bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration of relational and hierarchical network information for protein function prediction
Authors: Jiang Xiaoyu , Nariai Naoki , Steffen Martin , Kasif Simon , Kolaczyk Eric D
Published: August 2008

Background

In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO) database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions.

Results

We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing.

Conclusion

A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor) and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased positive predictive value), and that this increase is consistent uniformly with GO-term depth. Additional in silico validation on a collection of new annotations recently added to GO confirms the advantages suggested by the cross-validation study. Taken as a whole, our results show that a hierarchical approach to network-based protein function prediction, that exploits the ontological structure of protein annotation databases in a principled manner, can offer substantial advantages over the successive application of 'flat' network-based methods.
Differential screening identifies transcripts with depot-dependent expression in white adipose tissues
Authors: Wu Yu , Kim Ji Young , Zhou Shengli , Smas Cynthia M
Published: August 2008

Background

The co-morbidities of obesity are tied to location of excess fat in the intra-abdominal as compared to subcutaneous white adipose tissue (WAT) depot. Genes distinctly expressed in WAT depots may impart depot-dependent physiological functions. To identify such genes, we prepared subtractive cDNA libraries from murine subcutaneous (SC) or intra-abdominal epididymal (EP) white adipocytes.

Results

Differential screening and qPCR validation identified 7 transcripts with 2.5-fold or greater enrichment in EP vs. SC adipocytes. Boc, a component of the hedgehog signaling pathway demonstrated highest enrichment (~12-fold) in EP adipocytes. We also identified a dramatic enrichment in SC adipocytes vs. EP adipocytes and in SC WAT vs. EP WAT for transcript(s) for the major urinary proteins (Mups), small secreted proteins with pheromone functions that are members of the lipocalin family. Expression of Boc and Mup transcript was further assessed in murine tissues, adipogenesis models, and obesity. qPCR analysis reveals that EP WAT is a major site of expression of Boc transcript. Furthermore, Boc transcript expression decreased in obese EP WAT with a concomitant upregulation of Boc transcript in the obese SC WAT depot. Assessment of the Boc binding partner Cdon in adipose tissue and cell fractions thereof, revealed transcript expression similar to Boc; suggestive of a role for the Boc-Cdon axis in WAT depot function. Mup transcripts were predominantly expressed in liver and in the SC and RP WAT depots and increased several thousand-fold during differentiation of primary murine preadipocytes to adipocytes. Mup transcripts were also markedly reduced in SC WAT and liver of ob/ob genetically obese mice compared to wild type.

Conclusion

Further assessment of WAT depot-enriched transcripts may uncover distinctions in WAT depot gene expression that illuminate the physiological impact of regional adiposity.
Survey of extrachromosomal circular DNA derived from plant satellite repeats
Authors: Navrátilová Alice , Koblížková Andrea , Macas Jiří
Published: August 2008

Background

Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes.

Results

We performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (Arabidopsis, Oryza, Pisum, Secale, Triticum and Vicia). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths.

Conclusion

This work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity.
Results of emergency Hartmann's operation for obstructive or perforated left-sided colorectal cancer
Authors: Charbonnet Pierre , Gervaz Pascal , Andres Axel , Bucher Pascal , Konrad Béatrice , Morel Philippe
Published: August 2008

Background

Up to 15% of colorectal cancer (CRC) patients present with obstructive or perforated tumours, and require emergency surgery. The Hartmann's procedure (HP) provides the opportunity to achieve a potentially curative (R0) resection, while minimizing surgical trauma in poor-risk patients. The aim of this study was to assess the surgical (operative mortality), and oncological (long-term survival after curative resection) results of emergency HP for obstructive or perforated left-sided CRC.

Methods

A retrospective review of 50 patients who underwent emergency HP for perforated/obstructive CRC in our institution between 1995 and 2006.

Results

Median age of patients was 75 (range 22–95) years and the indications for HP were obstruction (32) and perforation (18 patients). Operative mortality and morbidity were 8% and 26% respectively. 35 patients (70%) were operated with a curative intent; in this group, overall 1-, 3- and 5-year survival rates were 80%, 54% and 40%. In univariate analysis, the presence of lymph node metastases was associated with poor 5-year survival (62% [Stage II] vs. 27% [Stage III], log-rank test, p = 0.02). Eleven patients (22%) had their operation reversed with a median delay of 225 (range 94–390) days. In this subgroup, two patients died from distant metastases, but there were no instances of loco-regional recurrence.

Conclusion

Hartmann's operation remains a good option to palliate symptoms in 30% of patients with left-sided CRC who are not candidates to a curative resection. For those who have a curative resection, the oncological outcome is acceptable, especially stage II patients, who appear to benefit the most from this surgical strategy.
Does preoperative analysis of intrahepatic venous anastomoses improve the surgeon's intraoperative decision making? Pilot data from a case report
Authors: Fischer Lars , Schoebinger Max , Neumann Jan-Oliver , Müller Sascha , Meinzer Hans-Peter , Büchler Markus W , Schmied Bruno M
Published: August 2008

Background

Three-dimensional (3D) visualization is thought to improve the anatomical understanding of clinicians, thus improving patient safety.

Case presentation

A 58-year-old male was admitted to our hospital in April 2007 with a suspected metastasis of a sigmoid cancer in the Couinaud segment (CS) 7. The anatomical situation of this patient was analyzed using both a CT scan and 3D images. The initial CT scan revealed that the proximal part of the middle hepatic vein was completely missing and the metastasis in the CS 7 was closely attached to the right hepatic vein. After analyzing additional 3D images, it became clear that due to the close proximity of metastasis and right hepatic vein, the resection of the right hepatic vein was inevitable. Based on this 3D analysis, it was decided to perform a right-sided hemihepatectomy. In this case report, 3D visualization resulted in a faster and clearer understanding of the unique anatomical situation in a patient with complicated liver anatomy than transversal CT images.

Conclusion

The here presented data shows for the first time 3D visualization of intravenous anastomoses in the human liver. The information offered by 3D visualization is not redundant but rather serves as a true source of additional information, indicating the potential benefit of 3D visualization in surgical operation planning.
Nuclear Factor-κB Mediates the Inhibitory Effects of Tumor Necrosis Factor-α on Growth Hormone-Inducible Gene Expression in Liver
Authors: Buzzelli Mark D. , Nagarajan Murali , Radtka John F. , Shumate Margaret L. , Navaratnarajah Maithili , Lang Charles H. , Cooney Robert N.
Published: August 2008

TNF inhibits serine protease inhibitor 2.1 (Spi 2.1) and IGF-I gene expression by GH in CWSV-1 hepatocytes. The current study describes construction of a GH-inducible IGF-I promoter construct and investigates mechanisms by which TNF and nuclear factor-κB (NFκB) inhibit GH-inducible gene expression. CWSV-1 cells were transfected with GH-inducible Spi 2.1 or IGF-I promoter luciferase constructs, incubated with TNF signaling inhibitors (fumonisin B1 for sphingomyelinase and SP600125 for c-Jun N-terminal kinase), treated with or without TNF, and then stimulated with recombinant human GH. The 5- to 6-fold induction of Spi 2.1 and IGF-I promoter activity by GH was inhibited by TNF. Neither fumonisin B1 nor SP600125 prevented the inhibitory effects of TNF on GH-inducible promoter activity. Dominant-negative inhibitor-κBα (IκBα) expression vectors (IκBαS/A or IκBαTrunc), p65 and p50 expression vectors, and p65 deletion constructs were used to investigate the NFκB pathway. IκBαS/A and IκBαTrunc ameliorated the inhibitory effects of TNF on GH-inducible Spi 2.1 and IGF-I promoter activity. Cotransfection of CWSV-1 cells with expression vectors for p65 alone or p50 and p65 together inhibited GH-inducible Spi 2.1 and IGF-I promoter activity. Cotransfection with a C-terminal p65 deletion (1–450) enhanced GH-inducible promoter activity, whereas the N-terminal deletion (31–551) was inhibitory for IGF-I but not Spi 2.1. Cycloheximide did not antagonize the inhibitory effects of TNF on GH-inducible IGF-I expression. We conclude the inhibitory effects of TNF on GH-inducible promoter activity are mediated by NFκB, especially p65, by a mechanism that does not require protein synthesis.
Signaling Pathways Involved in Sphingosine Kinase Activation and Sphingosine-1-Phosphate Release in Rat Myometrium in Late Pregnancy: Role in the Induction of Cyclooxygenase 2
Authors: Serrano-Sanchez Martin , Tanfin Zahra , Leiber Denis
Published: August 2008

We investigated the regulation of the sphingosine kinase (SphK)/sphingosine-1-phosphate (S1P) axis and its role during pregnancy in the rat myometrium. SphK1 and SphK2 were coexpressed in myometrium during gestation. The levels and activity of SphK1/2 were modest at midgestation (d 12), increased at d 19 and progressively declined to low at postpartum. Similar patterns were observed for the phosphorylation of ERK and protein kinase C (PKC). Inhibition of PKC and ERK reduced SphK1/2 activity. In late pregnancy, levels of cyclooxygenase 2 (COX2) increased in parallel to SphK levels. Using a pharmacological approach, we demonstrated that in primary cultures of myometrial cells from d-19 pregnant rats, induction of COX2 was mediated by 4β-phorbol 12,13-dibutyrate and IL-1β through sequential activation of PKC, ERK1/2, and SphK1. S1P produced by SphK1 was released in the medium. Addition of S1P, IL-1β or 4β-phorbol 12,13-dibutyrate enhanced COX2 levels via Gi protein. Interestingly, S1P was also released by myometrial tissues at late gestation. This event was dependent on PKC/ERK/SphK1. By contrast, in d-12 myometrial tissues, the release of S1P was markedly reduced in association with low levels of SphK1 and COX2. However, prolonged incubation of myometrium from midgestation led to the induction of COX2. This effect was blocked by SphK inhibitors, providing evidence of the close relationship between SphK activity and COX2 induction in rat myometrium. Overall, our findings provided insight into the physiological relevance of the SphK activation and S1P release in uterine smooth muscle during gestation.
Predicting acoustic orientation in complex real-world environments
Authors: Mhatre Natasha , Balakrishnan Rohini
Published: August 2008

Animals have to accomplish several tasks in their lifetime, such as finding food and mates and avoiding predators. Animals that locate these using sound need to detect, recognize and localize appropriate acoustic objects in their environment, typically in noisy, non-ideal conditions. Quantitative models attempting to explain or predict animal behaviour should be able to accurately simulate behaviour in such complex, real-world conditions. Female crickets locate potential mates in choruses of simultaneously calling males. In the present study, we have tested field cricket acoustic orientation behaviour in complex acoustic conditions in the field and also successfully predicted female orientation and paths under these conditions using a simulation model based on auditory physiology. Such simulation models can provide powerful tools to predict and dissect patterns of behaviour in complex, natural environments.
lsm1mutations impairing the ability of the Lsm1p-7p-Pat1p complex to preferentially bind to oligoadenylated RNA affect mRNA decay in vivo
Authors: Chowdhury Ashis , Tharun Sundaresan
Published: August 2008

The poly(A) tail is a crucial determinant in the control of both mRNA translation and decay. Poly(A) tail length dictates the triggering of the degradation of the message body in the major 5′ to 3′ and 3′ to 5′ mRNA decay pathways of eukaryotes. In the 5′ to 3′ pathway oligoadenylated but not polyadenylated mRNAs are selectively decapped in vivo, allowing their subsequent degradation by 5′ to 3′ exonucleolysis. The conserved Lsm1p-7p-Pat1p complex is required for normal rates of decapping in vivo, and the purified complex exhibits strong binding preference for oligoadenylated RNAs over polyadenylated or unadenylated RNAs in vitro. In the present study, we show that twolsm1mutants produce mutant complexes that fail to exhibit such higher affinity for oligoadenylated RNA in vitro. Interestingly, these mutant complexes are normal with regard to their integrity and retain the characteristic RNA binding properties of the wild-type complex, namely, binding near the 3′-end of the RNA, having higher affinity for unadenylated RNAs that carry U-tracts near the 3′-end over those that do not and exhibiting similar affinities for unadenylated and polyadenylated RNAs. Yet, theselsm1mutants exhibit a strong mRNA decay defect in vivo. These results underscore the importance of Lsm1p-7p-Pat1p complex–mRNA interaction for mRNA decay in vivo and imply that the oligo(A) tail mediated enhancement of such interaction is crucial in that process.
Influence of Mn(III) availability on the phase transformation from layered buserite to tunnel-structured todorokite
Authors: Cui Haojie , Liu Xiangwen , Tan Wenfeng , Feng Xionghan , Liu Fan , Ruan Huada Daniel
Published: August 2008

Todorokite is a common Mn oxide mineral in terrestrial and ocean-floor environments, and it is commonly synthesized from layered Na-buserite. Pyrophosphate, which is known to form strong complexes with Mn(III) at a pH range of 1–8, was added to a suspension of Na-buserite in order to sequester the available Mn(III) in Na-buserite. No Mn(III)-pyrophosphate complex was formed in solution at pH 10, and the treated Na-buserites were converted completely to todorokite. Significant transformation reductions were observed when Na-buserite was treated with pyrophosphate solution at pH 7. The presence of Mn(III) within the MnO6 octahedral sheets of Na-buserite is critical for the transformation from layered buserite to tunnel-structured todorokite at atmospheric pressure. At lower pH, two effects are combined to reduce the amount of Mn(III) in the layers: (1) the complexing power of pyrophosphate is increased; and (2) the transformation from Na-buserite to H-birnessite, which is concomitant with the migration of Mn(III) from layers to the interlayer, and the partial disproportionation of Mn(III). The results showed that Mn(III) played a key role in the transformation of layered Na-buserite to tunnel-structured todorokite at atmospheric pressure.
Preferred orientation of mineral grains in sample mounts for quantitative XRD measurements: How random are powder samples?
Authors: Kleeberg Reinhard , Monecke Thomas , Hillier Stephen
Published: August 2008

The degree of preferred orientation of mineral grains in powder X-ray diffraction (XRD) samples prepared by standard techniques has been evaluated by means of a correction model implemented in the Rietveld program, BGMN. It is demonstrated that neither front- nor side-loading of mineral powders obtained by wet grinding in a McCrone micronizing mill yield powder mounts with randomly oriented particles. Despite fine grinding, the primary sizes and shapes of mineral grains contained in multi-phase samples influence the degree of preferred orientation in XRD powder mounts. Two minerals, both of platy habit, were found to show different degrees of preferred orientation in front- and side-loaded samples. In contrast to these methods of sample preparation, the spray-drying technique yielded perfect randomness of the particles. The experiments on artificial mineral mixtures demonstrate that the model applied can effectively correct for preferred orientation allowing reliable Rietveld quantitative phase analysis of moderately textured samples prepared by standard techniques.
Role of Microbial Fe(III) Reduction and Solution Chemistry in Aggregation and Settling of Suspended Particles in the Mississippi River Delta Plain, Louisiana, USA
Authors: Jaisi Deb P. , Ji Shanshan , Dong Hailiang , Blake Ruth E. , Eberl Dennis D. , Kim Jinwook
Published: August 2008

River-dominated delta areas are primary sites of active biogeochemical cycling, with productivity enhanced by terrestrial inputs of nutrients. Particle aggregation in these areas primarily controls the deposition of suspended particles, yet factors that control particle aggregation and resulting sedimentation in these environments are poorly understood. This study was designed to investigate the role of microbial Fe(III) reduction and solution chemistry in aggregation of suspended particles in the Mississippi Delta. Three representative sites along the salinity gradient were selected and sediments were collected from the sediment-water interface. Based on quantitative mineralogical analyses 88–89 wt.% of all minerals in the sediments are clays, mainly smectite and illite. Consumption of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:c="http://cambridge.org/core/content" xmlns:core="http://cambridge.org/core" xmlns:m="http://cambridge.org/core/metadata" xmlns:cup="http://contentservices.cambridge.org" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mnf="http://cambridge.org/core/manifest">SO42−\$\end{document} and the formation of H2S and pyrite during microbial Fe(III) reduction of the non-sterile sediments by Shewanella putrefaciens CN32 in artificial pore water (APW) media suggest simultaneous sulfate and Fe(III) reduction activity. The pHPZNPC of the sediments was ⩽3.5 and their zeta potentials at the sediment-water interface pH (6.9–7.3) varied from −35 to −45 mV, suggesting that both edges and faces of clay particles have negative surface charge. Therefore, high concentrations of cations in pore water are expected to be a predominant factor in particle aggregation consistent with the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Experiments on aggregation of different types of sediments in the same APW composition revealed that the sediment with low zeta potential had a high rate of aggregation. Similarly, addition of external Fe(II) (i.e. not derived from sediments) was normally found to enhance particle aggregation and deposition in all sediments, probably resulting from a decrease in surface potential of particles due to specific Fe(II) sorption. Scanning and transmission electron microscopy (SEM, TEM) images showed predominant face-to-face clay aggregation in native sediments and composite mixtures of biopolymer, bacteria, and clay minerals in the bioreduced sediments. However, a clear need remains for additional information on the conditions, if any, that favor the development of anoxia in deep- and bottom-water bodies supporting Fe(III) reduction and resulting in particle aggregation and sedimentation.
The trapping of B from water by exfoliated and functionalized vermiculite
Authors: Kehal Mohamed , Reinert Laurence , Maurin David , Bantignies Jean-Louis , Ohashi Fumihiko , Mennour Ammar , Duclaux Laurent
Published: August 2008

Micron-grade natural vermiculite was modified by several physical and chemical treatments in order to increase the adsorption capacity of this material for B. A thermal exfoliation (T = 600°C) of pristine material, a chemical exfoliation through reaction with hydrogen peroxide (H2O2 35%), or grafting of a specific B complexant (i.e. N-methyl-D-glucamine: NMDG) led to an increase in the uptake of B at low initial concentrations of the aqueous solutions ([B] ≈ 5 mg L−1). The more efficient material is the NMDG-grafted clay, for which the adsorption uptake is four times greater than that of raw vermiculite, and reaches 0.04 mmol g−1. For all modified materials, the effect of the pH on B adsorption and the adsorption kinetics were studied and compared to raw vermiculite. Adsorption isotherms were also plotted and fitted well with the Freundlich equation.
XRD, FTIR, and thermal analysis of bauxite ore-processing waste (red mud) exchanged with heavy metals
Authors: Castaldi Paola , Silvetti Margherita , Santona Laura , Enzo Stefano , Melis Pietro
Published: August 2008

The present work shows the results of X-ray diffraction (XRD), Fourier transform infrared (FTIR), and thermal analysis of untreated (RMnt) and acid-treated red mud (RMa), a bauxite ore-processing waste, exchanged with Pb2+, Cd2+, and Zn2+ cations. These studies were performed in order to investigate the changes in the sorbent structure caused by the exchange with metals of different ionic radii.

The XRD pattern of RMnt, analyzed according to the Rietveld method, showed a mixture of eight different phases. However, just three phases made up 78 wt.% of the RMnt: cancrinite (33 wt.%), hematite (29 wt.%), and sodalite (16 wt.%). X-ray diffraction patterns of RMnt exchanged with Pb2+ and Cd2+ cations revealed two additional phases, namely hydrocerussite [Pb3(CO3)2(OH)2 (10 wt.%))] and octavite [CdCO3 (8 wt.%)].

These two phases probably originated from the carbonate precipitation processes which were due to the decarbonation of cancrinite. Hydrocerussite and octavite were not found in the case of acid-treated red mud samples.

In the FTIR spectra, the introduction of cations caused a distinct shift to higher wavenumbers in the peak at ∼1100 cm−1, which is attributed to the asymmetric stretch of Si-O-Al. This effect may be associated with the Pb2+, Cd2+, and Zn2+ adsorbed by the red muds which caused a deformation of the initial structure.

Thermal analysis data of the red mud samples were obtained by thermogravimetric/differential thermogravimetric analysis, and these methods were employed to evaluate the desorption behavior of water and to clarify the thermal stability of the chemical phases of the different red mud samples. The loss of metal-bound water in the red mud samples was found to depend on the size of non-framework cations and water loss consistently followed the order: Zn2+>Cd2+>Pb2+.
Does the feedback from previous trials influence current decisions? A study on the role of feedback processing in making decisions under explicit risk conditions
Authors: Brand Matthias.
Published: August 2008

Decision situations frequently provide information about the amount of gains and losses and winning probabilities. In decisions under these conditions, also called risk conditions, both the use of feedback and executive functions have been shown to influence the decision‐making process, as revealed in different patient populations. However, the influence of offering feedback in tasks examining decisions under risk conditions has not been investigated experimentally, so far. This was the aim of the present study. For this purpose, a sample of healthy individuals was examined with the Game of Dice Task, a decision‐making task that explicitly provides the rules for gains and losses and in which participants receive feedback after each trial. In addition, a modified version of this task was performed, in which the feedback after each trial and all associated feedback components were removed. Results indicate that participants had a lower performance in the modified Dice Task without feedback. They selected the disadvantageous alternatives more frequently, when they did not receive feedback following their choices. Task performance in either version was correlated with executive functioning. Conclusion: In decisions under risk conditions, both executive functions as well as the use of feedback following previous trials are important components for optimal performance. Results have implications for the interpretation of deficient decision making in patients with neuropsychological impairments as both disturbances in categorization and other cognitive processes as well as emotional dysfunctions can compromise decision making in risky situations.
Improved Granulocyte Colony-Stimulating Factor Mobilization of Hemopoietic Progenitors Using Cytokine Combinations in Primates
Authors: Larsen Stephen R. , Chng Keefe , Battah Fiona , Martiniello-Wilks Rosetta , Rasko John E.J.
Published: August 2008

Peripheral blood stem cells (PBSCs), usually mobilized with granulocyte colony-stimulating factor (G-CSF) alone or in combination with chemotherapy, are the preferred source of cells for hemopoietic stem cell transplantation. Up to 25% of otherwise eligible transplant recipients fail to harvest adequate PBSCs. Therefore it is important to investigate existing and novel reagents to improve PBSC mobilization. Because of marked interindividual variation in humans, we developed a robust nonhuman primate model that allows the direct comparison of the efficacy of two PBSC mobilization regimens within the same animal. Using this model, we compared pegylated G-CSF (pegG-CSF) with standard G-CSF and compared the combination of G-CSF and pegylated megakaryocyte growth and development factor (pegMGDF) with G-CSF plus stem cell factor (SCF) by measuring the levels of CD34+ cells, colony-forming cells (CFCs), and SCID repopulating cells (SRCs) before and after cytokine administration. Mobilization of CD34+ cells, CFCs and SRCs using pegG-CSF achieved similar levels to those resulting from 5 days of standard G-CSF. The combination of G-CSF+pegMGDF mobilized progenitors to levels similar to G-CSF+SCF but greater than standard G-CSF for CD34+ cells and CFC. This first direct comparison of PBSC mobilization in individual primates demonstrates that peg-G-CSF is equivalent to daily G-CSF and that the addition of pegMGDF to G-CSF improves mobilization. In light of the development of new thrombopoietin agonists, these data offer the potential for improved stem cell mobilization strategies.

Disclosure of potential conflicts of interest is found at the end of this article.
Consumer Preferences for Detailed versus Summary Formats of Nutrition Information on Grocery Store Shelf Labels
Authors: Berning Joshua P , Chouinard Hayley H , McCluskey Jill J
Published: August 2008

The health-related problems caused by poor diet choices has elevated the policy importance of how to communicate nutrition information more effectively to consumers at the point of purchase. At the same time, food retailers want to provide their customers with nutrition information in the format their shoppers prefer. The shopping environment, which includes the provision of nutrition information, is a way that food retailers can differentiate themselves from the competition. In this article, we present a simple model of the demand for nutrition information and empirically evaluate consumer preferences for two different formats. We compare nutrition information on grocery store shelf labels in the Greater San Francisco Area presented in detailed and summary formats. The detailed nutrition information provides an explicit description of specific nutrients but may be more costly to process and difficult to understand. Summary nutrition information reduces processing effort but provides a condensed description of nutritional content. The results indicate that there are higher mean preferences for detailed nutrition labels but also a greater dispersion of preferences. Nutrition-conscious consumers are more likely to prefer detailed information. The summary format may benefit shoppers who are less likely to use other forms of information.
Prediction of the Heat Transfer Coefficient in a Bubble Column Using an Artificial Neural Network
Authors: Al-Hemiri Adel A. , Ahmedzeki Nada S.
Published: August 2008

An artificial neural network (ANN) was applied for the prediction of the heat transfer coefficient in bubble columns, in order to obtain a general model and to facilitate the scale up of these multiphase contactors, covering a wide range of operating conditions, physical properties, and column dimensions, obtained from literature. A large number of data was collected (more than 1000) via a comprehensive literature survey. Selected parameters affecting the heat transfer coefficient were organized in six groups to serve as the input parameters. These were: gas superficial velocity, gas density, liquid density, diameter of the column, liquid viscosity, and gas hold-up. Four Back-Propagation Networks (BPNNS) were built. Two were trained using a different number of input parameters. The first ANN was trained with six inputs, which were the aforementioned parameters. The second was trained with three inputs only. These were gas velocity, liquid viscosity and gas hold-up. Each ANN was examined for two structures i.e., one hidden layer and two hidden layers. Comparison between these networks was made to find the optimal ANN structure with minimum %AARE and the maximum correlation coefficient (%R). It was found that the ANN structure of [6-13-1] with a %AARE of 16.2 and a %R of 94 was the best.
Advanced Concepts for the Kinetic Modeling of Fatty Acid Methyl Esters Hydrogenation
Authors: Cabrera Maria Ines , Grau Ricardo J.
Published: August 2008

Kinetic studies of the catalytic hydrogenation of vegetable oils and fatty acid methyl esters in liquid-phase are commonly performed in the framework of the Langmuir-Hinshelwood-Hougen-Watson (LHHW) formalism using the competitive and non-competitive adsorption models, which are certainly extreme. Based on the advanced concepts of multicentered adsorption and semi-competitive adsorption, mechanistic kinetic models including a distinction between occupied-sites and covered-sites by the large molecules of FAMEs were formulated without expressing an opinion a priori on whether the adsorption regime is competitive or non-competitive. The theoretical basis of the advanced kinetic modeling is described and successfully applied to three application examples of increasing complexity, including: (a) the hydrogenation of methyl oleate without cis-trans isomerization distinction, (b) the cis-trans isomerization and hydrogenation of the methyl oleate, and (c) the methyl linoleate hydrogenation including the cis-trans isomerization of the methyl oleate. The kinetic studies were carried out using a Ni/?-Al2O3, at 398, 413, 428 and 443 K, under isobaric conditions at hydrogen pressures of 370, 510, and 650 kPa, in the absence of mass-transport limitation. After model discrimination based on statistical analysis and taking into account the physical meaning of the estimated parameters, semi-competitive adsorption models were found to be more realistic than the classical LHHW competitive and non-competitive ones, mainly because they give additional information indicating that the adsorbed molecules of methyl linoleate and methyl oleate could cover up to 12 and 7 surface sites, respectively. These values are in adequate agreement with those expected from a rough computational simulation and seem to be the most interesting result, since they are factual and unattainable from the classical LHHW approaches.
Scale Up Parameter for Surface Aeration Systems
Authors: Rao Achanta Ramakrishna , Bimlesh Kumar
Published: August 2008

Based on the scale up parameter, X (theoretical power per unit volume = F4/3 R1/3, where F is the impeller Froude number and R is the impeller Reynolds number), it is presented that the said parameter is useful in scaling up the micromixing time in surface aeration systems. Scale up equations correlating X with micromixing time have been presented for the geometrically similar circular surface aeration systems.
Kinetic Study of Advanced Oxidation of Eosin Dye by Fenton's Reagent
Authors: Banerjee Phalguni , DasGupta Sunando , De Sirshendu
Published: August 2008

An advanced oxidation study using Fenton's reagent, i.e., ferrous sulfate and hydrogen peroxide was carried out for studying oxidation of eosin dye. Effects of concentration of various reagents on the degradation of dye were explored during an advanced oxidation process. It was found that ferrous concentration plays a major role in dye decomposition. Rate of dye decomposition is faster with an increase in ferrous sulfate concentration compared to the increase in hydrogen peroxide concentration. A detailed kinetic model was proposed. Profiles for eosin, hydrogen peroxide and various intermediates were also generated. The rate constant of the reaction of eosin with a hydroxyl radical was found to be of the order of 109 l/mol.s.
Synthesis and Characterization of Ordered Mesoporous Carbon/Silica Hybrid Thin Films
Authors: Wang Xiaoxian , Li Tiehu , Lin Qilang , Wang Dawei , Zhao Tingkai
Published: August 2008

Carbon/silica nanocomposite films with a hexagonal P6mm structure were fabricated directly by the oxidation and carbonization of surfactant/silica nanocomposite films, which were obtained by a dip-coating technique through a combination of sol-gel and evaporation-induced self-assembly. The as-synthesized nanocomposite films were characterized by scanning electron microscopy, X-ray diffraction, transmission electron microscopy and N2 adsorption-desorption. These analyses reveal that the carbon/silica nanocomposite films, with a narrow pore size distribution of mesopores, have an ordered symmetric structure. The pore sizes of this hybrid film can be controlled within a certain range by changing the carbonization temperature. In addition, the films are composed of a continuous silica matrix and a continuous carbon coating in about 1 nm adhered well to the silica matrix. The formation of carbon coatings from surfactant acts as a framework support to prevent the pore size of the silica matrix from shrinking.
Steady State Model for Heat Transfer in a Packed Bed Reactor of Elliptic Cylindrical Shape
Authors: Oliveira Laércio G. , Swarnakar Ramdayal , de Lima Antonio G. B.
Published: August 2008

The fixed-bed reactors of circular cylindrical geometry with heated or cooled walls are frequently used to carry out heterogeneous reactions of solid-gas type in engineering applications. The design of a fixed bed reactor requires an extensive knowledge of heat transfer characteristics within the packed bed. In this sense, this work presents a three-dimensional mathematical model to predict the heat transfer inside a fixed bed elliptical cylinder heat exchanger. The model considers uniform velocity and temperature profiles of the fluid phase at the entrance of the reactor, and constant thermo-physical properties. The surface of the equipment convective boundary condition is assumed to be constant. The energy equation, written in the elliptical cylindrical coordinates, was discretized using a finite-volume method considering a fully implicit formulation, and WUDS interpolation scheme. Numerical results of the dimensionless temperature profiles inside the packed bed reactor at a steady state are presented and temperature distribution is interpreted. To validate the model, numerical results obtained for the circular cylinder are compared with analytical results from literature and a good agreement was obtained.
Biosorption of Acid Blue 5 by Biomass Derived from Eichhornia crassipes: Batch and Column Studies
Authors: Ramasamy Ramamoorthy , Sahadevan Renganathan , Manikam Velan , Mahendradas Dharmendira Kumar , Muniswamy Raajenthiren
Published: August 2008

Biosorption of Acid Blue 5 dye by the Eichhornia crassipes was investigated in batch and column studies. Batch experiments were conducted to study the effect of initial solution pH and dye concentration. Langmuir and Freundlich sorption models were used to represent the equilibrium data. Experimental breakthrough curves in a column were obtained with bed height (5, 10 and 15 cm), flow rate (20, 25 and 30mL/min) and initial dye concentration (50, 75 and 100 mg/L). An increase in bed height and initial dye concentration favors the dye biosorption, while the minimum flow rate produced maximum dye biosorption. It was observed that the uptake of Acid Blue 5 using a bed height of 15 cm, flow rate of 20 mL/min and initial dye concentration of 100 mg/L was found to be more when compared to all other bed height, flow rate and initial dye concentration studied in the present investigation. The Bed Depth Service Time (BDST) model was used for the evaluation of continuous sorption data.
Effect of Argan Oil on Platelet Aggregation and Bleeding Time: A Beneficial Nutritional Property
Authors: Mekhfi Hassane , Gadi Dounia , Bnouham Mohammed , Ziyyat Abderrahim , Legssyer Abdelkhaleq , Aziz Mohammed
Published: August 2008

Platelet hyperactivity is one of the most important factors responsible for thrombosis and incidence of cardiovascular diseases. In this study, we investigated the effect of argan oil (0.2, 0.5, 1 and 2 %) on blood platelet aggregation (in vitro and ex vivo) and on tail bleeding time (in vivo) on rats. The in vitro aggregation was monitored after pre-incubation of platelets with argan oil for one minute. The in vivo bleeding time and ex vivo aggregation were performed after 4 weeks of oral treatment (10 ml/Kg/day). Argan oil was found to possess a maximum inhibition of the in vitro (46.4±4.3 %) and ex vivo platelet aggregation induced by different agonists (43.4±5.51 %). The ex vivo aggregation inhibition was not accompanied by a change in the platelets amount, neither in the bleeding time (5.5±0.3 min). These results suggest that argan oil may probably act directly on the common and an ultimate step of aggregation: attachment of fibrinogen to GpIIb/IIIa platelet receptors without affecting platelet adhesiveness to the vascular endothelium. These findings give evidence that the dietary intake of argan oil may be beneficial in the normalization of platelet hyperactivation and in the nutritional prevention of cardiovascular diseases.
Effect of Pretreatments on Air Drying of Papaya Cubes
Authors: Pandey Digvijay Kumar , Verma RadhaCharan , Chahar Vijay Kumar
Published: August 2008

Among various methods of preservation for fruits and vegetables, drying being simple, it is widely practiced from very ancient times. Papaya cubes were treated with Sodium meta bisulphite, Calcium chloride, blanching and their combination as pretreatments before air drying at 50oC and compared with the control sample. The time required for dehydration was comparatively less for the pretreated samples than control samples. The rehydration ratio of samples pretreated with blanching and Sodium meta bisulphite was observed maximum as 2.96.
Flow Behaviors of High Acyl Gellan Aqueous Solutions as Affected by Temperature, and Calcium and Gellan Concentrations
Authors: Huang Yiqun , Takhar Pawan Singh , Tang Juming , Swanson Barry G
Published: August 2008

Rheological behaviors of high acyl (HA) gellan are not well understood partially because of its relatively late commercialization compared to low acyl gellan. The objective of this study was to investigate the effect of temperature (5-30 °C), calcium (0, 1 and 10 mM) and gellan concentrations (0.0044-0.1000% w/v) on the flow behaviors of high acyl gellan aqueous solutions using rheological tests. Gellan solutions with 0 or 1 mM added Ca++ exhibited shear thinning behavior at gellan concentrations above 0.0125%. The influence of temperature on apparent viscosity (shear rate, 100 s-1) of gellan solutions can be described with an Arrhenius relationship. The apparent viscosity of gellan solution at low concentrations was more sensitive to temperature changes. The addition of Ca++ led to a decrease in flow resistance for a dilute gellan solution (<0.0125%), but an increased resistance for a relatively concentrated gellan solution (>0.0125%).
Effects of Heat and Pulsed Electric Fields on Bioactive Components and Color of Green Tea Infusions
Authors: Wang Mo , Yang Ruijin , Zhao Wei
Published: August 2008

Green tea is an unfermented tea containing a higher quantity of bioactive components. It has received a great deal of attention due to many biological activities, such as antioxidative, anticarcinogenic and antitumour activities. However, deterioration in quality after heating processes, in particular sterilization, was technical barrier for commercial ready-to-drink green tea production. It has already been demonstrated that pulsed electric fields (PEF) processing can alternatively be applied to deliver safe and shelf-stable products. In this paper the effect of conventional heat treatment (121 oC, 3min) and PEF treatment on the bioactive components (polyphenols, catechins and free amino acids) and color of green tea infusions was studied. There was a significant (P<0.05) decline in polyphenols, total catechins and total free amino acids induced by heat treatment, and the green tea infusions darkened and became less green and deeper yellow after the heating. Compared to heat processing, PEF can efficiently retain the bioactive components and original color of green tea infusions.
Physical-Mechanical Properties and Chemical Composition of Balangu (Lallemantia royleana (Benth. in Walla.)) Seed
Authors: Razavi Seyed Mohammad Ali , Mohammadi Moghaddam Toktam , Mohammad Amini Asad
Published: August 2008

Physical and mechanical properties of Balangu seed and other crops are necessary for the design of equipment to handling, transporting, processing and storing. In this paper, physico-mechanic properties and chemical composition of Balangu seed have been determined at a moisture content of 7.82% (d.b.). The results showed that the seeds contained averagely amounts of dry matter (92.75%), ash (3.63%), crude protein (25.60%), crude fat (18.27%), crude fiber (1.29%), NDF (30.67%) and ADF (47.80%). The average values of length, diameter, geometric mean diameter, sphericity and surface area were established as 3.148 mm, 0.720 mm, 1.176 mm, 37.4% and 4.362 mm2, respectively. The average unit mass, thousand mass, true and apparent volumes, true density, bulk density, porosity, terminal velocity and filling and emptying angles of repose were determined as 0.0016 g, 1.67 g, 1.51 mm3, 2.467 mm3, 1046.68 kg/m3, 739.50 kg/m3, 29.19% and 4.05 m/s, 27.24°, and 17.23°, respectively. The static coefficient of friction varied from 0.221 on glass to 0.432 on rubber. In the same moisture content, the average rupture force, hardness and toughness obtained 1482.06 g, 3280.76 g, 12902.83 gs, respectively.
Improving Nutritional Value of Dried Blueberries (Vaccinium corymbosum L.) Combining Microwave-Vacuum, Hot-Air Drying and Freeze Drying Technologies
Authors: Mejia-Meza Esteban I , Yanez Jaime A. , Davies Neal M. , Rasco Barbara , Younce Frank , Remsberg Connie M , Clary Carter
Published: August 2008

Blueberries (Vaccinium corymbosum L.) were dried combining microwave-vacuum, hot-air drying and freeze drying technologies to retain their nutritional value. Polyphenol retention, total polyphenols, anthocyanins, and antioxidant activity were evaluated in dried blueberries. Glycoside compounds for ellagic acid, quercetin, and kaempferol exhibited a higher retention than phloridzin, and R- and S-naringin in dried blueberries following dehydration. Freeze and HA-MIVAC® dried blueberries had a higher retention of total polyphenols and anthocyanins. Freeze dried blueberries had higher antioxidant activity, followed by the combination of HA-MIVAC®, MIVAC® and HA drying methods. FD, HA-MIVAC® and MIVAC® treated blueberries had a higher retention of individual polyphenols than HA treated blueberries, indicating that the nutritional properties of berries may be retained to a greater extent when these processes are employed.