bluuebunny/crossref_metadata_2025 huggingface dataset:
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

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

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

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

Background

Open cholecystectomy through a small incision is an alternative to laparoscopic cholecystectomy.

Methods

From 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.

Results

182 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.

Conclusion

Open, 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

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

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

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

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.
Adjusting for dependent comorbidity in the calculation of healthy life expectancy
Authors: Mathers Colin D , Iburg Kim M , Begg Stephen
Published: April 2006

Background

Healthy life expectancy – sometimes called health-adjusted life expectancy (HALE) – is a form of health expectancy indicator that extends measures of life expectancy to account for the distribution of health states in the population. The World Health Organization has estimated healthy life expectancy for 192 WHO Member States using information from health interview surveys and from the Global Burden of Disease Study. The latter estimates loss of health by cause, age and sex for populations. Summation of prevalent years lived with disability (PYLD) across all causes would result in overestimation of the severity of the population average health state because of comorbidity between conditions. Earlier HALE calculations made adjustments for independent comorbidity in adding PYLD across causes. This paper presents a method for adjusting for dependent comorbidity using available empirical data.

Methods

Data from five large national health surveys were analysed by age and sex to estimate "dependent comorbidity" factors for pairs of conditions. These factors were defined as the ratio of the prevalence of people with both conditions to the product of the two total prevalences for each of the conditions. The resulting dependent comorbidity factors were used for all Member States to adjust for dependent comorbidity in summation of PYLD across all causes and in the calculation of HALE. A sensitivity analysis was also carried out for order effects in the proposed calculation method.

Results

There was surprising consistency in the dependent comorbidity factors across the five surveys. The improved estimation of dependent comorbidity resulted in reductions in total PYLD per capita ranging from a few per cent in younger adult ages to around 8% in the oldest age group (80 years and over) in developed countries and up to 15% in the oldest age group in the least developed countries. The effect of the dependent comorbidity adjustment on estimated healthy life expectancies is small for some regions (high income countries, Eastern Europe, Western Pacific) and ranges from an increase of 0.5 to 1.5 years for countries in Latin America, South East Asia and Sub-Saharan Africa.

Conclusion

The available evidence suggests that dependent comorbidity is important, and that adjustment for it makes a significant difference to resulting HALE estimates for some regions of the world. Given the data limitations, we recommend a normative adjustment based on the available evidence, and applied consistently across all countries.
Comparison of the Genome Structure of the Self-Incompatibility (S) Locus in Interspecific Pairs of S Haplotypes
Authors: Fujimoto Ryo , Okazaki Keiichi , Fukai Eigo , Kusaba Makoto , Nishio Takeshi
Published: April 2006

The determinants of recognition specificity of self-incompatibility in Brassica are SRK in the stigma and SP11/SCR in the pollen, both of which are encoded in the S locus. The nucleotide sequence analyses of many SRK and SP11/SCR alleles have identified several interspecific pairs of S haplotypes having highly similar sequences between B. oleracea and B. rapa. These interspecific pairs of S haplotypes are considered to be derived from common ancestors and to have maintained the same recognition specificity after speciation. In this study, the genome structures of three interspecific pairs of S haplotypes were compared by sequencing SRK, SP11/SCR, and their flanking regions. Regions between SRK and SP11/SCR in B. oleracea were demonstrated to be much longer than those of B. rapa and several retrotransposon-like sequences were identified in the S locus in B. oleracea. Among the seven retrotransposon-like sequences, six sequences were found to belong to the ty3 gypsy group. The gag sequences of the retrotransposon-like sequences were phylogenetically different from each other. In Southern blot analysis using retrotransposon-like sequences as probes, the B. oleracea genome showed more signals than the B. rapa genome did. These findings suggest a role for the S locus and genome evolution in self-incompatible plant species.
Fission Yeast Num1p Is a Cortical Factor Anchoring Dynein and Is Essential for the Horse-Tail Nuclear Movement During Meiotic Prophase
Authors: Yamashita Akira , Yamamoto Masayuki
Published: April 2006

During meiotic prophase in the fission yeast Schizosaccharomyces pombe, the nucleus oscillates between the two ends of a cell. This oscillatory nuclear movement is important to promote accurate pairing of homologous chromosomes and requires cytoplasmic dynein. Dynein accumulates at the points where microtubule plus ends contact the cell cortex and generate a force to drive nuclear oscillation. However, it remains poorly understood how dynein associates with the cell cortex. Here we show that S. pombe Num1p functions as a cortical-anchoring factor for dynein. Num1p is expressed in a meiosis-specific manner and localized to the cell cortex through its C-terminal PH domain. The num1 deletion mutant shows microtubule dynamics comparable to that in the wild type. However, it lacks cortical accumulation of dynein and is defective in the nuclear oscillation as is the case for the dynein mutant. We also show that Num1p can recruit dynein independently of the CLIP-170 homolog Tip1p.
A Coalescent-Based Estimator of Admixture From DNA Sequences
Authors: Wang Jinliang
Published: April 2006

A variety of estimators have been developed to use genetic marker information in inferring the admixture proportions (parental contributions) of a hybrid population. The majority of these estimators used allele frequency data, ignored molecular information that is available in markers such as microsatellites and DNA sequences, and assumed that mutations are absent since the admixture event. As a result, these estimators may fail to deliver an estimate or give rather poor estimates when admixture is ancient and thus mutations are not negligible. A previous molecular estimator based its inference of admixture proportions on the average coalescent times between pairs of genes taken from within and between populations. In this article I propose an estimator that considers the entire genealogy of all of the sampled genes and infers admixture proportions from the numbers of segregating sites in DNA sequence samples. By considering the genealogy of all sequences rather than pairs of sequences, this new estimator also allows the joint estimation of other interesting parameters in the admixture model, such as admixture time, divergence time, population size, and mutation rate. Comparative analyses of simulated data indicate that the new coalescent estimator generally yields better estimates of admixture proportions than the previous molecular estimator, especially when the parental populations are not highly differentiated. It also gives reasonably accurate estimates of other admixture parameters. A human mtDNA sequence data set was analyzed to demonstrate the method, and the analysis results are discussed and compared with those from previous studies.
Concordant Genetic Estimators of Migration Reveal Anthropogenically Enhanced Source-Sink Population Structure in the River Sculpin,Cottus gobio
Authors: Hänfling B , Weetman D
Published: April 2006

River systems are vulnerable to natural and anthropogenic habitat fragmentation and will often harbor populations deviating markedly from simplified theoretical models. We investigated fine-scale population structure in the sedentary river fish Cottus gobio using microsatellites and compared migration estimates from three FST estimators, a coalescent maximum-likelihood method and Bayesian recent migration analyses. Source-sink structure was evident via asymmetry in migration and genetic diversity with smaller upstream locations emigration biased and larger downstream subpopulations immigration biased. Patterns of isolation by distance suggested that the system was largely, but not entirely, in migration-drift equilibrium, with headwater populations harboring a signal of past colonizations and in some cases also recent population bottlenecks. Up- vs. downstream asymmetry in population structure was partly attributable to the effects of flow direction, but was enhanced by weirs prohibiting compensatory upstream migration. Estimators of migration showed strong correspondence, at least in relative terms, especially if pairwise FST was used as an indirect index of relative gene flow rather than being translated to Nm. Since true parameter values are unknown in natural systems, comparisons among estimators are important, both to determine confidence in estimates of migration and to validate the performance of different methods.
Chemical and Biological Characteristics of Physically Uncomplexed Organic Matter
Authors: Gregorich E. G. , Beare M. H. , McKim U. F. , Skjemstad J. O.
Published: April 2006

Physical fractionation methods are based on the premise that soil organic matter (SOM) can be divided into pools of functional relevance. Physically uncomplexed organic matter (OM) is isolated on the basis of particle size and/or density. Our objective here is to review research on the biological and chemical characteristics of physically uncomplexed OM that demonstrates its value (or otherwise) as a meaningful pool of SOM. Chemical characterization indicates that fractions isolated by size are not identical to those separated by density; even materials separated using variations of a particular fractionation method (i.e., different sizes or different densities) have different chemical and biological properties. Physically uncomplexed OM often contains a substantial portion of whole soil carbon (C) and nitrogen (N) and, compared with the whole soil or heavy fraction, has a wide C/N ratio and high O‐alkyl (i.e., carbohydrates) and low carbonyl (i.e., proteins) C contents. The response of physically uncomplexed OM to changes in land use and management practices is greater than that of other labile OM fractions or the whole soil C and N. Studies to elucidate the nutrient availability of physically uncomplexed OM suggest that it is not an immediate source of nutrients. That the quantity of physically uncomplexed OM is not always related to the amount of plant residue inputs suggests that other factors may control its accumulation in soil. Thus the quantity and the biological and chemical properties of physically uncomplexed OM are affected by the amount, composition, and accessibility of plant residues entering the soil; environmental conditions that may enhance or constrain decomposition; and the fractionation technique used.
Taverner's Use of Erasmus and the Protestantization of English Humanism
Authors: Yost John K.
Published: April 2006

It is of course now obvious that the execution of More and Fisher did not bring about the collapse of the humanist movement in England during the middle third of the sixteenth century. Little attention, however, has been given to the fact that the loss of the two outstanding leaders of the older generation of humanists was followed by a decline of Catholic and the substantial growth of Protestant humanism. The primary aim of recent studies has been, rather, to establish the continuity of English humanism in the period that was not long ago widely believed to be its dark age. These recent works, to be sure, have persuasively traced its continuity in the analytical and realistic discussion of social and economic problems, the ideological bases of Henrician policy, and the interaction of Erasmian religious thought and the political Reformation.
Durer's ‘Four Apostles’ and the Dedication as a Form of Renaissance Art Patronage
Authors: Christensen Carl C.
Published: April 2006

In early October 1526 Albrecht Dürer dedicated the greatest of his paintings, the two panels commonly known as the ‘Four Apostles,' to the city council of his native Nuernberg. Although the work was accompanied by a letter explaining the reasons for the gift, modern scholars nonetheless have continued to speculate as to the full intentions of the artist. The subject matter of the painting, as well as the Biblical passages incorporated as an inscription at the base of the work, has turned the attention of most commentators to the contemporary religious scene, i.e., the recent establishment of the Lutheran Reformation in the free imperial city. One can also, however, consider this problem profitably from a different perspective, taking as a point of departure the question of art patronage and the art market in the early sixteenth century. Existing evidence, when viewed in this manner, not only sheds new light on this particular donation but also serves as an interesting commentary on the economic situation of the artist of the period.
A Greek Collection in Padua: The Library of Gian Vincenzo Pinelli (1535-1601
Authors: Grendler Marcella
Published: April 2006

The name Gian Vincenzo Pinelli is hardly known today, even among specialists in the Italian Renaissance. This was not always so. Four hundred years ago every Italian intellectual and most non- Italian intellectuals would have responded to the name Pinelli with enthusiasm and appreciation, since he possessed one of the best, perhaps the best private library in Italy in the second half of the sixteenth century. He not only collected books and manuscripts, he also put them at the disposal of serious readers. Moreover, he personally encouraged scholars in every imaginable field. Pinelli and his library deserve to be better known.
Titian's Pastoral Scene: A Unique Rendition of Lot and His Daughters
Authors: Mellinkoff Ruth
Published: April 2006

Titian's drawing called Pastoral Scene or Landscape with a Sleeping Nude and Animals is no ordinary landscape, its unordinariness underscored by an unusual combination of elements, which I maintain reveals a new and unique version of Lot and His Daughters. I contend that the large, naked woman in the right foreground is one of Lot's daughters; the two small figures resting or sleeping beneath the trees are Lot and his other daughter; the thatched houses in the middle left represent the little town of Segor where Lot first fled; the sheep represent livestock that Lot brought out of Sodom, as do the boar and goat; the boar and goat, however, also serve as symbols of lust and lechery; and the distant city with burning buildings in the city's right quarter is Sodom. Titian's inventiveness created an iconographic variation of an ancient theme.
Systematic optimization of an H2 PEM fuel cell power generation system with heat integration
Authors: Xu Cong , Biegler Lorenz T. , Jhon Myung S.
Published: April 2006

An H2 Polymer Electrolyte Membrane (PEM) Fuel Cell power generation system composed of three subsystems: fuel reforming, fuel cell stack, and post combustion is examined. The system is simulated and optimized with a fuel cell model integrated within the process flow sheet. A case study optimization of the entire power generation system is presented and the influence of heat integration on the optimization is demonstrated. Our objectives are to maximize the energy and system efficiencies as well as the system profit. Here, optimization formulations with heat integration are used to realize our objectives, which explore the synergy between optimization and heat integration. Our results showed that we can achieve an energy efficiency as high as 58.30% and a system efficiency as high as 28.35%. For comparison, we provide results obtained from sequential process optimization followed by heat integration. The gain from the synergy is mostly exemplified in the profit maximization study, where the profit increases by almost 27.15% in the best case. Finally, we obtain optimization results that include feed vaporization of water to steam as a comparison for the heat integration. These results demonstrate the importance of simultaneous optimal heat integration for fuel cell‐based processes. © 2006 American Institute of Chemical Engineers AIChE J, 2006
Direction‐oriented routing scheme for intervehicle multihop wireless networks
Authors: Shingu Masahisa , Masubuchi Tomohiro , Uehara Hideyuki , Yokoyama Mitsuo
Published: April 2006

This paper presents a direction‐oriented routing protocol (DORP) which exploits the features of the intervehicle multihop wireless communications (IVC) environment. Assuming a one‐dimensional highway as the IVC environment, the topology of the IVC network will be straight lines along the road. The relative position of neighboring vehicles will be limited to two directions, and the destination must be in one of two directions. In addition, once the direction of the destination is fixed, each node will just forward a packet in that direction rather than choose a relay node. Therefore, direction information is very attractive as routing information. We consider a group of vehicles driving on a one‐dimensional highway as a traffic model, and evaluate the performance of the proposed scheme by computer simulation. It is found that the proposed scheme can provide a higher packet delivery ratio and a lower number of redundant packets than DSR. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 3, 89(10): 11–22, 2006; Published online in Wiley InterScience (www.interscience. wiley.com). DOI 10.1002/ecjc.20182
A probability‐density‐based autoregressive model using support vector method and higher‐order spectra estimation
Authors: Nishiguchi Yoshitomo , Toda Naohiro , Usui Shiro
Published: April 2006

When the characteristics of non‐Gaussian time series such as biological signals are described, not only power spectra but also higher‐order spectra are required. In order to obtain estimated values with few statistical fluctuations, some parametric estimation method has to be established. As the parametric model, regression‐function‐based autoregressive models such as the neural network autoregressive model have been studied so far. On the other hand, probability‐density‐based autoregressive models in which the correlation information of the time series is represented by the conditional probability density function have been proposed. However, in the existing probability‐density‐based autoregressive models, higher‐order spectral estimation is not assumed. So, if we adopt the probability‐density‐based autoregressive model for the estimation of higher‐order spectra, some problems such as the stationarity arise. In this paper, we proposed a new probability‐density‐based autoregressive model using the support vector method. Further, we estimated higher‐order spectra of the time series by the proposed model. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 3, 89(10): 1–10, 2006; Published online in Wiley InterScience (www.interscience. wiley.com). DOI 10.1002/ecjc.20225
Octahedral RuII Complexes with [PNO] Hydrazonic Ligands: Synthesis, Structure, Reactivity and Catalytic Activity in the Addition of Benzoic Acid to Alkynes
Authors: Pelagatti Paolo , Bacchi Alessia , Balordi Marcella , Bolaño Sandra , Calbiani Francesca , Elviri Lisa , Gonsalvi Luca , Pelizzi Corrado , Peruzzini Maurizio , Rogolino Dominga
Published: April 2006

A series of RuII complexes containing [(H)PNO] hydrazonic ligands were synthesised using different ruthenium sources such as [Ru(PPh3)3Cl2], [Ru(dmso)4Cl2] and [Ru(p‐cymene)Cl2]2. The complexes were characterised by 1H NMR, 31P{1H} NMR, IR, FAB‐MS, microanalysis and in some cases by X‐ray diffraction analysis on a single crystal. The ligands show a great variety of different coordinating behaviours such as κ3‐(H)PNO, κ2‐(H)PN, κ1‐(H)P and κ3‐PNO, depending on the ruthenium precursor and on the synthetic experimental conditions. The complexes trans‐[Ru(κ3‐(H)PNO)(PPh3)Cl2] reacted with dmso to give the bis‐chelate complex [Ru(κ3‐PNO)2], [Ru(dmso)4]Cl2, OPPh3, HCl and Me2S, through an oxygen‐transfer reaction from dmso to PPh3. A catalytic version of this reaction was also developed. The complexes obtained from [Ru(PPh3)3Cl2] were tested as homogeneous pre‐catalysts for the coupling between benzoic acid and terminal alkynes to give the corresponding enol esters. High stereo‐ and regio‐selectivity, up to 100 % (determined by 1H NMR), in favour of the (Z)‐anti‐Markovnikov products (Z)‐alk‐1‐en‐1‐yl benzoate was observed. An ESI‐MS monitoring of the catalytic couplings revealed that the enol ester formation occurs through an intermolecular attack of an external carboxylate anion onto a vinylidene–Ru intermediate of the type [Ru(PNO)(PPh3)(C=CH–C4H9)Cl]. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Oxidized low-density lipoprotein inhibits hepatitis C virus cell entry in human hepatoma cells
Authors: von Hahn Thomas , Lindenbach Brett D. , Boullier Agnès , Quehenberger Oswald , Paulson Matthew , Rice Charles M. , McKeating Jane A.
Published: April 2006

Cell entry of hepatitis C virus, pseudoparticles (HCVpp) and cell culture grown virus (HCVcc), requires the interaction of viral glycoproteins with CD81 and other as yet unknown cellular factors. One of these is likely to be the scavenger receptor class B type I (SR-BI). To further understand the role of SR-BI, we examined the effect of SR-BI ligands on HCVpp and HCVcc infectivity. Oxidized low-density lipoprotein (oxLDL), but not native LDL, potently inhibited HCVpp and HCVcc cell entry. Pseudoparticles bearing unrelated viral glycoproteins or bovine viral diarrhea virus were not affected. A dose-dependent inhibition was observed for HCVpp bearing diverse viral glycoproteins with an approximate IC50 of 1.5 μg/mL apolipoprotein content, which is within the range of oxLDL reported to be present in human plasma. The ability of lipoprotein components to bind to target cells associated with their antiviral activity, suggesting a mechanism of action which targets a cell surface receptor critical for HCV infection of the host cell. However, binding of soluble E2 to SR-BI or CD81 was not affected by oxLDL, suggesting that oxLDL does not act as a simple receptor blocker. At the same time, oxLDL incubation altered the biophysical properties of HCVpp, suggesting a ternary interaction of oxLDL with both virus and target cells.

In conclusion

, the SR-BI ligand oxLDL is a potent cell entry inhibitor for a broad range of HCV strains

in vitro

. These findings suggest that SR-BI is an essential component of the cellular HCV receptor complex. (Hepatology 2006;43:932–942.)
Effects of angiogenic factor overexpression by human and rodent cholangiocytes in polycystic liver diseases
Authors: Fabris Luca , Cadamuro Massimiliano , Fiorotto Romina , Roskams Tania , Spirlì Carlo , Melero Saida , Sonzogni Aurelio , Joplin Ruth E. , Okolicsanyi Lajos , Strazzabosco Mario
Published: April 2006

Liver involvement in autosomal dominant polycystic kidney disease (ADPKD) is characterized by altered remodeling of the embryonic ductal plate (DP) with presence of biliary cysts and aberrant portal vasculature. The genetic defect causing ADPKD has been identified, but mechanisms of liver cyst growth remain uncertain. To investigate the possible role of angiogenic mechanisms, we have studied the immunohistochemical expression of vascular endothelial growth factor (VEGF), angiopoietin–1 (Ang-1), angiopoietin-2 (Ang-2) and their receptors (VEGFR-1, VEGFR-2, Tie-2) in ADPKD, Caroli's disease, normal and fetal livers. In ADPKD and control livers Ang-1 and Ang-2 gene expression was studied by real-time-PCR. Effects of VEGF on cholangiocyte proliferation were studied by PCNA Western Blot in isolated rat cholangiocytes and by MTS assay in cultured cholangiocytes isolated from ADPKD patients and from an ADPKD mouse model (Pkd2WS25/−). Cholangiocytes were strongly positive for VEGF, VEGFR-1, VEGFR-2 and Ang-2 in ADPKD and Caroli, and also for Ang-1 and Tie-2 in ADPKD, similar to fetal ductal plate cells. VEGF stimulated proliferation in both normal and ADPKD cholangiocytes, but the effect was particularly evident in the latter. Ang-1 alone had no effect, but was synergic to VEGF. VEGF expression on cholangiocytes positively correlated with microvascular density.

In conclusion

, consistent with the immature phenotype of the cystic epithelium, expression of VEGF, VEGFRs, Ang-1 and Tie-2 is strongly upregulated in cholangiocytes from polycystic liver diseases. VEGF and Ang-1 have autocrine proliferative effect on cholangiocyte growth and paracrine effect on portal vasculature, thus promoting the growth of the cysts and their vascular supply.

Supplementary material for this article can be found on the HEPATOLOGY website (

http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html

).

(Hepatology 2006;43:1001–1012.)
Identification of a hepatitis C virus–reactive T cell receptor that does not require CD8 for target cell recognition
Authors: Callender Glenda G. , Rosen Hugo R. , Roszkowski Jeffrey J. , Lyons Gretchen E. , Li Mingli , Moore Tamson , Brasic Natasha , McKee Mark D. , Nishimura Michael I.
Published: April 2006

Hepatitis C virus (HCV) has been reported to elicit B and T cell immunity in infected patients. Despite the presence of antiviral immunity, many patients develop chronic infections leading to cirrhosis, hepatocellular carcinoma, and liver failure that can require transplantation. We have previously described the presence of HLA-A2–restricted, HCV NS3–reactive cytotoxic T lymphocytes (CTL) in the blood of HLA-A2− liver transplantation patients that received an HLA-A2+ liver allograft. These T cells are analogous to the “allospecific” T cells that have been described in hematopoietic stem cell transplantation patients. It has been speculated that allospecific T cells express high-affinity T cell receptors (TCRs). To determine if our HCV-reactive T cells expressed TCRs with relatively high affinity for antigen, we identified and cloned a TCR from an allospecific HLA-A2–restricted, HCV:NS3:1406-1415–reactive CD8+ T cell clone and expressed this HCV TCR in Jurkat cells. Tetramer binding to HCV TCR–transduced Jurkat cells required CD8 expression, whereas antigen recognition did not.

In conclusion

, based on the reactivity of the TCR-transduced Jurkat cells, we have identified a TCR that transfers anti-HCV reactivity to alternate effectors. These data suggest this high affinity HCV-specific TCR might have potential new immunotherapic implications. (Hepatology 2006;43:973–981.)
Prevention of first overt episode of hepatic encephalopathy after TIPS: No easy task
Authors: Mullen Kevin D. , Ghanta Ravi K. , Putka Brian S.
Published: April 2006

Abstract

Background/Aims:

Hepatic encephalopathy is a frequent event after transjugular-intrahepatic-portosystemic-shunt (TIPS), especially during the first months. Aim of this study was to compare two different treatments (lactitol 60 g/day, rifaximin 1200 mg/day) with no-treatment in the prevention of post-TIPS hepatic encephalopathy.

Methods:

Seventy-five consecutive cirrhotics submitted to TIPS were randomized to receive either one of the above treatments or no-treatment. The main end-point was the occurrence of an episode of overt hepatic encephalopathy during the first month post-TIPS. Before the procedure and weekly thereafter the patients were evaluated by examining their mental status, asterixis, ammonia and trail-making-test Part-A (TMT-A).

Results:

The three groups were comparable for age, sex, etiology, Child-Pugh-score, post-TIPS porto-systemic gradient, previous hepatic encephalopathy, basal values of ammonia and psychometric performance. Twenty-five patients developed hepatic encephalopathy (33%, CI 95%=22-45%). One-month incidence was similar in the three groups (P=0.97). Previous hepatic encephalopathy (Relative Hazard=3.79;1.27-11.31) and basal-TMT-A Z-score1.5 (RH=3.55;1.24-10.2) were predictors of post-TIPS encephalopathy at multivariate analysis. A <5 mmHg porto-systemic gradient was also significantly related to the occurrence of encephalopathy.

Conclusions:

Our data show that treatment with lactitol or rifaximin is not effective in the prophylaxis of hepatic encephalopathy during the first month after a TIPS.
Duration of peginterferon therapy in acute hepatitis C: A randomized trial
Authors: Kamal Sanaa M. , Moustafa Khairy N. , Chen Jason , Fehr Jutta , Moneim Azza Abdel , Khalifa Khalifa E. , El Gohary Leila A. , Ramy Amr H. , Madwar Mohamed A. , Rasenack Jens , Afdhal Nezam H.
Published: April 2006

Spontaneous resolution of acute hepatitis C virus infection cannot be predicted, and chronic evolution of the disease occurs in a majority of cases. To assess the efficacy and safety of peginterferon alpha-2b administered for 8, 12, or 24 weeks in patients with acute hepatitis C virus infection a total of 161 patients were identified with acute hepatitis C virus infection. Of these, 30 patients refused treatment but were retained in the study as a nonrandomized comparison group. Of the 131 patients who consented to treatment, 29 patients spontaneously resolved, leaving 102 patients randomly assigned to peginterferon alpha-2b (1.5 μg/kg) for 8 weeks (group A; n = 34), 12 weeks (group B; n = 34), and 24 weeks (group C; n = 34). The primary end point was sustained virologic response. An intent-to-treat analysis was used for efficacy and safety end points. Sustained virologic response was achieved in 23/34 (67.6%), 28/34 (82.4%), and 31/34 (91.2%) of patients in groups A, B, and C, respectively; all had undetectable hepatitis C virus RNA 48 weeks after the end of therapy. Treatment for 8 or 12 weeks was effective in genotypes 2, 3, and 4, whereas genotype 1 required 24 weeks of therapy. The 8- and 12-week regimens were associated with fewer adverse events compared with the 24-week regimen.

In conclusion

, peginterferon alpha-2b effectively induces high sustained virologic response rates in patients with acute hepatitis C virus infection, thus preventing development of chronic hepatitis C. Duration of treatment should be further optimized based on genotype and rapid virologic response at week 4. (Hepatology 2006;43:923–931.)
Hydrophilic nanofibrous structure of polylactide; fabrication and cell affinity
Authors: Bhattarai Shanta Raj , Bhattarai Narayan , Viswanathamurthi Periasamy , Yi Ho Keun , Hwang Pyoung Han , Kim Hak Yong
Published: April 2006

Microstructure and architecture of the scaffolds along with the surface chemistry exert profound effect on biological activity (cell distribution, proliferation, and differentiation). For the biological activity, scaffolds in tissue engineering have been widely designed. The objective of this study was to develop hydrophilic nanofibrous structure of polylactides (PLLA) polymer in the form of nonwoven mat by electrospinning technique, and further evaluate the fibroblast NIH3T3 cell proliferation, morphology, and cell–matrix interaction. Hydrophilicity of the PLLA fibers was improved by adding small fraction of low molecular weight polyethylene glycol (PEG) into the electrospinning solution. Four different ratio types (100/0, 80/20, 70/30, and 50/50) of PLLA/PEG electrospun matrices were fabricated, and the pore characteristics, tensile properties, contact angle, and hydrolytic degradation were observed. Furthermore, scanning electron microscope (SEM) and fluorescence actin staining images were used for micro‐observation of cell–matrix interaction and cell morphology. It was found that the electrospun mat of PLLA/PEG (80/20), composed of fibers with diameters in the range 540–850 nm, majority of pore diameter less than 100 μm, tensile strength 8 MPa, elongation 150%, porosity more than 90%, and improved hydrophilicity with slow hydrolytic degradation, is favorable for biological activity of NIH3T3 fibroblast cell. Based on these results, the correct composition of PLLA and PEG in the porous electrospun matrix (i.e., PLLA/PEG (80/20)) will be a better candidate rather than other compositions of PLLA/PEG as well as hydrophobic PLLA for application in tissue engineering. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res, 2006