bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proliferative activity of cells from remaining dental pulp in response to treatment with dental materials
Authors: Lutfi AN , Kannan TP , Fazliah MN , Jamaruddin MA , Saidi J 
Published: March 2010

AbstractBackground:  The biological examination of pulp injury, repair events and response of dental pulp stem cells to dental restorative materials is important to accomplish restorative treatment, especially to commonly used dental materials in paediatric dentistry, such as glass ionomer cement (GIC) and calcium hydroxide (Ca(OH)2) lining cement.Methods:  Healthy patients aged between 9 to 11 years with carious primary molars without pulp exposure were selected and divided into two groups: Group 1 (teeth restored with GIC) and Group 2 (teeth lined using Ca(OH)2 and restored with GIC). The proliferative activity of stem cells of teeth between these two groups was compared using colourimetric cell proliferation reagent, alamarBlue. Immunocytochemistry and flow cytometry confirmation were performed using mesenchymal stem cell markers, CD105 and CD166.Results:  The proliferative activity using alamarBlue™ assay showed that cells derived from the remaining dental pulp of exfoliated deciduous teeth were positive for CD105 and CD166 and exhibited no difference between the two groups.Conclusions:  It can be concluded that the use of Ca(OH)2 or GIC as a lining material in indirect pulp capping procedures has the same effect on cells derived from the remaining dental pulp of exfoliated deciduous teeth which have responded favourably to the restorative treatments.
A primer on the application of Markov chains to the study of wildlife disease dynamics
Authors: Zipkin Elise F. , Jennelle Christopher S. , Cooch Evan G. 
Published: March 2010

Summary1. For wildlife researchers, disease specialists and policy analysts unfamiliar with the mathematical/statistical language of disease models, translation of probability statements into meaningful terms for disease research and control may be challenging. Markov chain models are powerful tools, applicable to the study of disease dynamics that allow straightforward calculations of easily interpretable metrics of interest including probabilities of infection/recovery, expected times to initial infection, duration of illness and life expectancies for susceptible and infected individuals.2. We present the basic principles and assumptions behind Markov chain modelling with an intuitive interpretation of parameter estimates and a step‐by‐step guide (including software code) for implementing this approach in the study of wildlife diseases. We also include an explanation of the estimation process necessary to implement Markov chain modelling (i.e. estimating the probability of state transitions between consecutive time steps) from typical survey data.3. We demonstrate the usefulness and ease of calculation of Markov chains through an example using a house finchCarpodacus mexicanus–Mycoplasma gallisepticum(MG) system. Our results show how semi‐weekly transition estimates of susceptible and infected individuals can be used to estimate a wide array of seasonal disease‐associated metrics.4. Markov chain modelling can provide a basic understanding of parameters estimated from wildlife disease studies, and can aid in understanding the implications of disease on wildlife populations and in evaluation of control measures. We envision this paper serving as an entry point into the extensive literature and potential applications of Markov chains in epidemiological modelling.
Monte
Carlo Study of Phonon Heat Conduction in Silicon Thin Films Including Contributions of Optical
Phonons
Authors: Mittal Arpit , Mazumder Sandip 
Published: March 2010

Abstract
The Monte Carlo method has found prolific use in the solution of the Boltzmann transport equation for phonons for the prediction of nonequilibrium heat conduction in crystalline thin films. This paper contributes to the state-of-the-art by performing a systematic study of the role of the various phonon modes on thermal conductivity predictions, in particular, optical phonons. A procedure to calculate three-phonon scattering time-scales with the inclusion of optical phonons is described and implemented. The roles of various phonon modes are assessed. It is found that transverse acoustic (TA) phonons are the primary carriers of energy at low temperatures. At high temperatures (T&gt;200 K), longitudinal acoustic (LA) phonons carry more energy than TA phonons. When optical phonons are included, there is a significant change in the amount of energy carried by various phonons modes, especially at room temperature, where optical modes are found to carry about 25% of the energy at steady state in silicon thin films. Most importantly, it is found that inclusion of optical phonons results in better match with experimental observations for silicon thin-film thermal conductivity. The inclusion of optical phonons is found to decrease the thermal conductivity at intermediate temperatures (50–200 K) and to increase it at high temperature (&gt;200 K), especially when the film is thin. The effect of number of stochastic samples, the dimensionality of the computational domain (two-dimensional versus three-dimensional), and the lateral (in-plane) dimension of the film on the statistical accuracy and computational efficiency is systematically studied and elucidated for all temperatures.
Differentiation of Clonal Complex 59 Community-Associated Methicillin-Resistant
Staphylococcus aureus
in Western Australia
Authors: Coombs Geoffrey W. , Monecke Stefan , Ehricht Ralf , Slickers Peter , Pearson Julie C. , Tan Hui-Leen , Christiansen Keryn J. , O'Brien Frances G. 
Published: March 2010

ABSTRACT

Clonal complex 59 (CC59) community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) strains were characterized using pulsed-field gel electrophoresis,
spa
typing, multilocus sequence typing, diagnostic DNA microarrays, and PCRs targeting staphylococcal cassette chromosome
mec
(SCC
mec
) elements and Panton-Valentine leukocidin (PVL). Six distinct groups within CC59 were characterized. At least seven different variants of SCC
mec
elements were identified (IVa [2B], IVb [2B], IVd [2B], IV variant [2B], IVa [2B&5], V variant [5C2], and V [5C2&5]). (The structural type is indicated by a Roman numeral, with a lowercase letter indicating the subtype, and the
ccr
complex and the
mec
complex are indicated by an Arabic numeral and an uppercase letter, respectively. Where there is an extra
ccr
element, this is indicated by “&” and an Arabic numeral designating the
ccr
type.) The first group is similar to the American sequence type 59 (ST59) MRSA-IV CA-MRSA strain USA1000. The second group includes a PVL-negative ST87 strain with an SCC
mec
element of subtype IVb (2B). The third group comprises PVL-variable ST59 MRSA-IV strains harboring multiple SCC
mec
IV subtypes. PVL-negative ST59 MRSA strains with multiple or composite SCC
mec
elements (IVa [2B&5]) form the fourth group. Group 5 corresponds to the internationally known “Taiwan clone,” a PVL-positive strain with a variant SCC
mec
element (V [5C2&5]). This strain proved to be the most common CC59 MRSA strain isolated in Western Australia. Finally, group 6 encompasses the ST59 MRSA-V variant (5C2). The differentiation of CC59 into groups and strains indicates a rapid evolution and spread of SCC
mec
elements. Observed differences between groups of strains as well as intrastrain variability within a group facilitate the tracing of their spread.
Cyclotide Interactions with the Nematode External Surface
Authors: Colgrave Michelle L. , Huang Yen-Hua , Craik David J. , Kotze Andrew C. 
Published: March 2010

ABSTRACTCyclotides are a large family of cyclic cystine knot-containing plant peptides that have anthelminthic activities againstHaemonchus contortusandTrichostrongylus colubriformis, two important gastrointestinal nematodes of sheep. In this study, we investigated the interaction of the prototypic cyclotide kalata B1 with the external surface ofH. contortuslarvae and adult worms. We show that cyclotides do not need to be ingested by the worms to exert their toxic effects but that an interaction with the external surface alone is toxic. Evidence for this was the toxicity toward adult worms in the presence of a chemically induced pharyngeal ligature and toxicity of cyclotides toward nonfeeding larval life stages. Uptake of tritiated inulin in ligated adult worms was increased in the presence of cyclotide, suggesting that cyclotides increase the permeability of the external membranes of adult nematodes. Polyethylene glycols of various sizes showed protective effects on the nonfeeding larval life stage, as well as in hemolytic activity assays, suggesting that discrete pores are formed in the membrane surfaces by cyclotides and that these can be blocked by polyethylene glycols of appropriate size. This increased permeability is consistent with recently reported effects of cyclotides on membranes in which kalata B1 was demonstrated to form pores and cause leakage of vesicle/cellular contents. Our data, together with known size constraints on the movement of permeants across nematode cuticle layers, suggest that one action of the cyclotides involves an interaction with the lipid-rich epicuticle layer at the surface of the worm.
Antiviral Activity of a Small-Molecule Inhibitor of Filovirus Infection
Authors: Warren Travis K. , Warfield Kelly L. , Wells Jay , Enterlein Sven , Smith Mark , Ruthel Gordon , Yunus Abdul S. , Kinch Michael S. , Goldblatt Michael , Aman M. Javad , Bavari Sina 
Published: March 2010

ABSTRACT

There exists an urgent need to develop licensed drugs and vaccines for the treatment or prevention of filovirus infections. FGI-103 is a low-molecular-weight compound that was discovered through an
in
vitro
screening assay utilizing a variant of
Zaire
ebolavirus
(ZEBOV) that expresses green fluorescent protein.
In
vitro
analyses demonstrated that FGI-103 also exhibits antiviral activity against wild-type ZEBOV and
Sudan
ebolavirus
, as well as
M
arburgvirus
(MARV) strains Ci67 and Ravn.
In
vivo
administration of FGI-103 as a single intraperitoneal dose of 10 mg/kg delivered 24 h after infection is sufficient to completely protect mice against a lethal challenge with a mouse-adapted strain of either ZEBOV or MARV-Ravn. In a murine model of ZEBOV infection, delivery of FGI-103 reduces viremia and the viral burden in kidney, liver, and spleen tissues and is associated with subdued and delayed proinflammatory cytokine responses and tissue pathology. Taken together, these results identify a promising antiviral therapeutic candidate for the treatment of filovirus infections.
Synergistic Effects between Conventional Antibiotics and 2-Aminoimidazole-Derived Antibiofilm Agents
Authors: Rogers Steven A. , Huigens Robert W. , Cavanagh John , Melander Christian 
Published: March 2010

ABSTRACT

2-Aminoimidazoles are an emerging class of small molecules that possess the ability to inhibit and disperse biofilms across bacterial order, class, and phylum. Herein, we report the synergistic effect between a 2-aminoimidazole/triazole conjugate and antibiotics toward dispersing preestablished biofilms, culminating with a 3-orders-of-magnitude increase of biofilm dispersion toward
Staphylococcus aureus
biofilms. Furthermore, we document that the 2-aminoimidazole/triazole conjugate will also resensitize multidrug-resistant strains of bacteria to the effects of conventional antibiotics, including methicillin-resistant
Staphylococcus aureus
(MRSA) and multidrug-resistant
Acinetobacter baumannii.
Many Chromosomal Genes Modulate MarA-Mediated Multidrug Resistance in
Escherichia coli
Authors: Ruiz Cristian , Levy Stuart B. 
Published: March 2010

ABSTRACT

Multidrug resistance (MDR) in clinical isolates of
Escherichia coli
can be associated with overexpression of
marA
, a transcription factor that upregulates multidrug efflux and downregulates membrane permeability. Using random transposome mutagenesis, we found that many chromosomal genes and environmental stimuli affected MarA-mediated antibiotic resistance. Seven genes affected resistance mediated by MarA in an antibiotic-specific way; these were mostly genes encoding unrelated enzymes, transporters, and unknown proteins. Other genes affected MarA-mediated resistance to all antibiotics tested. These genes were
acrA
,
acrB
, and
tolC
(which encode the major MarA-regulated multidrug efflux pump AcrAB-TolC),
crp
,
cyaA
,
hns
, and
pcnB
(four genes involved in global regulation of gene expression), and the unknown gene
damX
. The last five genes affected MarA-mediated MDR by altering
marA
expression or MarA function specifically on
acrA
. These findings demonstrate that MarA-mediated MDR is regulated at multiple levels by different genes and stimuli, which makes it both complex and fine-tuned and interconnects it with global cell regulation and metabolism. Such a regulation could contribute to the adaptation and spread of MDR strains and may be targeted to treat antibiotic-resistant
E. coli
and related pathogens.
A comparison of flower-visiting insects to rare Symphyotrichum sericeum and common Solidago nemoralis (Asteraceae)
Authors: Robson Diana Bizecki 
Published: March 2010

Flower-visiting insect activity to the rare Symphyotrichum sericeum (Vent.) G.L. Nesom and the common Solidago nemoralis Ait. var. longipetiolata (Mack. & Bush) Pal. & Steyerm. was examined to detect compositional and temporal similarities. A hand pollination experiment was conducted to determine whether pollen was limiting seed set. Of the 31 insect taxa that visited these plants, Bombus bifarius Cresson was the most common visitor to both species. More insect visitors of the Halictidae and Bombyliidae were received by S. sericeum than S. nemoralis, which received more visitors of the Syrphidae and Tachinidae. The insect visitation rate was not significantly different between the two plant species. Solidago nemoralis was visited by fewer insect taxa per day than S. sericeum, but the constancy of its visitors was higher. The insect visitor composition changed over time, with B. bifarius ignoring S. sericeum plants initially, then visiting them more frequently as the number of receptive S. nemoralis capitula declined. Hand pollination increased seed set in the earliest flowering capitula of S. sericeum, but not for those flowering during the peak. This research shows that the quantity of insect visits to the rare plant is comparable with that of the common plant but that pollination quality may be lower, particularly for early blooming capitula.
STATISTICAL COMPARISON OF METHODS TO ESTIMATE THE ERROR PROBABILITY IN SHORT-READ ILLUMINA SEQUENCING
Authors: ABNIZOVA IRINA , SKELLY TOM , NAUMENKO FEDOR , WHITEFORD NAVA , BROWN CLIVE , COX TONY 
Published: March 2010

As was the case in the beginning of the sequencing era, the new generation of short-read sequencing technologies still requires both accuracy of data processing methods and reliable measures of that accuracy. Inspired by the classic of the genre, the Phred method, we generalized those findings in the area of base quality value calibration. We introduce a simple, straightforward statistically established way to measure the performance of a calibrator, and to find an optimal way to assess its reliability. We illustrate the method by assessing the performance of several calibrators/predictors for Illumina, Genome Analyser 2 (GA2) data. The choice of the best predictor is based on optimization of validity, discriminative ability and discrimination power for several candidate predictors. We applied the method on data from one experimental run for genome of the phage ϕX, and found the best predictor out of ten candidates to be 'Purity', a statistics derived from corrected cluster intensities. The source code for the comparison of the predictors is available from the authors by request.
The Potential of Genes and Other Markers to Inform about Risk
Authors: Pepe Margaret S. , Gu Jessie W. , Morris Daryl E. 
Published: March 2010

AbstractBackground: Advances in biotechnology have raised expectations that biomarkers, including genetic profiles, will yield information to accurately predict outcomes for individuals. However, results to date have been disappointing. In addition, statistical methods to quantify the predictive information in markers have not been standardized.Methods: We discuss statistical techniques to summarize predictive information, including risk distribution curves and measures derived from them, that relate to decision making. Attributes of these measures are contrasted with alternatives such as receiver operating characteristic curves, R2, percent reclassification, and net reclassification index. Data are generated from simple models of risk conferred by genetic profiles for individuals in a population. Statistical techniques are illustrated, and the risk prediction capacities of different risk models are quantified.Results: Risk distribution curves are most informative and relevant to clinical practice. They show proportions of subjects classified into clinically relevant risk categories. In a population in which 10% have the outcome event and subjects are categorized as high risk if their risk exceeds 20%, we identified some settings where more than half of those destined to have an event were classified as high risk by the risk model. Either 150 genes each with odds ratio of 1.5 or 250 genes each with odds ratio of 1.25 were required when the minor allele frequencies are 10%. We show that conclusions based on receiver operating characteristic curves may not be the same as conclusions based on risk distribution curves.Conclusions: Many highly predictive genes will be required to identify substantial numbers of subjects at high risk. Cancer Epidemiol Biomarkers Prev; 19(3); 655–65
Sequence Variants in the TLR4 and TLR6-1-10 Genes and Prostate Cancer Risk. Results Based on Pooled Analysis from Three Independent Studies
Authors: Lindström Sara , Hunter David J. , Grönberg Henrik , Stattin Pär , Wiklund Fredrik , Xu Jianfeng , Chanock Stephen J. , Hayes Richard , Kraft Peter 
Published: March 2010

Abstract
Background: Genetic variation in two members of the Toll-like receptor family, TLR4 and the gene cluster TLR6-1-10, has been implicated in prostate cancer in several studies but the associated alleles have not been consistent across reports.
Methods: We did a pooled analysis combining genotype data from three case-control studies, Cancer of the Prostate in Sweden, the Health Professionals Follow-up Study, and the Prostate, Lung, Colon and Ovarian Cancer Screening Trial, with data from 3,101 prostate cancer cases and 2,523 controls. We did imputation to obtain dense coverage of the genes and comparable genotype data for all cohorts. In total, 58 single nucleotide polymorphisms in TLR4 and 96 single nucleotide polymorphisms in TLR6-1-10 were genotyped or imputed and analyzed in the entire data set. We did a cohort-specific analysis as well as meta-analysis and pooled analysis. We also evaluated whether the analyses differed by age or disease severity.
Results: We observed no overall association between genetic variation at the TLR4 and TLR6-1-10 loci and risk of prostate cancer.
Conclusions: Common germ line genetic variation in TLR4 and TLR6-1-10 did not seem to have a strong association with risk of prostate cancer.
Impact: This study suggests that earlier associations between prostate cancer risk and TLR4 and TLR6-1-10 sequence variants were chance findings. To definitely assess the causal relationship between TLR sequence variants and prostate cancer risk, very large sample sizes are needed. Cancer Epidemiol Biomarkers Prev; 19(3); 873–6
Adolescent Diet in Relation to Breast Cancer Risk among Premenopausal Women
Authors: Linos Eleni , Willett Walter C. , Cho Eunyoung , Frazier Lindsay 
Published: March 2010

Abstract
Background: Although the association between adult diet and breast cancer has been investigated extensively, large prospective studies have generally not shown a direct link between intakes of carbohydrate, fat, fiber, and other nutrients and risk of breast cancer. Adolescence may be a period of increased susceptibility to risk factors that predispose to breast cancer. Dietary risk factors could therefore be more important during early life than later in adulthood.
Methods: This is a prospective observational study of 39,268 premenopausal women in the Nurses' Health Study II who completed a 124-item food frequency questionnaire on their diet during high school (HS-FFQ) in 1998, at which time participants were 34 to 53 years of age. Cox proportional hazards regression was used to estimate relative risks and 95% CIs.
Results: Four hundred fifty-five incident cases of invasive breast cancer were diagnosed between 1998 and 2005. Compared with women in the lowest quintile of intake, the relative risk of breast cancer in the highest quintile of adolescent total fat consumption was 1.35 (95% confidence interval, 1.00-1.81). Adolescent consumption of saturated, monounsaturated, polyunsaturated, and trans fats was not significantly associated with breast cancer risk. Total dairy, milk, carbohydrate intake, glycemic index, glycemic load, and fiber consumed during adolescence were not significantly related to breast cancer incidence.
Conclusion: Dietary fat consumed during adolescence may be associated with an elevated risk of breast cancer. Further studies to assess this relationship among postmenopausal women, and confirm these results in premenopausal women, are needed. Cancer Epidemiol Biomarkers Prev; 19(3); 689–96
Association Between Cytokine Gene Polymorphisms and Gastric Precancerous Lesions: Systematic Review and Meta-analysis
Authors: Peleteiro Bárbara , Lunet Nuno , Carrilho Carla , Durães Cecília , Machado José Carlos , La Vecchia Carlo , Barros Henrique 
Published: March 2010

Abstract
Polymorphisms within interleukin-1 (IL1) and tumor necrosis factor α (TNFA) gene clusters are associated with an increased risk of gastric cancer. However, their role in gastric precancerous lesions remains poorly understood. Our objective was to perform a meta-analysis of studies addressing the association between IL1B-511, IL1RN variable number of tandem repeat, and TNFA-308 gene polymorphisms and gastric precancerous lesions, including original data from Portugal and Mozambique. Published studies on the association between these cytokine gene polymorphisms and gastric precancerous lesions were identified by systematic review, and estimates of the association were combined using random-effects meta-analysis taking into account new data obtained from Portuguese volunteer shipyard workers (n = 215) and Mozambican dyspeptic patients (n = 96) who underwent endoscopic and pathologic evaluation following the same protocol. Odds ratio (OR) estimates for intestinal metaplasia were 2.83 [95% confidence interval (95% CI), 1.15-6.96] for the IL1RN*22 genotype, 1.86 (95% CI, 1.03-3.36) for IL1B-511 T carriers, and 0.59 (95% CI, 0.12-3.04) for the TNFA-308*AA genotype in the Portuguese sample. All Mozambican subjects with intestinal metaplasia were T carriers for IL1B-511 and none had the 2 allele for IL1RN. In meta-analysis, IL1RN*22 genotype was associated with an increased risk of gastric precancerous lesions (22 versus LL: OR, 2.27; 95% CI, 1.40-3.70; I2 = 26.4%; 12 studies). No such association was found for the IL1B-511 (TT versus CC: OR, 1.34; 95% CI, 0.87-2.07; I2 = 65.7%; 13 studies) or TNFA-308 genotypes (AA versus GG: OR, 0.93; 95% CI, 0.35-2.43; I2 = 0.0%; 7 studies). The IL1RN*22 genotype seems to consistently increase the risk of gastric precancerous lesions, supporting a role for this polymorphism in the early stages of gastric carcinogenesis. Cancer Epidemiol Biomarkers Prev; 19(3); 762–76