bluuebunny/crossref_metadata_2025_split huggingface dataset:
The trapping and vertical focusing of internal waves in a pycnocline due to the horizontal inhomogeneities of density and currents
Authors: Badulin S. I. , Shrira V. I. , Tsimring L. Sh. 
Published: April 2006

This paper studies the propagation of a wave packet in regions where the central packet frequency ω is close to the local maximum of the effective Väisälä frequency Nf(z) = N(z)/[1 − k·U(z)/ω], where k is the central wavevector of the packet and U is the mean current with a vertical velocity shear. The wave approaches the layer ω = Nfm asymptotically, i.e. trapping of the wave takes place. The trapping of guided internal waves is investigated within the framework of the linearized equations of motion of an incompressible stratified fluid in the WKB approximation, with viscosity, spectral bandwidth of the packet, vertical shear of the mean current and non-stationarity of the environment taken into account. As the packet approaches the layer of trapping, the growth of the wavenumber k is restricted only by possible wave-breaking and viscous dissipation. The growth of k is accompanied by the transformation of the vertical structure of internal-wave modes. The wave motion focuses at a certain depth determined by the maximum effective Väisälä frequency Nfm. The trapping of the wave packet results in power growth of the wave amplitude and steepness. At larger times the viscous dissipation becomes a dominating factor of evolution as a result of strong slowing down of the packet motion.The role of trapping in the energy exchange of internal waves, currents and small-scale turbulence is discussed.
Interannual climatic variation mediates elevated CO2 and O3 effects on forest growth
Authors: KUBISKE MARK E. , QUINN VANESSA S. , HEILMAN WARREN E. , McDONALD EVAN P. , MARQUARDT PAULA E. , TECLAW RON M. , FRIEND ALEXANDER L. , KARNOSKY DAVID F. 
Published: April 2006

AbstractWe analyzed growth data from model aspen (Populus tremuloides Michx.) forest ecosystems grown in elevated atmospheric carbon dioxide ([CO2]; 518 μL L−1) and ozone concentrations ([O3]; 1.5 × background of 30–40 nL L−1 during daylight hours) for 7 years using free‐air CO2 enrichment technology to determine how interannual variability in present‐day climate might affect growth responses to either gas. We also tested whether growth effects of those gasses were sustained over time. Elevated [CO2] increased tree heights, diameters, and main stem volumes by 11%, 16%, and 20%, respectively, whereas elevated ozone [O3] decreased them by 11%, 8%, and 29%, respectively. Responses similar to these were found for stand volume and basal area. There were no growth responses to the combination of elevated [CO2+O3]. The elevated [CO2] growth stimulation was found to be decreasing, but relative growth rates varied considerably from year to year. Neither the variation in annual relative growth rates nor the apparent decline in CO2 growth response could be explained in terms of nitrogen or water limitations. Instead, growth responses to elevated [CO2] and [O3] interacted strongly with present‐day interannual variability in climatic conditions. The amount of photosynthetically active radiation and temperature during specific times of the year coinciding with growth phenology explained 20–63% of the annual variation in growth response to elevated [CO2] and [O3]. Years with higher photosynthetic photon flux (PPF) during the month of July resulted in more positive growth responses to elevated [CO2] and more negative growth responses to elevated [O3]. Mean daily temperatures during the month of October affected growth in a similar fashion the following year. These results indicate that a several‐year trend of increasingly cloudy summers and cool autumns were responsible for the decrease in CO2 growth response.
Extramammary Paget's disease—a proliferation of adnexal origin?
Authors: Regauer S 
Published: April 2006

Aim : To investigate a possible follicular origin of extramammary Paget's disease (EPD). EPD is a predominantly intraepidermal tumour with extensive involvement of adnexal structures and high recurrence rates suggesting a follicular stem cell origin. Cytokeratin (CK) 15 and CK19 are considered markers for follicular stem cells located in the hair follicle bulge region.Methods and results : Formalin‐fixed paraffin‐embedded tissues of 12 cases of primary EPD (three anal, nine vulvar) were studied immunohistochemically with antibodies to CK15 and CK19. All cases of EPD showed polygonal Paget cells in the interfollicular epidermis, hair follicles, sebaceous and apocrine glands distributed individually, in nests and in gland‐like areas. The polygonal Paget cells were intimately associated with small, flat, mitotically active, ‘compressed’ keratinocytes. The large Paget cells uniformly expressed CK19 in 12/12 EPD. The small ‘compressed’ keratinocytes showed strong cytoplasmic CK15 staining in 9/12 EPD with focal accentuation, while the polygonal Paget cells were negative.Conclusions : These histological and immunohistochemical observations allow the following conclusions: (i) the small, flat, ‘compressed’ keratinocytes are an integral part of EPD; (ii) the dual cell population is reminiscent of sebaceous glands with mature sebocytes and germinative keratinocytes; (iii) since both cell types express cytokeratins typical for follicular differentiation, EPD may be a proliferation of adnexal stem cells residing in the infundibulo‐sebaceous unit of hair follicles and adnexal structures.
An autonomous mobile agent‐based distributed learning architecture: a proposal and analytical analysis
Authors: Ahmed Iftikhar , Sadeq Muhammad Jafar 
Published: April 2006

AbstractCurrent distance learning systems are increasingly packing highly data‐intensive contents on servers, resulting in the congestion of network and server resources at peak service times. A distributed learning system based on faded information field (FIF) architecture that employs mobile agents (MAs) has been proposed and simulated in this work. The learning contents are decentralised in the proposed system, and these are dynamically distributed around the main education site server on different nodes in response to network congestion and server overload. The system simulation results have been presented and analysed. The proposed system holds the potential to address the network congestion and server‐overload problems in distance learning systems.
Role of acetylcholine and polyspecific cation transporters in serotonin-induced bronchoconstriction in the mouse
Authors: Kummer Wolfgang , Wiegand Silke , Akinci Sibel , Wessler Ignatz , Schinkel Alfred H , Wess Jürgen , Koepsell Hermann , Haberberger Rainer V , Lips Katrin S 
Published: April 2006

Abstract

Background
It has been proposed that serotonin (5-HT)-mediated constriction of the murine trachea is largely dependent on acetylcholine (ACh) released from the epithelium. We recently demonstrated that ACh can be released from non-neuronal cells by corticosteroid-sensitive polyspecific organic cation transporters (OCTs), which are also expressed by airway epithelial cells. Hence, the hypothesis emerged that 5-HT evokes bronchoconstriction by inducing release of ACh from epithelial cells via OCTs.

Methods
We tested this hypothesis by analysing bronchoconstriction in precision-cut murine lung slices using OCT and muscarinic ACh receptor knockout mouse strains. Epithelial ACh content was measured by HPLC, and the tissue distribution of OCT isoforms was determined by immunohistochemistry.

Results
Epithelial ACh content was significantly higher in OCT1/2 double-knockout mice (42 ± 10 % of the content of the epithelium-denuded trachea, n = 9) than in wild-type mice (16.8 ± 3.6 %, n = 11). In wild-type mice, 5-HT (1 μM) caused a bronchoconstriction that slightly exceeded that evoked by muscarine (1 μM) in intact bronchi but amounted to only 66% of the response to muscarine after epithelium removal. 5-HT-induced bronchoconstriction was undiminished in M2/M3 muscarinic ACh receptor double-knockout mice which were entirely unresponsive to muscarine. Corticosterone (1 μM) significantly reduced 5-HT-induced bronchoconstriction in wild-type and OCT1/2 double-knockout mice, but not in OCT3 knockout mice. This effect persisted after removal of the bronchial epithelium. Immunohistochemistry localized OCT3 to the bronchial smooth muscle.

Conclusion
The doubling of airway epithelial ACh content in OCT1/2-/- mice is consistent with the concept that OCT1 and/or 2 mediate ACh release from the respiratory epithelium. This effect, however, does not contribute to 5-HT-induced constriction of murine intrapulmonary bronchi. Instead, this activity involves 1) a non-cholinergic epithelium-dependent component, and 2) direct stimulation of bronchial smooth muscle cells, a response which is partly sensitive to acutely administered corticosterone acting on OCT3. These data provide new insights into the mechanisms involved in 5-HT-induced bronchoconstriction, including novel information about non-genomic, acute effects of corticosteroids on bronchoconstriction.
mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code
Authors: Karpievitch Yuliya V , Almeida Jonas S 
Published: April 2006

Abstract

Background
Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke.

Results
mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server.

Conclusion
Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet.
Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data
Authors: Vinciotti Veronica , Liu Xiaohui , Turk Rolf , de Meijer Emile J , 't Hoen Peter AC 
Published: April 2006

Abstract

Background
The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literature do not fully exploit the temporal ordering in the dataset and are not suited to the case where temporal profiles are measured for a number of different biological conditions. We present a statistical test that makes explicit use of the temporal order in the data by fitting polynomial functions to the temporal profile of each gene and for each biological condition. A Hotelling T
2-statistic is derived to detect the genes for which the parameters of these polynomials are significantly different from each other.

Results
We validate the temporal Hotelling T
2-test on muscular gene expression data from four mouse strains which were profiled at different ages: dystrophin-, beta-sarcoglycan and gamma-sarcoglycan deficient mice, and wild-type mice. The first three are animal models for different muscular dystrophies. Extensive biological validation shows that the method is capable of finding genes with temporal profiles significantly different across the four strains, as well as identifying potential biomarkers for each form of the disease. The added value of the temporal test compared to an identical test which does not make use of temporal ordering is demonstrated via a simulation study, and through confirmation of the expression profiles from selected genes by quantitative PCR experiments. The proposed method maximises the detection of the biologically interesting genes, whilst minimising false detections.

Conclusion
The temporal Hotelling T
2-test is capable of finding relatively small and robust sets of genes that display different temporal profiles between the conditions of interest. The test is simple, it can be used on gene expression data generated from any experimental design and for any number of conditions, and it allows fast interpretation of the temporal behaviour of genes. The R code is available from V.V. The microarray data have been submitted to GEO under series GSE1574 and GSE3523.
Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein
Authors: Pawlik Timothy M , Hawke David H , Liu Yanna , Krishnamurthy Savitri , Fritsche Herbert , Hunt Kelly K , Kuerer Henry M 
Published: April 2006

Abstract

Background
Isotope-coded affinity tag (ICAT) tandem mass spectrometry (MS) allows for qualitative and quantitative analysis of paired protein samples. We sought to determine whether ICAT technology could quantify and identify differential expression of tumor-specific proteins in nipple aspirate fluid (NAF) from the tumor-bearing and contralateral disease-free breasts of patients with unilateral early-stage breast cancer.

Methods
Paired NAF samples from 18 women with stage I or II unilateral invasive breast carcinoma and 4 healthy volunteers were analyzed using ICAT labeling, sodium dodecyl sulfate-polyacrylamide gel (SDS-PAGE), liquid chromatography, and MS. Proteins were identified by sequence database analysis. Western blot analysis of NAF from an independent sample set from 12 women (8 with early-stage breast cancer and 4 healthy volunteers) was also performed.

Results
353 peptides were identified from tandem mass spectra and matched to peptide sequences in the National Center for Biotechnology Information database. Equal numbers of peptides were up- versus down-regulated. Alpha2HS-glycoprotein [Heavy:Light (H:L) ratio 0.63] was underexpressed in NAF from tumor-bearing breasts, while lipophilin B (H:L ratio 1.42), beta-globin (H:L ratio 1.98), hemopexin (H:L ratio 1.73), and vitamin D-binding protein precursor (H:L ratio 1.82) were overexpressed. Western blot analysis of pooled samples of NAF from healthy volunteers versus NAF from women with breast cancer confirmed the overexpression of vitamin D-binding protein in tumor-bearing breasts.

Conclusion
ICAT tandem MS was able to identify and quantify differences in specific protein expression between NAF samples from tumor-bearing and disease-free breasts. Proteomic screening techniques using ICAT and NAF may be used to find markers for diagnosis of breast cancer.
Open cholecystectomy for all patients in the era of laparoscopic surgery – a prospective cohort study
Authors: Leo Jonas , Filipovic Goran , Krementsova Julia , Norblad Rickard , Söderholm Mattias , Nilsson Erik 
Published: April 2006

AbstractBackgroundOpen cholecystectomy through a small incision is an alternative to laparoscopic cholecystectomy.MethodsFrom 1 January 2002 through 31 December 2003, all operations upon the gallbladder in a district hospital with emergency admission and responsibility for surgical training were done as intended small-incision open cholecystectomy.Results182 women and 90 men with a median age of 56 (interquartile range 45 to 68 years) underwent cholecystectomy for symptomatic gallbladder disease, 170 as elective and 102 as emergency cases. Trainee surgeons assisted by consultants or registrars having passed an examination for open cholecystectomy performed surgery in 194 cases (71%). The common bile duct was explored in 52 patients. Total postoperative morbidity was six percent. Median postoperative stay was one day and mean total (pre- and postoperative) hospital stay 3.1 days. 32 operations (12%) were done as day surgery procedures. Nationally in Sweden in 2002, mean total hospital stay was 4.4 days, and 13% of all cholecystectomies were performed on an outpatient basis.ConclusionOpen, small-incision cholecystectomy for all patients is compatible with short hospital stay, evidence-based gall-bladder surgery, and training of surgical residents.
Secretion of functional human enzymes by Tetrahymena thermophila
Authors: Weide Thomas , Herrmann Lutz , Bockau Ulrike , Niebur Nadine , Aldag Ingo , Laroy Wouter , Contreras Roland , Tiedtke Arno , Hartmann Marcus WW 
Published: April 2006

Abstract

Background
The non-pathogenic ciliate Tetrahymena thermophila is one of the best-characterized unicellular eucaryotes used in various research fields. Previous work has shown that this unicellular organism provides many biological features to become a high-quality expression system, like multiplying to high cell densities with short generation times in bioreactors. In addition, the expression of surface antigens from the malaria parasite Plasmodium falciparum and the ciliate Ichthyophthirius multifiliis suggests that T. thermophila might play an important role in vaccine development. However, the expression of functional mammalian or human enzymes remains so far to be seen.

Results
We have been able to express a human enzyme in T. thermophila using expression modules that encode a fusion protein consisting of the endogenous phospholipase A1 precursor and mature human DNaseI. The recombinant human enzyme is active, indicating that also disulfide bridges are correctly formed. Furthermore, a detailed N-glycan structure of the recombinant enzyme is presented, illustrating a very consistent glycosylation pattern.

Conclusion
The ciliate expression system has the potential to become an excellent expression system. However, additional optimisation steps including host strain improvement as wells as measures to increase the yield of expression are necessary to be able to provide an alternative to the common E. coli and yeast-based systems as well as to transformed mammalian cell lines.
Insertional protein engineering for analytical molecular sensing
Authors: Ferraz Rosa María , Vera Andrea , Arís Anna , Villaverde Antonio 
Published: April 2006

Abstract
The quantitative detection of low analyte concentrations in complex samples is becoming an urgent need in biomedical, food and environmental fields. Biosensors, being hybrid devices composed by a biological receptor and a signal transducer, represent valuable alternatives to non biological analytical instruments because of the high specificity of the biomolecular recognition. The vast range of existing protein ligands enable those macromolecules to be used as efficient receptors to cover a diversity of applications. In addition, appropriate protein engineering approaches enable further improvement of the receptor functioning such as enhancing affinity or specificity in the ligand binding. Recently, several protein-only sensors are being developed, in which either both the receptor and signal transducer are parts of the same protein, or that use the whole cell where the protein is produced as transducer. In both cases, as no further chemical coupling is required, the production process is very convenient. However, protein platforms, being rather rigid, restrict the proper signal transduction that necessarily occurs through ligand-induced conformational changes. In this context, insertional protein engineering offers the possibility to develop new devices, efficiently responding to ligand interaction by dramatic conformational changes, in which the specificity and magnitude of the sensing response can be adjusted up to a convenient level for specific analyte species. In this report we will discuss the major engineering approaches taken for the designing of such instruments as well as the relevant examples of resulting protein-only biosensors.
Operational strategies, monitoring and control of heterologous protein production in the methylotrophic yeast Pichia pastoris under different promoters: A review
Authors: Cos Oriol , Ramón Ramón , Montesinos José Luis , Valero Francisco 
Published: April 2006

Abstract
The methylotrophic yeast Pichia pastoris has been widely reported as a suitable expression system for heterologous protein production. The use of different phenotypes under PAOX promoter, other alternative promoters, culture medium, and operational strategies with the objective to maximize either yield or productivity of the heterologous protein, but also to obtain a repetitive product batch to batch to get a robust process for the final industrial application have been reported. Medium composition, kinetics growth, fermentation operational strategies from fed-batch to continuous cultures using different phenotypes with the most common PAOX promoter and other novel promoters (GAP, FLD, ICL), the use of mixed substrates, on-line monitoring of the key fermentation parameters (methanol) and control algorithms applied to the bioprocess are reviewed and discussed in detail.
The characteristics of the spectra of superior venae cavae in patients with right heart failure
Authors: Jia Hua-Ping , Duan Yun-You , Cao Tie-Sheng , Yuan Li-Jun , Li Juan 
Published: April 2006

Abstract

Background
Aimed to elucidate the characteristics of the spectra of superior venae cavae (SVC) in respiratory cycles in patients with right heart failure.

Methods
The spectra of SVC of 30 patients with right heart failure and 30 paired healthy subjects were recorded through right supraclavicular fossa view. The profiles of spectra of superior venae cavae were observed, and peak velocity and velocity time integral (VTI) of every wave of SVC under spontaneous respiration were measured for statistical analysis.

Results
In healthy subjects, the peak velocities and VTI of S wave and D wave increased in inspiratory phase and diminished in expiratory phase, and which of S wave were larger than which of D wave in whole respiratory cycle. In patients with right heart failure, spectral variations of SVC could be classified into three patterns: Pattern I: peak velocities and VTI of S wave were larger than that of D wave in early inspiratory phase, but peak velocities and VTI of D wave were larger than those of S wave in late inspiratory phase and early expiratory phase [Pattern I-1], even in whole respiratory cycle [Pattern I-2]; Pattern II: the S wave disappeared and was substituted by inverse wave with low amplitude in whole respiratory cycle. Pattern III: the profiles of the spectra of SVC in patients were similar to those of healthy subjects. In the whole, the respiratory variation ratios of peak velocities and VTI of S wave and D wave were diminished in patients compared with those in healthy subjects.

Conclusion
The spectra of superior venae cavae in patients with right heart failure were abnormal, and these characteristics could be used as signs in evaluating right heart failure.