles counted in this study), and in particular from the UK (15.63%) and Greece (15.63%). There were no contributions from Africa or South America.

Conclusion
A detailed discussion and interpretation of these results and ideas for future analyses are provided. MetaCarta can prove very useful as a bibliometric research tool.
Interpretation of the post-surgical Somatostatin Receptor Scintigram of a Primary Neuroendocrine Tumor of the Thymus: a case report and literature review
Authors: Leondi Anastasia , Koutsikos John , Zerva Cherry 
Published: March 2005

AbstractA case of a thymic neuroendocrine tumor and the interpretation problems in a post-surgical Somatostatin Receptor Scintigraphy are presented. In a 53-year-old man with superior vena cava obstruction syndrome an atypical carcinoid of the thymus (neuroendocrine carcinoma of intermediate grade 2), was found at surgery.During his first year of follow-up a Somatostatin Receptor Scintigraphy was recommended. An area of abnormal concentration of the radiopharmaceutical was revealed in the mediastinum at this time.A thorough understanding of the mechanisms of the radiopharmaceutical uptake and of the various clinical settings in which uptake can occur are essential for a proper evaluation of the scintigraphic findings and result in the optimal use of this valuable modality.The literature review provides an overview of this rare type of tumor and insight into the clinical significance of Somatostatin Receptor Scintigraphy.
Optimising surgical management of elderly cancer patients
Authors: Ramesh Hodigere Sripathy Jois , Pope Daniel , Gennari Roberto , Audisio Riccardo A 
Published: March 2005

Abstract
Background
Elderly population is on rise. It is an ethical dilemma how aggressive one should be when it comes to treat cancer in elderly. Presumed fear of increased postoperative morbidity and mortality has resulted in delivery of sub-optimal cancer surgery.

Methods
In this review article we visit physiology of the aged, tools available to assess surgical risks in oncogeriatric patients, and current practice in the management of common cancers encountered in surgical oncology, with the view of increasing awareness on optimising surgical management of senior patients with cancer. A pubmed search for cancer, surgery, elderly, was carried out.

Results
Cancer is on rise with increasing age predominantly affecting breast, gastrointestinal tract and lung. Increasingly more surgeons are offering surgery to elderly cancer patient but selection bias is prevalent. Available data reflect short and long-term outcome of cancer surgery in elderly is not greatly different to that of younger patient. Declining physiological reserve along with inability to respond adequately to physiological stress are salient age related changes. C omprehensive G eriatric A ssessment (CGA) is not tested in surgical patient. There is need for a tool to define individualised operative risk. Preoperative assessment of cancer in elderly is designed to offer this information based on functional status of an individual utilising currently available tools of risk assessment.

Conclusion
All elderly cancer patients should be offered optimal treatment depending on their functional status not on chronological age. Oncogeriatric patient would benefit from dedicated multidisciplinary approach. Recruitment of elderly cancer patients to more clinical trials is needed to enhance our knowledge and to offer optimum treatment to this unique subgroup.
CTLA4-CD80/CD86 interactions on primary mouse CD4+ T cells integrate signal-strength information to modulate activation with Concanavalin A
Authors: Mukherjee Sambuddho , Ahmed Asma , Nandi Dipankar 
Published: March 2005

AbstractThe mechanisms by which concanavalin A (Con A), a lectin, activates T cells are poorly studied. A low dose of Con A is stimulatory for T cells, whereas a high dose of Con A results in suppression of proliferation and enhanced T cell death. The expression and functional roles of costimulatory receptors, CD28 and cytotoxic T-lymphocyte antigen 4 (CTLA4), and their ligands, CD80 and CD86, on primary mouse CD4+ T cells after activation with different doses of Con A were studied. CTLA4-CD80/CD86 interactions in this T:T cell activation model demonstrate distinct outcomes depending on the dose of Con A. CTLA4-CD80/CD86 interactions inhibit CD4+ T cell cycling and survival after activation with a suppressive dose of Con A by increasing oxidative stress and decreasing levels of BclXL. The enhanced CD4+ T cell death with a suppressive dose of Con A is dependent on excess H2O2 and nitric oxide but is independent of Fas and caspase activity. It is surprising that the increased proliferation of CD4+ T cells with a suppressive dose of Con A on blocking CTLA4-CD80/CD86 interactions is largely interleukin (IL)-2-independent but is cyclosporine A-sensitive. On activation with a stimulatory dose of Con A, CTLA4-CD80/CD86 interactions enhance T cell activation and survival by reducing the production of reactive oxygen species, increasing IL-2 and BclXL levels. Here IL-10 but not transforming growth factor-β plays a functional role. In summary, CTLA4-CD80/CD86 interactions on T cells integrate signal strength, based on the dose of Con A, to enhance or inhibit primary mouse CD4+ T cell cycling and survival.
Kinetics of diffusion in polyacrylonitrile fiber formation
Authors: Hou Chen , Qu Rong‐jun , Liang Ying , Wang Cheng‐guo 
Published: March 2005

AbstractA H2O/dimethyl sulfoxide (DMSO) mixture was used as the coagulation bath of the wet‐spun process for polyacrylonitrile fibers. Diffusion behaviors of coagulate and solvent of the protofibers were studied. Diffusion coefficients of H2O and DMSO of the protofibers, prepared by acrylonitrile (AN) homopolymers, were also determined. It was found that diffusion coefficients of H2O and DMSO in the protofibers prepared by AN homopolymers, synthesized by DMSO solution polymerization, are highest compared with those of AN homopolymers synthesized by H2O/DMSO mixture suspension polymerization and aqueous suspension polymerization. With increasing polyacrylonitrile concentration in the dope, diffusion coefficients of H2O and DMSO decreased continuously. Diffusion coefficients of H2O and DMSO increased concomitantly with increasing bath temperature, but the changes of diffusion coefficient values were less prominent when the temperature increased beyond 60°C. When DMSO concentration in the coagulation bath was 55 wt %, the values of diffusion coefficients of H2O and DMSO were minimal. Diffusion coefficients increased with increasing jet stretch minus ratio. When the protofiber radius was increased, there was a corresponding increase of diffusion coefficients of H2O and DMSO. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 1529–1533, 2005
Synthesis and characterization of aniline and o‐toluidine conducting copolymer microtubes with the template‐synthesis method
Authors: Xin Ling‐Yun , Zhang Xiao‐Gang , Zhang Guo‐Qing , Shen Cheng‐Min 
Published: March 2005

AbstractCopolymer microtubes composed of aniline and o‐toluidine were prepared through the synthesis of the desired polymer within the pores of a microporous anodic aluminum oxide (AAO) template. Scanning electron microscopy and transmission electron microscopy revealed that the obtained copolymer microtubes had uniform and well‐aligned arrays, and the aspect ratios of the AAO membranes could be controlled through their diameter and length. Infrared spectrometry and X‐ray photoelectron spectroscopy supported the surface analysis for the microtubes and also proved the formation of copolymers. Ultraviolet–visible/near‐infrared spectra proved that the doping effect decreased with an increase of o‐toluidine in the copolymers, but the solubility greatly improved (up to 3.83 g/L in N,N‐dimethylformamide), and the conductivity was as high as approximately 17.4 S cm−1. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 1539–1543, 2005
Inferential estimation of molecular weights of polybutadiene rubber by neural networks
Authors: Padmavathi G. , Mandan M. G. , Mitra S. P. , Chaudhuri K. K. , Patel Shital J. , Dabke S. P. 
Published: March 2005

AbstractMolecular weight distribution, which is characterized by its averages like number average (Mn) and weight average (Mw), is one of the important properties of polybutadiene rubber (PBR), and it is difficult to measure. The objective of this work is to develop models to predict Mn and Mw from readily available process variables. Neural networks that are capable of mapping highly complex and non‐linear dependencies have been adapted to develop models for the Mn and Mw of PBR. The molecular weight distribution and its averages of PBR samples collected over a wide range of operating conditions were measured by the conventional Gel Permeable Chromatograph (GPC) method. Neural networks were trained with relevant data to predict Mn and Mw from process variables. The trained networks were found to generalize well when tested with new data. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 1611–1618, 2005
Swelling behavior of poly(acrylamide‐co‐N‐vinylimidazole) hydrogels under different environment conditions
Authors: Işık Belma , Doǧantekin Banu 
Published: March 2005

AbstractA series of random copolymers of acrylamide and N‐vinylimidazole, poly(AAm‐co‐NVI), with various compositions were prepared using redox copolymerization. The influence of environmental conditions such as pH, temperature, and ionic strength on the swelling behavior of the copolymeric hydrogels was investigated. The hydrogels exhibited the highest equilibrium swelling in basic medium at high temperature. Equilibrium swelling decreased with rising ionic strength at pH 5.0. As pH increased, equilibrium swelling of the hydrogels increased at pH 11.0 and I = 0.20 M. Swelling kinetics of the hydrogels was found to be non‐Fickian at 25°C. The process tended to be Fickian at higher pH and temperature. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 1783–1788, 2005
Determination of gelation temperature of poly(vinyl chloride) by thermomechanical and thermogravimetric parameters
Authors: Boztuǧ Ali , Zengin H. Bayram , Basan Satılmış 
Published: March 2005

AbstractPreheating between the temperatures of 200 and 280°C is done to a film‐structured poly(vinyl chloride) (PVC) sample, which has a gelation temperature ∼ 250°C. After this preheat, the PVC's thermomechanical and thermal differences, at temperatures before and after thermal gelation, are observed. Consequently, when some thermomechanical and thermal parameters, obtained at temperatures before and after gelation, are compared, it can be said that this is an easier method to determine the gelation temperature of a polymer. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 1635–1640, 2005
Reaction kinetics and characteristics of polyurethane/clay nanocomposites
Authors: Kim Dae Su , Kim Jin‐Tae , Woo Won Bum 
Published: March 2005

AbstractThe reaction behavior and physical properties of polyurethane (PU)/clay nanocomposite systems were investigated. Organically modified clay was used as nanofillers to formulate the nanocomposites. Differential scanning calorimetry was used to study the reaction behavior of the PU/clay nanocomposite systems. The reaction rate of the nanocomposite systems increased with increasing clay content. The reaction kinetic parameters of proposed kinetic equations were determined by numerical methods. The glass transition temperatures of the PU/clay nanocomposite systems increased with increasing clay content. The thermal decomposition behavior of the PU/clay nanocomposites was measured by using thermogravimetric analysis. X‐ray diffractometer and transmission electronic microscope data showed the intercalation of PU resin between the silicate layers of the clay in the PU/clay nanocomposites. A universal testing machine was used to investigate the tensile properties of the PU/clay nanocomposites. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 1641–1647, 2005
Adhesion property of novel polyimides with 1‐[3′,5′‐bis(trifluoromethyl)phenyl] pyromellitic dianhydride
Authors: Myung B. Y. , Ahn C. J. , Yoon T. H. 
Published: March 2005

AbstractNovel polyimides were synthesized from 1‐[3′,5′‐bis(trifluoromethyl)phenyl] pyromellitic dianhydride (6FPPMDA) by a conventional two‐step process: the preparation of poly(amic acid) followed by solution imidization via refluxing in p‐chlorophenol. The diamines used for polyimide synthesis included bis(3‐aminophenyl)‐3,5‐bis(trifluoromethyl)phenyl phosphine oxide, bis(3‐aminophenyl)‐4‐trifluoromethylphenyl phosphine oxide, and bis(3‐aminophenyl)phenyl phosphine oxide. The synthesized polyimides were designed to have a molecular weight of 20,000 g/mol by off‐stoichiometry and were characterized by Fourier transform infrared, NMR, differential scanning calorimetry, and thermogravimetric analysis. In addition, their intrinsic viscosity, solubility, water absorption, and coefficient of thermal expansion (CTE) were also measured. The adhesion properties of the polyimides were evaluated via a T‐peel test with bare and silane/Cr‐coated Cu foils, and the failure surfaces were investigated with scanning electron microscopy. The 6FPPMDA‐based polyimides exhibited high glass‐transition temperatures (280–299°C), good thermal stability (>530°C in air), low water absorption (1.46–2.16 wt %), and fairly low CTEs (32–40 ppm/°C), in addition to good adhesion properties (83–88 g/mm) with silane/Cr‐coated Cu foils. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 1801–1809, 2005