bluuebunny/crossref_metadata_2025_split huggingface dataset:
Traditional versus novel forecasting techniques: how much do we gain?
Authors: Fernandez Viviana 
Published: May 2008

AbstractThis article applies two novel techniques to forecast the value of US manufacturing shipments over the period 1956–2000: wavelets and support vector machines (SVM). Wavelets have become increasingly popular in the fields of economics and finance in recent years, whereas SVM has emerged as a more user‐friendly alternative to artificial neural networks. These two methodologies are compared with two well‐known time series techniques: multiplicative seasonal autoregressive integrated moving average (ARIMA) and unobserved components (UC). Based on forecasting accuracy and encompassing tests, and forecasting combination, we conclude that UC and ARIMA generally outperform wavelets and SVM. However, in some cases the latter provide valuable forecasting information that it is not contained in the former. Copyright © 2008 John Wiley & Sons, Ltd.
Improving moving average trading rules with boosting and statistical learning methods
Authors: Andrada‐Félix Julián , Fernández‐Rodríguez Fernando 
Published: May 2008

AbstractWe present a system for combining the different types of predictions given by a wide category of mechanical trading rules through statistical learning methods (boosting, and several model averaging methods like Bayesian or simple averaging methods). Statistical learning methods supply better out‐of‐sample results than most of the single moving average rules in the NYSE Composite Index from January 1993 to December 2002. Moreover, using a filter to reduce trading frequency, the filtered boosting model produces a technical strategy which, although it is not able to overcome the returns of the buy‐and‐hold (B&H) strategy during rising periods, it does overcome the B&H during falling periods and is able to absorb a considerable part of falls in the market. Copyright © 2008 John Wiley & Sons, Ltd.
Isolation and characterization of mesenchymal stem cell population entrapped in bone marrow collection sets
Authors: Dvorakova Jana , Hruba Alena , Velebny Vladimir , Kubala Lukas 
Published: May 2008

AbstractBone marrow is an important source of mesenchymal stem cells (MSCs), and a promising tool for cytotherapy. MSC utilization is limited by low cell yields obtained under standard isolation protocols. Herein, used bone marrow collection sets were evaluated as a valuable source of MSCs. Adherent cells washed from the collection sets were examined for widely accepted criteria defining MSCs. Significant numbers of cells (median 9 million per set in passage 1) with colony‐forming activity and high proliferative potential at low seeding densities were obtained. These cells were positive for essential MSC surface molecules (CD90, CD105, CD166, CD44, CD29) and negative for most haematopoietic and endothelial cell markers (CD45, CD34, CD11a, CD235a, HLA‐DR, CD144). The cells were capable of differentiation along adipogenic, osteogenic and chondrogenic pathways. Washing out bone marrow collection sets may constitute a highly ethical source of MSCs for research purposes and may be utilized also in clinical applications.
Prolactin decreases the expression ratio of receptor activator of nuclear factor κB ligand/osteoprotegerin in human fetal osteoblast cells
Authors: Seriwatanachai Dutmanee , Charoenphandhu Narattaphol , Suthiphongchai Tuangporn , Krishnamra Nateetip 
Published: May 2008

AbstractProlactin (PRL) enhanced bone remodeling leading to net bone loss in adult and net bone gain in young animals. Studies in PRL‐exposed osteoblasts derived from adult humans revealed an increase in the expression ratio of receptor activator of nuclear factor κB ligand (RANKL) and osteoprotegerin (OPG), thus supporting the previous finding of PRL‐induced bone loss in adults. This study thus investigated the effects of PRL on the osteoblast functions and the RANKL/OPG ratio in human fetal osteoblast (hFOB) cells which strongly expressed PRL receptors. After 48 h incubation, PRL increased osteocalcin expression, but had no effect on cell proliferation. However, the alkaline phosphatase activity was decreased in a dose—response manner within 24 h. The effect of PRL on alkaline phosphatase was abolished by LY294002, a phosphoinositide 3‐kinase (PI3K) inhibitor. PRL also decreased the RANKL/OPG ratio by downregulating RANKL and upregulating OPG expression, implicating a reduction in the osteoblast signal for osteoclastic bone resorption. It could be concluded that, unlike the osteoblasts derived from adult humans, PRL‐exposed hFOB cells exhibited indices suggestive of bone gain, which could explain the in vivo findings in young rats. The signal transduction of PRL in osteoblasts involved the PI3K pathway.
Expression mapping of ectonucleotide pyrophosphatase/phosphodiesterase 1‐3 (E‐NPP1–3) in different brain structures during rat development
Authors: Cognato Giana de Paula , Czepielewski Rafael Sanguinetti , Sarkis João José Freitas , Bogo Maurício Reis , Bonan Carla Denise 
Published: May 2008

AbstractEcto‐nucleotide pyrophosphatases/phosphodiesterases (E‐NPPs) are membrane‐bound ecto‐enzymes involved in the modulation of purinergic signaling. Important physiological roles related to brain development have been associated to purinergic neurotransmission. NPP1, two splice isoforms of NPP2, and NPP3 have already been identified in adult rat brain. However, there are no studies evaluating the mRNA expression of these NPP members during the brain development. The effort of the present study was to map NPP gene expression pattern in olfactory bulb, hippocampus, cerebral cortex, striatum, and cerebellum at crucial ages for rat development (7, 14, 21, 60, and 150 days old) by a semi‐quantitative reverse transcriptase‐polymerase chain reaction (RT‐PCR) strategy. Our results demonstrated an increase in the relative expression of NPP1 throughout the aging in all structures analyzed, except in hippocampus, where the higher expression has been detected in 14 days old rats. Both NPP2 isoforms have shown a similar pattern of expression among all structures. The relative expression of NPP3 decreased during the aging mainly on cerebellum, hippocampus, and olfactory bulb. Altogether, the different patterns of NPP gene expression during rat brain development reinforce the idea that each enzyme may play a distinct role on modulating the purinergic signaling throughout aging.
Identification of Trimeric Peptides That Bind Porcine Parvovirus from Mixtures Containing Human Blood Plasma
Authors: Heldt Caryn L. , Gurgel Patrick V. , Jaykus Lee‐Ann , Carbonell Ruben G. 
Published: May 2008

AbstractVirus contamination in human therapeutics is of growing concern as more therapeutic products from animal or human sources come into the market. All biopharmaceutical processes are required to have at least two distinct viral clearance steps to remove viruses. Most of these steps work well for enveloped viruses and large viruses, whether enveloped or not. That leaves a class of small non‐enveloped viruses, like parvoviruses and hepatitis A, which are not easily removed by these typical steps. In this study, we report the identification of trimeric peptides that bind specifically to porcine parvovirus (PPV) and their potential use to remove this virus from process solutions. All of the trimeric peptides isolated completely removed all detectable PPV from buffer in the first nine column volumes, corresponding to a clearance of 4.5–5.5 log of infectious virus. When the virus was spiked into a more complex matrix consisting of 7.5% human blood plasma, one of the trimers, WRW, was able to remove all detectable PPV in the first three column volumes, after which human blood plasma began to interfere with the binding of the virus to the peptide resin. These trimer resins removed considerably more virus than weak ion exchange resins. The results of this work indicate that small peptide ligand resins have the potential to be used in virus removal processes where removal of contaminating virus is necessary to ensure product safety.
Microbial Oxidation of Naphthalene to cis‐1,2‐Naphthalene Dihydrodiol Using Naphthalene Dioxygenase in Biphasic Media
Authors: McIver Angela M. , Garikipati SVB Janardhan , Bankole Kehinde S. , Gyamerah Michael , Peeples Tonya L. 
Published: May 2008

AbstractThe selective oxidation of aryl substrates to chiral cis‐1,2‐dihydrodiols is an industrially important reaction for the production of intermediates that can be used to produce fine chemicals, pharmaceuticals, and many other bioactive natural products. More specifically, the oxidation of naphthalene to produce optically pure (+)‐ cis‐(1 R,2 S)‐1,2‐napthalene dihydrodiol (NDHD) to be used as a chiral synthon for specialty chemicals has gained much interest. Escherichia coli JM109(DE3) pDTG141 expresses naphthalene dioxygenase which catalyzes this reaction. Poor substrate solubility and substrate toxicity are barriers to using the power of these enzymes in large‐scale aqueous whole cell systems. A biphasic reaction system was chosen to overcome these barriers. The optimal biphasic conditions for E. coli JM109(DE3) pDTG141 were determined to be 20% dodecane as the organic solvent containing 40 g/L naphthalene. The productivity of the biotransformation using resting cells was 1.75 g‐diol/g‐cdw/h for the first 6 h with 20% organic phase, which was increased from 0.59 g‐diol/g‐cdw/h for growing cells with 40% organic phase. The biocatalytic activity was retained for at least 12 h. The biocatalyst could be recycled for at least four runs in both suspended and immobilized form. The stability of the 12 h recycle was improved by immobilization in calcium alginate beads. The process has been improved both environmentally and economically by reducing the amount of solvent used and by recycling the biocatalyst.
Application of Multivariate Data Analysis for Identification and Successful Resolution of a Root Cause for a Bioprocessing Application
Authors: Kirdar Alime Ozlem , Green Ken D. , Rathore Anurag S. 
Published: May 2008

AbstractMultivariate Data Analysis (MVDA) can be used for supporting key activities required for successful bioprocessing. These activities include process characterization, process scale‐up, process monitoring, fault diagnosis and root cause analysis. This paper examines an application of MVDA towards root cause analysis for identifying scale‐up differences and parameter interactions that adversely impact cell culture process performance. Multivariate data analysis and modeling were performed using data from small‐scale (2 L), pilot‐scale (2,000 L) and commercial‐scale (15,000 L) batches. The input parameters examined included bioreactor pCO2, glucose, lactate, ammonium, raw materials and seed inocula. The output parameters included product attributes, product titer, viable cell density, cell viability and osmolality. Time course performance variables (daily, initial, peak and end point) were also evaluated. Application of MVDA as a diagnostic tool was successful in identifying the root cause and designing experimental conditions to demonstrate and correct it. Process parameters and their interactions that adversely impact cell culture performance and product attributes were successfully identified. MVDA was successfully used as an effective tool for collating process knowledge and increasing process understanding.
Residue‐Specific Contact Order and Contact Breadth in Single‐Domain Proteins: Implications for Folding as a Function of Chain Elongation
Authors: Kurt Neşe , Mounce Bryan C. , Ellison Paul A. , Cavagnero Silvia 
Published: May 2008

AbstractCotranslational protein misfolding and aggregation are often responsible for inclusion body formation during in vivo protein expression. This study addresses the relations between protein folding/misfolding and the distribution of intramolecular interactions across different regions of the polypeptide chain in soluble single‐domain proteins. The sequence regions examined here include the C terminus, which is synthesized last in the cell. Emphasis is placed on two parameters reporting on short‐ and long‐range interactions, i.e., residue‐specific contact order ( RCO) and a new descriptor of intramolecular protein interaction networks denoted as residue‐specific contact breadth ( RCB). RCB illustrates the average spread in sequence of the residues serving as interaction counterparts. We show that both RCO and RCB are maximized at the chain termini for a large fraction of single‐domain soluble proteins. A direct implication of this result is that the C terminus of the polypeptide chain, which is synthesized last during ribosome‐assisted translation, plays a key role in the generation of native‐like structure by establishing long‐range interactions and generating contacts with interaction counterparts widely distributed across the sequence. Comparison of our computational predictions with the experimental behavior of selected proteins shows that the presence and absence of large RCO and RCB at the chain termini correlates with the protein's ability to properly fold either after the C terminus has been synthesized or during chain elongation, respectively.
Signals Derived fromYABBYGene Activities in Organ Primordia Regulate Growth and Partitioning ofArabidopsisShoot Apical Meristems
Authors: Goldshmidt Alexander , Alvarez John Paul , Bowman John L. , Eshed Yuval 
Published: May 2008

AbstractShoot apical meristems (SAMs) are self-sustaining groups of cells responsible for the ordered initiation of all aerial plant tissues, including stems and lateral organs. The precise coordination of these processes argues for crosstalk between the different SAM domains. The products of YABBY (YAB) genes are limited to the organ primordium domains, which are situated at the periphery of all SAMs and which are separated by a margin of three to seven cells from the central meristem zone marked by WUSCHEL and CLAVATA3 expression. Mutations in the two related YAB1 genes, FILAMENTOUS FLOWER and YABBY3 (YAB3), cause an array of defects, including aberrant phyllotaxis. We show that peripheral YAB1 activity nonautonomously and sequentially affects the phyllotaxis and growth of subsequent primordia and coordinates the expression of SAM central zone markers. These effects support a role for YAB1 genes in short-range signaling. However, no evidence was found that YAB1 gene products are themselves mobile. A screen for suppression of a floral YAB1 overexpression phenotype revealed that the YAB1-born signals are mediated in part by the activity of LATERAL SUPPRESSOR. This GRAS protein is expressed at the boundary of organ primordia and the SAM central zone, distinct from the YAB1 expression domain. Together, these results suggest that YAB1 activity stimulates signals from the organs to the meristem via a secondary message or signal cascade, a process essential for organized growth of the SAM.
A Mutant Impaired in the Production of Plastome-Encoded Proteins Uncovers a Mechanism for the Homeostasis of Isoprenoid Biosynthetic Enzymes inArabidopsisPlastids
Authors: Flores-Pérez Úrsula , Sauret-Güeto Susanna , Gas Elisabet , Jarvis Paul , Rodríguez-Concepción Manuel 
Published: May 2008

AbstractThe plastid-localized methylerythritol phosphate (MEP) pathway synthesizes the isoprenoid precursors for the production of essential photosynthesis-related compounds and hormones. We have identified an Arabidopsis thaliana mutant, rif1, in which posttranscriptional upregulation of MEP pathway enzyme levels is caused by the loss of function of At3g47450, a gene originally reported to encode a mitochondrial protein related to nitric oxide synthesis. However, we show that nitric oxide is not involved in the regulation of the MEP pathway and that the encoded protein is a plastid-targeted homolog of the Bacillus subtilis YqeH protein, a GTPase required for proper ribosome assembly. Consistently, in rif1 seedlings, decreased levels of plastome-encoded proteins were observed, with the exception of ClpP1, a catalytic subunit of the plastidial Clp protease complex. The unexpected accumulation of ClpP1 in plastids with reduced protein synthesis suggested a compensatory mechanism in response to decreased Clp activity levels. In agreement, a negative correlation was found between Clp protease activity and MEP pathway enzyme levels in different experiments, suggesting that Clp-mediated degradation of MEP pathway enzymes might be a mechanism used by individual plastids to finely adjust plastidial isoprenoid biosynthesis to their functional and physiological states.
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all‐atom statistical energy functions
Authors: Yang Yuedong , Zhou Yaoqi 
Published: May 2008

AbstractOne of the common methods for assessing energy functions of proteins is selection of native or near‐native structures from decoys. This is an efficient but indirect test of the energy functions because decoy structures are typically generated either by sampling procedures or by a separate energy function. As a result, these decoys may not contain the global minimum structure that reflects the true folding accuracy of the energy functions. This paper proposes to assess energy functions by ab initio refolding of fully unfolded terminal segments with secondary structures while keeping the rest of the proteins fixed in their native conformations. Global energy minimization of these short unfolded segments, a challenging yet tractable problem, is a direct test of the energy functions. As an illustrative example, refolding terminal segments is employed to assess two closely related all‐atom statistical energy functions, DFIRE (distance‐scaled, finite, ideal‐gas reference state) and DOPE (discrete optimized protein energy). We found that a simple sequence‐position dependence contained in the DOPE energy function leads to an intrinsic bias toward the formation of helical structures. Meanwhile, a finer statistical treatment of short‐range interactions yields a significant improvement in the accuracy of segment refolding by DFIRE. The updated DFIRE energy function yields success rates of 100% and 67%, respectively, for its ability to sample and fold fully unfolded terminal segments of 15 proteins to within 3.5 Å global root‐mean‐squared distance from the corresponding native structures. The updated DFIRE energy function is available as DFIRE 2.0 upon request.
Cooperativity of complex salt bridges
Authors: Gvritishvili Anzor G. , Gribenko Alexey V. , Makhatadze George I. 
Published: May 2008

AbstractThe energetic contribution of complex salt bridges, in which one charged residue (anchor residue) forms salt bridges with two or more residues simultaneously, has been suggested to have importance for protein stability. Detailed analysis of the net energetics of complex salt bridge formation using double‐ and triple‐mutant cycle analysis revealed conflicting results. In two cases, it was shown that complex salt bridge formation is cooperative, i.e., the net strength of the complex salt bridge is more than the sum of the energies of individual pairs. In one case, it was reported that complex salt bridge formation is anti‐cooperative. To resolve these different findings, we performed analysis of the geometries of salt bridges in a representative set of structures from the PDB and found that over 87% of all complex salt bridges anchored by Arg/Lys have a geometry such that the angle formed by their Cα atoms, Θ, is <90°. This preferred geometry is observed in the two reported instances when the energetics of complex salt bridge formation is cooperative, while in the reported anti‐cooperative complex salt bridge, Θ is close to 160°. Based on these observations, we hypothesized that complex salt bridges are cooperative for Θ < 90° and anti‐cooperative for 90° < Θ < 180°. To provide a further experimental test for this hypothesis, we engineered a complex salt bridge with Θ = 150° into a model protein, the activation domain of human procarboxypeptidase A2 (ADA2h). Experimentally derived stabilities of the ADA2h variants allowed us to show that the complex salt bridge in ADA2h is anti‐cooperative.
Phosphorus Availability Influences Elemental Uptake in the Mycorrhizal Fungus
Glomus intraradices
, as Revealed by Particle-Induced X-Ray Emission Analysis
Authors: Olsson Pål Axel , Hammer Edith C. , Wallander Håkan , Pallon Jan 
Published: May 2008

ABSTRACT

We investigated element accumulation in the arbuscular mycorrhizal fungus
Glomus intraradices
. Fungal spores and mycelia growing in monoxenic cultures were analyzed. The elemental composition was quantified using particle-induced X-ray emission (PIXE) in combination with scanning transmission ion microscopy. In the spores, Ca and Fe were associated mainly with the spore wall, while P and K showed patchy distributions and their concentrations were correlated. Excess of P in the hyphal growth medium increased the P and Si concentrations in spores and increased the K/Ca ratio in spores. Increased P availability decreased the concentration of Zn and Mn in spores. We concluded that the availability of P influences the uptake and accumulation of several elements in spores. It is demonstrated that PIXE analysis is a powerful tool for quantitative analysis of elemental accumulation in fungal mycelia.
Monitoring Bacterial Diversity of the Marine Sponge
Ircinia strobilina
upon Transfer into Aquaculture
Authors: Mohamed Naglaa M. , Rao Venkateswara , Hamann Mark T. , Kelly Michelle , Hill Russell T. 
Published: May 2008

ABSTRACT

Marine sponges in the genus
Ircinia
are known to be good sources of secondary metabolites with biological activities. A major obstacle in the development of sponge-derived metabolites is the difficulty in ensuring an economic, sustainable supply of the metabolites. A promising strategy is the ex situ culture of sponges in closed or semiclosed aquaculture systems. In this study, the marine sponge
Ircinia strobilina
(order Dictyoceratida: family Irciniidae) was collected from the wild and maintained for a year in a recirculating aquaculture system. Microbiological and molecular community analyses were performed on freshly collected sponges and sponges maintained in aquaculture for 3 months and 9 months. Chemical analyses were performed on wild collected sponges and individuals maintained in aquaculture for 3 months and 1 year. Denaturing gradient gel electrophoresis was used to assess the complexity of and to monitor changes in the microbial communities associated with
I. strobilina
. Culture-based and molecular techniques showed an increase in the
Bacteroidetes
and
Alpha
- and
Gammaproteobacteria
components of the bacterial community in aquaculture. Populations affiliated with
Beta
- and
Deltaproteobacteria
,
Clostridia
, and
Planctomycetes
emerged in sponges maintained in aquaculture. The diversity of bacterial communities increased upon transfer into aquaculture.