bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Contour Intervals and Grid Cell Size on the Accuracy of DEMs and Slope Derivatives
Authors: Ziadat Feras M 
Published: January 2007

AbstractDigital Elevation Models (DEMs) are indispensable tools in many environmental and natural resource applications. DEMs are frequently derived from contour lines. The accuracy of such DEMs depends on different factors. This research investigates the effect of sampling density used to derive contours, vertical interval between contours (spacing), grid cell size of the DEM (resolution), terrain complexity, and spatial filtering on the accuracy of the DEM and the slope derivative. The study indicated different alternatives to achieve an acceptable accuracy depending on the contour interval, the DEM resolution and the complexity of the terrain. The effect of these factors on the accuracy of the DEM and the slope derivative was quantified using models that determine the level of accuracy (RMSE). The implementation of the models will guide users to select the best combination to improve the results in areas with similar topography. For areas with variable terrain complexity, the suggestion is to generate DEMs and slope at a suitable resolution for each terrain separately and then to merge the results to produce one final layer for the whole area. This will provide accurate estimates of elevation and slope, and subsequently improve the analyses that rely on these digital derivatives.
Ontological Engineering for Interpreting Geospatial Queries
Authors: Peachavanish Ratchata , Karimi Hassan A 
Published: January 2007

AbstractDespite advancements in geographic information system (GIS) technology, the efficient and effective utilization of GIS to solve geospatial problems is a daunting process requiring specialized knowledge and skills. Two of the most important and burdensome tasks in this process are interpretation of geospatial queries and mapping the interpreted results into geospatial data models and geoprocessing operations. With the current state of GIS, there exists a gap between the knowledge user's possess and the knowledge and skills they need to utilize GIS for solving problems. Currently, users resort to training and practice on GIS technology or involving GIS experts. Neither of these options is optimal and there is a need for a new approach that automates geoprocessing tasks using GIS technology. This paper presents an ontological engineering methodology that uses multiple ontologies and the mappings among them to automate certain tasks related to interpretation of geospatial queries and mapping the interpreted results into geospatial data models and geoprocessing operations. The presented methodology includes conceptualization of geospatial queries, knowledge representation for queries, techniques for relating elements in different ontologies, and an algorithm that uses ontologies to map queries to geoprocessing operations.
Empirical-Likelihood-Based Inference in Missing Response Problems and Its Application in Observational Studies
Authors: Qin Jing , Zhang Biao 
Published: January 2007

SummaryThe problem of missing response data is ubiquitous in medical and social science studies. In the case of responses that are missing at random (depending on some covariate information), analyses focused only on the complete data may lead to biased results. Various debias methods have been extensively studied in the literature, particularly the weighting method that was motivated by Horvitz and Thompson's estimators. To improve efficiency, Robins, Rotnitzky and Zhao proposed augmented estimating equations based on corrected complete-case analyses. A nice feature of the augmented method is its ‘double robustness’, i.e. the estimator that is derived from the augmented method is asymptotically unbiased if either the underlying missing data mechanism or the underlying regression function is correctly specified. Furthermore, the augmented estimator can achieve full efficiency if both the missing data mechanism and the regression function are correctly specified. In general, however, it is very difficult to specify the regression function correctly, especially when the dimension of covariates is high— this is the so-called curse of dimensionality problem. The augmented estimator has much lower efficiency if the ‘working regression model’ is not close to the true regression model. In this paper, the empirical likelihood method is employed to seek a constrained empirical likelihood estimation of mean response with the assumption that responses are missing at random. The empirical-likelihood-based estimators enjoy the double-robustness property. Moreover, it is possible that the empirical-likelihood-based inference can produce asymptotically unbiased and efficient estimators even if the true regression function is not completely known. Simulation results indicate that the empirical-likelihood-based estimators are very robust to a misspecification of the propensity score and dominate other competitors in the sense of having smaller mean-square errors. Methods that are developed in this paper have a nice application in observational causal inferences. The propensity score is used to adjust for differences in pretreatment variables in the estimation of average treatment effects.
IGF‐I‐induced oligodendrocyte progenitor proliferation requires PI3K/Akt, MEK/ERK, and Src‐like tyrosine kinases
Authors: Cui Qiao‐Ling , Almazan Guillermina 
Published: January 2007

AbstractInsulin‐like growth factor‐I (IGF‐I) is required for the growth of oligodendrocytes, although the underlying mechanisms are not fully understood. Our aim was to investigate the role of phosphatidylinositol 3‐kinase (PI3K), mitogen‐activated protein kinase kinase (MEK1), and Src family tyrosine kinases in IGF‐I‐stimulated proliferation of oligodendrocyte progenitors. IGF‐I treatment increased the proliferation of cultured oligodendrocyte progenitors as determined by measuring incorporation of [3H]‐thymidine and bromodeoxy‐uridine (BrdU). IGF‐I stimulated a transient phosphorylation of 3‐phosphoinositide‐dependent kinase‐1 (PDK1) and extracellular signal‐regulated kinases (ERK1/2) (targets of MEK1), as well as a rapid and sustained activation of Akt (a target of PI3K). Furthermore, inhibitors of PI3K (LY294002 and Wortmannin), MEK1 (PD98059 and U0126), and Src family tyrosine kinases (PP2) decreased IGF‐I‐induced proliferation, and blocked ERK1/2 activation. LY294002, Wortmannin and PP2 also blocked Akt activation. To further determine whether Akt is required for IGF‐I stimulated oligodendrocyte progenitor proliferation, cultures were infected with adenovirus vectors expressing dominant‐negative mutants of Akt or treated with pharmacological inhibitors of Akt. All treatments reduced IGF‐I‐induced oligodendrocyte progenitor proliferation. Our data indicate that stimulation of oligodendrocyte progenitor proliferation by IGF‐I requires Src‐like tyrosine kinases as well as the PI3K/Akt and MEK1/ERK signaling pathways.
Purification of visual arrestin from squid photoreceptors and characterization of arrestin interaction with rhodopsin and rhodopsin kinase
Authors: Swardfager Walter , Mitchell Jane 
Published: January 2007

AbstractInvertebrate visual signal transduction involves photoisomerization of rhodopsin, activating a guanine nucleotide binding protein (G protein) of the Gq class, iGq, which stimulates a phospholipase C, increasing intracellular Ca2+. Arrestin binding to photoactivated rhodopsin is a key mechanism of desensitization. We have previously reported the cloning of a retina‐specific arrestin cDNA from Loligo pealei displaying 56–64% sequence similarity to other reported arrestin sequences. Here, we report the purification of the 55‐kDa squid visual arrestin. Purified squid visual arrestin is able to inhibit light‐activated GTPase activity dose‐dependently in arrestin‐depleted rhabdomeric membranes and associate with the membrane in a light‐dependent manner. Membrane association can be partially inhibited by inositol 1,2,3,4,5,6‐hexakisphosphate (IP6), a soluble analog of the membrane lipid phosphatidylinositol 3,4,5‐triphosphate. In reconstitution assays, we demonstrate arrestin phosphorylation by squid rhodopsin kinase, a novel function among the G protein‐coupled receptor kinase family. Phosphorylation of purified arrestin requires squid rhodopsin kinase, membranes, light‐activation, and the presence of Ca2+. This is the first large‐scale purification of an invertebrate arrestin and biochemical demonstration of arrestin function in the invertebrate visual system.
Behavior of CAL72 osteoblast‐like cells cultured on zirconia ceramics with different surface topographies
Authors: Bächle Maria , Butz Frank , Hübner Ute , Bakalinis Emmanouil , Kohal Ralf J. 
Published: January 2007

AbstractObjectives: Because of its inherent strength, biocompatibility, and tooth‐like color, zirconia ceramics have the potential to become an alternative to titanium as dental implant material. This study aimed at investigating the osteoblastic response to yttrium‐stabilized tetragonal zirconia polycrystal (Y‐TZP) with different surface topographies.Methods: CAL72 osteoblast‐like cells were cultured on machined (TZP‐m), airborne particle abraded (TZP‐s), and airborne particle abraded and acid‐etched Y‐TZP (TZP‐sa) surfaces. Polystyrene and airborne particle abraded with large grit and acid‐etched (SLA) titanium served as a reference control. The surface topography was examined by scanning electron microscopy (SEM) and profilometry. At culture days 3, 6, and 12, cell proliferation, at day 12 cell morphology, and cell‐covered surface area were determined.Results: The surface roughness of Y‐TZP was increased by airborne particle abrasion and additionally by acid etching. No statistically significant differences were found between average roughness (Ra) and maximum peak‐to‐valley height (Rp–v) values of airborne particle abraded and acid‐etched Y‐TZP and SLA titanium. Whereas the cell proliferation assay revealed statistically significant greater values at day 3 for surface‐treated Y‐TZP and polystyrene cultures as compared with machined Y‐TZP, no differences between the Y‐TZP groups, SLA titanium, and polystyrene were observed at culture days 6 and 12.Conclusions: Cell morphology and cell‐covered surface area were not affected by the type of substrate. The results suggest that roughened Y‐TZP is an appropriate substrate for the proliferation and spreading of osteoblastic cells.
Morphogenesis of the peri‐implant mucosa: an experimental study in dogs
Authors: Berglundh Tord , Abrahamsson Ingemar , Welander Maria , Lang Niklaus P. , Lindhe Jan 
Published: January 2007

AbstractPurpose: The objective of the present experiment was to study the morphogenesis of the mucosal attachment to implants made of c.p. titanium.Material and methods: All mandibular premolars were extracted in 20 Labrador dogs. After a healing period of 3 months, four implants (ITI® Dental Implant System) were placed in the right and left sides of the mandible. A non‐submerged implant installation technique was used and the mucosal tissues were secured to the conical marginal portion of the implants with interrupted sutures. The sutures were removed after 2 weeks and a plaque control program including daily cleaning of the remaining teeth and the implants was initiated. The animals were sacrificed and biopsies were obtained at various intervals to provide healing periods extending from Day 0 (2 h) to 12 weeks. The mandibles were removed and placed in the fixative. The implant sites were dissected using a diamond saw and processed for histological analysis.Results: Large numbers of neutrophils infiltrated and degraded the coagulum that occupied the compartment between the mucosa and the implant during the initial phase of healing. At 2 weeks after surgery, fibroblasts were the dominating cell population in the connective tissue interface but at 4 weeks the density of fibroblasts had decreased. Furthermore, the first signs of epithelial proliferation were observed in specimens representing 1–2 weeks of healing and a mature barrier epithelium occurred after 6–8 weeks of healing. The collagen fibers of the mucosa were organized after 4–6 weeks of healing.Conclusion: It is suggested that the soft‐tissue attachment to implants placed using a non‐submerged installation procedure is properly established after several weeks following surgery.
Bactericidal Activity and Resistance Development Profiling of Dalbavancin
Authors: Goldstein Beth P. , Draghi Deborah C. , Sheehan Daniel J. , Hogan Patricia , Sahm Daniel F. 
Published: January 2007

ABSTRACT

Dalbavancin, a semisynthetic lipoglycopeptide being developed for the treatment of skin and skin structure infections (SSSIs), has a half-life of 5 to 7 days in humans and offers promise for a convenient weekly dosing regimen. We studied the in vitro bactericidal activity of dalbavancin against target organisms, using the concentrations that are maintained in human blood with the proposed dosage regimen. Dalbavancin minimal bactericidal concentrations (MBCs) were ≤0.5 μg/ml for eight staphylococcal isolates; and for six of these strains, including one vancomycin-intermediate
Staphylococcus aureus
(VISA) isolate, the MBCs were equal to or within 1 doubling dilution of the MIC. Dalbavancin MICs for all three
Streptococcus pyogenes
strains were 0.008 μg/ml, as were the MBCs for two of the isolates. In time-kill studies conducted with a different set of seven strains (two methicillin-susceptible
S. aureus
isolates, three methicillin-resistant
S. aureus
isolates, one VISA isolate, and one
S. pyogenes
isolate), all strains exhibited a ≥3-log
10
decrease in their viable counts when they were exposed to ≥1 μg/ml of dalbavancin for 24 h. Resistance development studies by both direct selection (resistance frequency, <10
−10
) and serial passage failed to produce stable mutants with decreased susceptibility to dalbavancin. These observations suggest that dalbavancin will be an effective choice for the management of patients with SSSIs.
Population Pharmacokinetic Model for Gatifloxacin in Pediatric Patients
Authors: Rubino Christopher M. , Capparelli Edmund V. , Bradley John S. , Blumer Jeffrey L. , Kearns Gregory L. , Reed Michael , Jacobs Richard F. , Cirincione Brenda , Grasela Dennis M. 
Published: January 2007

ABSTRACT
The broad spectrum of antimicrobial activity, oral bioavailability, extensive tissue distribution, and once-daily intravenous or oral dosing of gatifloxacin, an expanded-spectrum 8-methoxy fluoroquinolone, make it a potentially useful agent for the treatment of pediatric infections. A population pharmacokinetic model was developed to describe the pharmacokinetics of gatifloxacin in children. Data for analysis were obtained from a single-dose safety/pharmacokinetic study utilizing intensive blood sampling in patients aged 6 months to 16 years. Each subject received a single oral dose of gatifloxacin as a suspension, at doses of 5, 10, or 15 mg/kg of body weight. A total of 845 samples were obtained from 82 patients. A one-compartment model with first-order absorption and elimination was the most appropriate to describe the gatifloxacin concentrations. Covariate analysis using forward selection and backward elimination found that apparent clearance was related to body surface area, and apparent volume of distribution was related to body weight. No effect of age on drug clearance could be identified once clearance was corrected for body surface area. Based on pharmacokinetic simulations, the 10-mg/kg (maximum, 400 mg) once-daily dose of gatifloxacin is expected to provide drug exposure similar to that in healthy adults. The population pharmacokinetic model described herein will be used for Bayesian analyses of sparse pharmacokinetic sampling in phase II/III clinical trials and for Monte Carlo simulation experiments. The success of this strategy provides a model for future pediatric drug development programs.
Mosaic Structure of p1658/97, a 125-Kilobase Plasmid Harboring an Active Amplicon with the Extended-Spectrum β-Lactamase Gene
bla
SHV-5
Authors: Zienkiewicz M. , Kern-Zdanowicz I. , Gołȩbiewski M. , Żyliñska J. , Mieczkowski P. , Gniadkowski M. , Bardowski J. , Cegłowski P. 
Published: January 2007

ABSTRACT

Escherichia coli
isolates recovered from patients during a clonal outbreak in a Warsaw, Poland, hospital in 1997 produced different levels of an extended-spectrum β-lactamase (ESBL) of the SHV type. The β-lactamase hyperproduction correlated with the multiplication of ESBL gene copies within a plasmid. Here, we present the complete nucleotide sequence of plasmid p1658/97 carried by the isolates recovered during the outbreak. The plasmid is 125,491 bp and shows a mosaic structure in which all modules constituting the plasmid core are homologous to those found in plasmids F and R100 and are separated by segments of homology to other known regions (plasmid R64,
Providencia rettgeri
genomic island R391,
Vibrio cholerae
STX transposon,
Klebsiella pneumoniae
or
E. coli
chromosomes). Plasmid p1658/97 bears two replication systems, IncFII and IncFIB; we demonstrated that both are active in
E. coli
. The presence of an active partition system (
sopABC
locus) and two postsegregational killing systems (
pemIK
and
hok/sok
) indicates that the plasmid should be stably maintained in
E. coli
populations. The conjugative transfer is ensured by the operons of the
tra
and
trb
genes. We also demonstrate that the plasmidic segment undergoing amplification contains the
bla
SHV-5
gene and is homologous to a 7.9-kb fragment of the
K. pneumoniae
chromosome. The amplicon displays the structure of a composite transposon of type I.
Gamma Interferon Loaded onto Albumin Nanoparticles: In Vitro and In Vivo Activities against
Brucella abortus
Authors: Segura S. , Gamazo C. , Irache J. M. , Espuelas S. 
Published: January 2007

ABSTRACT

The aim of this study was to evaluate the activity of gamma interferon (IFN-γ) when it was either adsorbed onto or loaded into albumin nanoparticles.
Brucella abortus
-infected macrophages and infected BALB/c mice were selected as the models for testing of the therapeutic potentials of these cytokine delivery systems, in view of the well-established role of IFN-γ-activated macrophages for the control of
Brucella
sp. infections. Whereas the encapsulation of IFN-γ inside the matrix of nanoparticles completely abrogated its activity, adsorbed IFN-γ increased by 0.75 log unit the bactericidal effect induced by RAW macrophages activated with free IFN-γ, along with a higher level of production of nitric oxide. In infected BALB/c-mice, IFN-γ adsorbed onto nanoparticles was also more active than free cytokine in reducing the number of bacteria in the spleens, and the effect was mediated by an increased ratio of IFN-γ-secreting (Th1) to interleukin-4-secreting (Th2) cells. Overall, albumin nanoparticles would be suitable as carriers that target IFN-γ to macrophages and, thus, potentiate their therapeutic activity.
Evolution of TEM-Type Enzymes: Biochemical and Genetic Characterization of Two New Complex Mutant TEM Enzymes, TEM-151 and TEM-152, from a Single Patient
Authors: Robin Frédéric , Delmas Julien , Schweitzer Cédric , Tournilhac Olivier , Lesens Olivier , Chanal Catherine , Bonnet Richard 
Published: January 2007

ABSTRACT

Two clinical isolates of
Escherichia coli
, CF1179 and CF1295, were isolated from a patient hospitalized in the hematology unit of the University Hospital of Clermont-Ferrand, Clermont-Ferrand, France. They were resistant to penicillin-clavulanate combinations and to ceftazidime. The double-disk synergy test was positive only for isolate CF1179. Molecular comparison of the isolates showed that they were clonally related.
E. coli
recombinant strains exhibiting the resistance phenotype of the clinical strains were obtained by cloning. The clones corresponding to strains CF1179 and CF1295 produced TEM-type beta-lactamases with pI values of 5.7 and 5.3, respectively. Sequencing analysis revealed two novel
bla
TEM
genes encoding closely related complex mutant TEM enzymes, designated TEM-151 (pI 5.3) and TEM-152 (pI 5.7). These two genes also harbored a new promoter region which presented a 9-bp deletion. The two novel β-lactamases differed from the parental enzyme, TEM-1, by the substitution Arg164His, previously observed in extended-spectrum beta-lactamases (ESBLs), and by the substitutions Met69Val and Asn276Asp, previously observed in the inhibitor-resistant penicillinase TEM-36/IRT-7. They differed by two amino acid substitutions: TEM-152 harbored a Glu240Lys ESBL-type substitution and TEM-151 had an Ala284Gly substitution. Functional analysis of TEM-151 and TEM-152 showed that both enzymes had hydrolytic activity against ceftazidime (
k
cat
, 5 and 16 s
−1
, respectively). TEM-152 was more resistant than TEM-151 to the inhibitor clavulanic acid (50% inhibitory concentrations, 1 versus 0.17 μM). These results confirm the evolution of TEM-type enzymes toward complex enzymes harboring the two kinds of substitutions which confer an extended spectrum of action against beta-lactam antibiotics and resistance to inhibitors.
EthA, a Common Activator of Thiocarbamide-Containing Drugs Acting on Different Mycobacterial Targets
Authors: Dover Lynn G. , Alahari Anuradha , Gratraud Paul , Gomes Jessica M. , Bhowruth Veemal , Reynolds Robert C. , Besra Gurdyal S. , Kremer Laurent 
Published: January 2007

ABSTRACT

Many of the current antimycobacterial agents require some form of cellular activation unmasking reactive groups, which in turn will bind to their specific targets. Therefore, understanding the mechanisms of activation of current antimycobacterials not only helps to decipher mechanisms of drug resistance but may also facilitate the development of alternative activation strategies or of analogues that do not require such processes. Herein, through the use of genetically defined strains of
Mycobacterium bovis
BCG we provide evidence that EthA, previously shown to activate ethionamide, also converts isoxyl (ISO) and thiacetazone (TAC) into reactive species. These results were further supported by the development of an in vitro assay using purified recombinant EthA, which allowed direct assessment of the metabolism of ISO. Interestingly, biochemical analysis of [
14
C]acetate-labeled cultures suggested that all of these EthA-activated drugs inhibit mycolic acid biosynthesis via different mechanisms through binding to specific targets. This report is also the first description of the molecular mechanism of action of TAC, a thiosemicarbazone antimicrobial agent that is still used in the treatment of tuberculosis as a second-line drug in many developing countries. Altogether, the results suggest that EthA is a common activator of thiocarbamide-containing drugs. The broad specificity of EthA can now be used to improve the activation process of these drugs, which may help overcome the toxicity problems associated with clinical thiocarbamide use.