bluuebunny/crossref_metadata_2025_split huggingface dataset:
The importance of and a method for including transfection efficiency into real‐time PCR data analyses
Authors: Godbey WT. , Zhang Xiujuan , Chang Fengqi 
Published: February 2008

AbstractThe polymerase chain reaction (PCR) is widely used to ascertain absolute or relative changes in the expression levels of specific genes as a function of cell type or in response to changes in environmental stimuli. Real‐time PCR is an advance which allows for the analysis of gene expression over a wide range of initial cDNA concentrations, where the cDNA is the product of reverse transcriptase reactions applied to RNA samples. With the advent and advances in gene delivery technologies, it is now common for the cellular responses under scrutiny to be initiated via the expression of an exogenously delivered gene. When transfection (or transduction) is a part of the procedure used to prepare cell samples for real‐time PCR, it is necessary to take the efficiency of gene delivery into account. Here a robust mathematical model for such analyses is derived, and validated with theoretical and experimental support. Comparison to existing analysis methods is presented to demonstrate the high significance of noting transfection, loading, and primer PCR efficiencies when processing PCR data./ Biotechnol. Bioeng. 2008;100: 765–772. © 2008 Wiley Periodicals, Inc.
Synthesis, characterization, bioactivity and biocompatibility of nanostructured materials based on the wollastonite‐poly(ethylmethacrylate‐co‐vinylpyrrolidone) system
Authors: Rodríguez‐Lorenzo L. M. , García‐Carrodeguas R. , Rodríguez M. A. , De Aza S. , Jiménez J. , López‐Bravo A. , Fernandez M. , Román J. San 
Published: February 2008

AbstractComposite materials are very promising biomaterials for hard tissue augmentation. The approach assayed in this work involves the manufacturing of a composite made of a bioactive ceramic, natural wollastonite (W) and a nanostructured copolymer of ethylmethacrylate (EMA) and vinylpyrrolidone (VP) to yield a bioresorbable and biocompatible VP–EMA copolymer. A bulk polymerization was induced thermally at 50°C, using 1 wt % azobis(isobutyronitrile) (AIBN) as free‐radical initiator. Structural characterization, compressive strength, flexural strength (FS), degradation, bioactivity, and biocompatibility were evaluated in specimens with a 60/40 VP/EMA ratio and ceramic content in the range 0–60%. A good integration between phases was achieved. Greater compression and FS, in comparison with the pure copolymer specimens was obtained only when the ceramic load got up to 60% of the total weight. The soaking in NaCl solution resulted in the initial swelling of the specimens tested. The maximum swelling was reached after 2–3 h of immersion and it was significantly greater for lower ceramic loads. This result makes the polymer component the main responsible for the interactions with the media. After soaking in SBF, microdomains segregation can be observed in the polymer component that can be related with a dramatic difference in the reactivity of both monomers in free radical polymerization, whereas the formation of an apatite‐like layer on the W surfaces can be observed. Biocompatibility in vitro studies showed the absence of cytotoxicity of all formulations. The cells were able to adhere on the polystyrene negative control and on specimens containing 60 wt % wollastonite forming a monolayer and showing a normal morphology. However, a low cellular growth was observed. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Surface immobilization of poly(ethyleneimine) and plasmid DNA on electrospun poly(L‐lactic acid) fibrous mats using a layer‐by‐layer approach for gene delivery
Authors: Sakai Shinji , Yamada Yusuke , Yamaguchi Tetsu , Ciach Tomasz , Kawakami Koei 
Published: February 2008

AbstractThe method of coating electrospun ultrafine poly(L‐lactic acid) fibers with DNA, by building up polyelectrolyte layer(s) of poly(ethyleneimine) (PEI) and plasmid DNA using an electrostatic layer‐by‐layer deposition method, for gene delivery is presented. The pGL3 encoding luciferase was applied as plasmid DNA. The quantity of pGL3 immobilized on individual fibers increased with increasing pGL3 concentration in the immersion solution (0.017–0.870 mg/mL) and increasing bilayer number of PEI/pGL3 (single–triple). With the exception of one specimen prepared under the condition 0.870 mg/mL pGL3 solution and double PEI/pGL3 layers, the transfection efficiency of COS‐7 cells, defined by the ratio of fluorescence intensity (resulting from the presence of luciferase) with respect to the quantity of cellular protein on the fibrous mat increased with increasing quantity of pGL3 on the fibers. In addition to the ease of controlling the quality of polyelectrolyte bilayer(s) by simply changing the concentrations of substances and number of immersing cycles, the features of the electrospun fibrous mat such as a very large surface‐to‐volume ratio and flexibility, could potentially be employed as a strategy for gene therapy combined with tissue engineering technology. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Effect of nicotine in matrix mineralization by human bone marrow and Saos‐2 cells cultured on the surface of plasma‐sprayed titanium implants
Authors: Pereira M. L. , Carvalho J. C. , Peres F. , Fernandes M. H. 
Published: February 2008

AbstractSmoking has an established negative impact in the clinical outcome of dental implants. This work analyses the response of human osteoblastic cells to nicotine, at the surface of plasma‐sprayed commercial titanium implants. Human bone marrow (HBM) and Saos‐2 cells, seeded on the surface of titanium implants and cultured in experimental conditions favoring osteoblastic differentiation, were exposed continuously to nicotine (0.0001 to 0.5 mg mL−1) and characterized for cell proliferation and function. Exposure of HBM cells resulted in increased cell proliferation, higher alkaline phosphatase (ALP) activity, and earlier onset of matrix mineralization at levels up to 0.2 mg mL−1, an initial inhibitory effect in cell growth and functional activity followed by a recovery in the presence of 0.3 mg mL−1 and a dose‐dependent deleterious effect at higher levels. By contrast, exposure to nicotine did not affect cell proliferation of Saos‐2 cells at levels up to 0.2 mg mL−1, and caused only a small positive effect in ALP activity in the presence of 0.05 and 0.1 mg mL−1; however, matrix mineralization by Saos‐2 cells also occurred earlier in the cultures exposed to levels of nicotine up to 0.1 mg mL−1. Higher concentrations caused dose‐dependent inhibitory effects. Considering the high diffusion potential of nicotine, results suggest a local role of nicotine in modulating bone formation events at the implant surface. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Ontogenetic Sequence Analysis: using parsimony to characterize developmental sequences and sequence polymorphism
Authors: Colbert Matthew W. , Rowe Timothy 
Published: February 2008

AbstractOntogenetic sequences are a pervasive aspect of development and are used extensively by biologists for intra‐ and interspecific comparisons. A tacit assumption behind most such analyses is that sequence is largely invariant within a species. However, recent embryological and experimental work emphasizes that ontogenetic sequences can be variable and that sequence polymorphism may be far more prevalent than is generally realized. We present a method that uses parsimony algorithms to map hierarchic developmental patterns that capture variability within a sample. This technique for discovering and formalizing sequences is called the “Ontogenetic Sequence Analysis” (OSA). Results of OSA include formalized diagrams of reticulating networks, describe all most parsimonious sequences, and can be used to develop statistics and metrics for comparison of both intraspecific and interspecific sequence variation. The method is tested with examples of human postnatal skeletal ossification, comprising a time‐calibrated data set of human hand and wrist epiphyseal unions, and a longitudinal data set of human wrist ossification. Results illustrate the validity of the method for discovering sequence patterns and for predicting morphologies not represented in analytic samples. OSA demonstrates the potential and challenges of incorporating ontogenetic sequences of morphological information into evolutionary analyses. J. Exp. Zool. (Mol. Dev. Evol.) 310B:398–416, 2008. © 2008 Wiley‐Liss, Inc.
Side populations of gastrointestinal cancers are not enriched in stem cells
Authors: Burkert J , Otto WR , Wright NA 
Published: February 2008

AbstractThe side population (SP) phenotype, defined as the reserpine‐blockable ability to efflux the nucleic acid dye Hoechst 33342, has been claimed to be enriched for stem cells in several human normal tissues, cancers and cell lines, and thus may be useful for the identification and isolation of cancer stem cells. We demonstrated the presence of SP fractions in all of seven tested gastrointestinal cancer cell lines. Four cell lines were selected (HT29, HGT101, Caco2 and HRA19a1.1) for detailed phenotypic and behavioural analysis with respect to stem cell characteristics. Cell surface marker analysis showed that, contrary to non‐SP cells, the SPs entirely lack the expression of CD34. This difference, however, disappeared when the cells were cultured, rendering both populations CD34‐positive. Expression of other putative stem cell markers (CD133, CD44, Hes‐1, β‐catenin, Musashi‐1, Oct‐4 and CD117) was identical on SP and non‐SPs before and after culturing. Sorted SP and non‐SP cells were similarly clonogenic in vitro, tumourigenic in vivo, and displayed similar multipotential differentiation potential in vitro and in vivo. Additionally, culturing cytometrically‐sorted SP and non‐SP cells showed that the populations are interconvertible, each giving rise to the other. Expression of ABCG2 and Mdr‐1, two membrane transporter proteins that have been suggested to be responsible for the drug‐effluxing capacities of SP cells, including Hoechst 33342, was identical in non‐SP and SP cells, indicating that there may be additional factors responsible for the Hoechst effluxing property in gastrointestinal cancer SP cells. Here, we show that the SP and non‐SP fractions, albeit phenotypically distinct populations, do not differ with respect to stem cell‐like cell number or behaviour. We thus conclude that the concept of the SP phenotype as a universal marker for stem cells does not apply to gastrointestinal cancer cells. These findings stand in contrast to the observations made in many other tissues and harbour important implications for the future search for intestinal cancer stem cell markers. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Poly(ether imide)/N‐methyl pyrrolidinone solutions: kinetics of water vapour absorption and surface layer formation
Authors: Pochat‐Bohatier Céline , Cohen‐Addad Jean‐Pierre , Chinpa Watchanida , Deratani André 
Published: February 2008

AbstractBACKGROUND: Water sorption by polymer solutions during film fabrication may affect the film morphology and thereby the film properties.RESULTS: Water vapour sorption isotherms at 40 °C of poly(ether imide) (PEI)/N‐methyl pyrrolidinone (NMP) solutions were experimentally determined. Considering PEI concentrations ranging from 0 to 20 wt%, results obtained from gravimetric measurements and near‐infrared (NIR) spectroscopy, indicative of the total weight uptake and the local water concentration in the bulk solution, respectively, showed that a first stage occurred featuring a quasi‐linear time dependence of the weight fraction of absorbed water. Deviations from linearity dependent on the PEI concentration were afterwards observed, this behaviour being more marked for concentrations higher than 14 wt%. To achieve good predictions, the mathematical description of the sorption results must take into consideration both the classical approach using diffusion equations and the possible time dependence of the surface concentration of water at the air‐facing interface.CONCLUSION: This paper presents an analysis of water vapour sorption in PEI/NMP solutions combining local and global quantifications of the water content through NIR and gravimetric methods. The development of a mathematical model suggests a possible surface layer formation at the air‐facing interface. Copyright © 2008 Society of Chemical Industry
Structural studies of shikimate 5‐dehydrogenase from Mycobacterium tuberculosis
Authors: Arcuri Helen A. , Borges Júlio C. , Fonseca Isabel O. , Pereira José H. , Neto João Ruggiero , Basso Luiz A. , Santos Diógenes S. , de Azevedo Walter F. 
Published: February 2008

AbstractTuberculosis (TB) remains the leading cause of mortality due to a single bacterial pathogen, Mycobacterium tuberculosis. The reemergence of TB as a potential public health threat, the high susceptibility of human immunodeficiency virus‐infected persons to the disease, the proliferation of multi‐drug‐resistant strains (MDR‐TB) and, more recently, of extensively drug resistant isolates (XDR‐TB) have created a need for the development of new antimycobacterial agents. Amongst the several proteins and/or enzymes to be studied as potential targets to develop novel drugs against M. tuberculosis, the enzymes of the shikimate pathway are attractive targets because they are essential in algae, higher plants, bacteria, and fungi, but absent from mammals. The mycobacterial shikimate pathway leads to the biosynthesis of chorismate, which is a precursor of aromatic amino acids, naphthoquinones, menaquinones, and mycobactins. Here we report the structural studies by homology modeling and circular dichroism spectroscopy of the shikimate dehydrogenase from M. tuberculosis (MtSDH), which catalyses the fourth step of the shikimate pathway. Our structural models show that the MtSDH has similar structure to other shikimate dehydrogenase structures previously reported either in presence or absence of NADP, despite the low amino acid sequence identity. The circular dichroism spectra corroborate the secondary structure content observed in the MtSDH models developed. The enzyme was stable up to 50°C presenting a cooperative unfolding profile with the midpoint of the unfolding temperature value of ∼63–64°C, as observed in the unfolding experiment followed by circular dichroism. Our MtSDH structural models and circular dichroism data showed small conformational changes induced by NADP binding. We hope that the data presented here will assist the rational design of antitubercular agents. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Determination of lopinavir and ritonavir in blood plasma, seminal plasma, saliva and plasma ultra‐filtrate by liquid chromatography/tandem mass spectrometry detection
Authors: Estrela Rita C. E. , Ribeiro Fabio S. , Seixas Brayan V. , Suarez‐Kurtz Guilherme 
Published: February 2008

AbstractA method based on liquid‐liquid extraction followed by high‐performance liquid chromatography (HPLC) with positive ion electrospray ionization tandem mass spectrometry (ESI‐MS/MS) detection was developed for the simultaneous determination of lopinavir (LPV) and ritonavir (RTV) in human blood, semen and saliva samples. The acquisition was performed in multiple reaction monitoring (MRM) mode, monitoring the transitions: m/z 629 > 447.1 for LPV, 721.18 > 268.02 for RTV and m/z 747.22 > 322.03 for the internal standard (IS). The limit of quantification was 1 ng/mL for both analytes in all matrices. The method was linear in the studied range (1–2000 ng/mL for LPV and 1–200 ng/mL for RTV), with r2 > 0.99 for each drug, and the run time was 4.5 min. The intra‐assay precisions (%) were in the ranges of 0.1–14.2 (LPV) and 0.4–12.7 (RTV), the inter‐assay precisions were in the ranges of 2.8–15.3 (LPV) and 1.1–12.8 (RTV) and the intra‐and inter‐assay recoveries were >85% for both drugs. The extraction efficiencies were 73.5–118.4% for LPV and 74.4–126.2% for RTV. The analytical method was applied to measure LPV and RTV concentrations in blood plasma (total and unbound fraction), saliva and semen of six HIV+ individuals under stable treatment with Kaletra® soft gel capsules. The results were consistent with previously published data. Copyright © 2008 John Wiley & Sons, Ltd.
An optimized forwarding protocol for lifetime extension of wireless sensor networks
Authors: Azim Mohammad Abdul , Kibria M. Rubaiyat , Jamalipour Abbas 
Published: February 2008

AbstractOptimized routing (from source to sink) in wireless sensor networks (WSN) constitutes one of the key design issues in prolonging the lifetime of battery‐limited sensor nodes. In this paper, we explore this optimization problem by considering different cost functions such as distance, remaining battery power, and link usage in selecting the next hop node among multiple candidates. Optimized selection is carried out through fuzzy inference system (FIS). Two differing algorithms are presented, namely optimized forwarding by fuzzy inference systems (OFFIS), and two‐layer OFFIS (2L‐OFFIS), that have been developed for flat and hierarchical networks, respectively. The proposed algorithms are compared with popular routing protocols that are considered as the closest counterparts such as minimum transmit energy (MTE) and low energy adaptive clustering hierarchy (LEACH). Simulation results demonstrate the superiority of the proposed algorithms in extending the WSN lifetime. Copyright © 2008 John Wiley & Sons, Ltd.
Differentiation of Insulin Secretion Patterns in Insulinoma
Authors: Saddig Christiane , Goretzki Peter E. , Starke Achim A. R. 
Published: February 2008

AbstractBackgroundIn patients with insulinoma, biochemical proof of inappropriately elevated insulin secretion during hypoglycemia is required prior to surgery. Because circulating insulin levels usually vary widely, we have used the combined OGTT‐fasting test to define new normative criteria for a retrospective systematic analysis.MethodsWe retrospectively analyzed insulin concentrations from OGTT‐fasting tests of 64 patients with surgically removed insulinomas. In addition, the response to intravenous somatostatin infusions was estimated. Normative criteria were defined to obtain comparable estimates of insulin concentrations: basal, glucose‐stimulated maximum, postglucose plateau, and secretory bursts.ResultsThree types of insulin secretion patterns were identified: (1) the autonomous secretion pattern (type 1, N = 17) with basal and post‐OGTT plateau insulin concentrations of approximately 50 mU/L, suppression after OGTT by 41%, virtual absence of distinctive secretory bursts, and resistance to somatostatin‐mediated suppression (25 %); (2) the inadequate suppression pattern (type 2, N = 28) with moderately elevated basal and post‐OGTT insulin concentrations of approximately 20 mU/L, suppression after OGTT by 73%, absence of secretory bursts, and incomplete somatostatin‐induced suppression (56 %); (3) the late‐burst secretion pattern (type 3, N = 19) with similar basal and post‐OGTT insulin concentrations of 17 mU/L, suppression after OGTT by 76%, true insulin bursts of Δ 13 ± 11 mU/L (184%), and nearly complete somatostatin‐induced suppression by 64%.ConclusionsBy means of a new normative analysis of the combined OGTT‐fasting test, three different patterns of insulin secretion can be described in patients with insulinoma: the autonomous secretion type, the inadequate suppression type, and the late‐burst secretion type.
The effects of milk as a food matrix for polyphenols on the excretion profile of cocoa ( − )-epicatechin metabolites in healthy human subjects
Authors: Roura Elena , Andrés-Lacueva Cristina , Estruch Ramon , Lourdes Mata Bilbao M. , Izquierdo-Pulido Maria , Lamuela-Raventós Rosa M. 
Published: February 2008

The effect of different food matrices on the metabolism and excretion of polyphenols is uncertain. The objective of the study was to evaluate the possible effect of milk on the excretion of ( − )-epicatechin metabolites from cocoa powder after its ingestion with and without milk. Twenty-one volunteers received the following three test meals each in a randomised cross–over design with a 1-week interval between meals: (1) 250 ml whole milk as a control; (2) 40 g cocoa powder dissolved in 250 ml whole milk (CC–M); (3) 40 g cocoa powder dissolved in 250 ml water (CC–W). Urine was collected before consumption and during the 0–6, 6–12 and 12–24 h periods after consumption. ( − )-Epicatechin metabolite excretion was measured using liquid chromatography–MS. One ( − )-epicatechin glucuronide and three ( − )-epicatechin sulfates were detected in urine excreted after the intake of the two cocoa beverages (CC–M and CC–W). The results show that milk does not significantly affect the total amount of metabolites excreted in urine. However, differences in metabolite excretion profiles were observed; there were changes in the glucuronide and sulfate excretion rates, and the sulfation position between the period of excretion and the matrix. The matrix in which polyphenols are consumed can affect their metabolism and excretion, and this may affect their biological activity. Thus, more studies are needed to evaluate the effect of these different metabolite profiles on the body.
Multitrophic effects of nutrient addition in upland grassland
Authors: Fountain M.T. , Brown V.K. , Gange A.C. , Symondson W.O.C. , Murray P.J. 
Published: February 2008

AbstractAlthough the effects of nutrient enhancement on aquatic systems are well documented, the consequences of nutritional supplements on soil food webs are poorly understood, and results of past research examining bottom-up effects are often conflicting. In addition, many studies have failed to separate the effects of nutrient enrichment and the physical effects of adding organic matter. In this field study, we hypothesised that the addition of nitrogen to soil would result in a trophic cascade, through detritivores (Collembola) to predators (spiders), increasing invertebrate numbers and diversity.Nitrogen and lime were added to plots in an upland grassland in a randomised block design. Populations of Collembola and spiders were sampled by means of pitfall traps and identified to species.Seventeen species of Collembola were identified from the nitrogen plus lime (N+L) and control plots. Species assemblage, diversity, richness, evenness and total number were not affected by nutrient additions. However, there was an increase in the number of Isotomidae juveniles and Parisotoma anglicana trapped in the N+L plots.Of the 44 spider species identified, over 80% were Linyphiidae. An effect on species assemblage from the addition of N+L to the plots was observed on two of the four sampling dates (July 2002 and June 2003). The linyphiid, Oedothorax retusus, was the only species significantly affected by the treatments and was more likely to be trapped in the control plots.The increased number of juvenile Collembola, and change in community composition of spiders, were consequences of the bottom-up effect caused by nutrient inputs. However, despite efforts to eliminate the indirect effects of nutrient inputs, a reduction in soil moisture in the N+L plots cannot be eliminated as a cause of the invertebrate population changes observed. Even so, this experiment was not confounded by the physical effects of habitat structure reported in most previous studies. It provides evidence of moderate bottom-up influences of epigeic soil invertebrate food webs and distinguishes between nutrient addition and plant physical structure effects. It also emphasises the importance of understanding the effects of soil management practices on soil biodiversity, which is under increasing pressure from land development and food production.