bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data
Authors: Annest Amalia , Bumgarner Roger E , Raftery Adrian E , Yeung Ka Yee 
Published: February 2009

AbstractBackgroundMicroarray technology is increasingly used to identify potential biomarkers for cancer prognostics and diagnostics. Previously, we have developed the iterative Bayesian Model Averaging (BMA) algorithm for use in classification. Here, we extend the iterative BMA algorithm for application to survival analysis on high-dimensional microarray data. The main goal in applying survival analysis to microarray data is to determine a highly predictive model of patients' time to event (such as death, relapse, or metastasis) using a small number of selected genes. Our multivariate procedure combines the effectiveness of multiple contending models by calculating the weighted average of their posterior probability distributions. Our results demonstrate that our iterative BMA algorithm for survival analysis achieves high prediction accuracy while consistently selecting a small and cost-effective number of predictor genes.ResultsWe applied the iterative BMA algorithm to two cancer datasets: breast cancer and diffuse large B-cell lymphoma (DLBCL) data. On the breast cancer data, the algorithm selected a total of 15 predictor genes across 84 contending models from the training data. The maximum likelihood estimates of the selected genes and the posterior probabilities of the selected models from the training data were used to divide patients in the test (or validation) dataset into high- and low-risk categories. Using the genes and models determined from the training data, we assigned patients from the test data into highly distinct risk groups (as indicated by a p-value of 7.26e-05 from the log-rank test). Moreover, we achieved comparable results using only the 5 top selected genes with 100% posterior probabilities. On the DLBCL data, our iterative BMA procedure selected a total of 25 genes across 3 contending models from the training data. Once again, we assigned the patients in the validation set to significantly distinct risk groups (p-value = 0.00139).ConclusionThe strength of the iterative BMA algorithm for survival analysis lies in its ability to account for model uncertainty. The results from this study demonstrate that our procedure selects a small number of genes while eclipsing other methods in predictive performance, making it a highly accurate and cost-effective prognostic tool in the clinical setting.
Prostaglandin E2-EP1 and EP2 receptor signaling promotes apical junctional complex disassembly of Caco-2 human colorectal cancer cells
Authors: Tanaka Marcelo N , Diaz Bruno L , de Souza Wanderley , Morgado-Diaz Jose A 
Published: February 2009

AbstractBackgroundThe apical junctional complex (AJC) is a dynamic structure responsible to maintain epithelial cell-cell adhesions and it plays important functions such as, polarity, mechanical integrity, and cell signaling. Alteration of this complex during pathological events leads to an impaired epithelial barrier by perturbation of the cell-cell adhesion system. Although clinical and experimental data indicate that prostaglandin E2(PGE2) plays a critical function in promoting cell motility and cancer progression, little is known concerning its role in AJC disassembly, an event that takes place at the beginning of colorectal tumorigenesis. Using Caco-2 cells, a cell line derived from human colorectal cancer, we investigated the effects of prostaglandin E2(PGE2) treatment on AJC assembly and function.ResultsExposition of Caco-2 cells to PGE2promoted differential alteration of AJC protein distribution, as evidenced by immunofluorescence and immunoblotting analysis and impairs the barrier function, as seen by a decrease in the transepithelial electric resistance and an increase in the permeability to ruthenium red marker. We demonstrated the involvement of EP1 and EP2 prostaglandin E2receptor subtypes in the modulation of the AJC disassembly caused by prostanoid. Furthermore, pharmacological inhibition of protein kinase-C, but not PKA and p38MAPK significantly prevented the PGE2effects on the AJC disassembly.ConclusionOur findings strongly suggest a central role of Prostaglandin E2-EP1 and EP2 receptor signaling to mediate AJC disassembly through a mechanism that involves PKC and claudin-1 as important target for the TJ-related effects in human colorectal cancer cells (Caco-2).
Global gene expression analysis reveals reduced abundance of putative microRNA targets in human prostate tumours
Authors: Sun Ruping , Fu Xuping , Li Yao , Xie Yi , Mao Yumin 
Published: February 2009

Abstract

Background
Recently, microRNAs (miRNAs) have taken centre stage in the field of human molecular oncology. Several studies have shown that miRNA profiling analyses offer new possibilities in cancer classification, diagnosis and prognosis. However, the function of miRNAs that are dysregulated in tumours remains largely a mystery. Global analysis of miRNA-target gene expression has helped illuminate the role of miRNAs in developmental gene expression programs, but such an approach has not been reported in cancer transcriptomics.

Results
In this study, we globally analysed the expression patterns of miRNA target genes in prostate cancer by using several public microarray datasets. Intriguingly, we found that, in contrast to global mRNA transcript levels, putative miRNA targets showed a reduced abundance in prostate tumours relative to benign prostate tissue. Additionally, the down-regulation of these miRNA targets positively correlated with the number of types of miRNA target-sites in the 3' untranslated regions of these targets. Further investigation revealed that the globally low expression was mainly driven by the targets of 36 specific miRNAs that were reported to be up-regulated in prostate cancer by a miRNA expression profiling study. We also found that the transcript levels of miRNA targets were lower in androgen-independent prostate cancer than in androgen-dependent prostate cancer. Moreover, when the global analysis was extended to four other cancers, significant differences in transcript levels between miRNA targets and total mRNA backgrounds were found.

Conclusion
Global gene expression analysis, along with further investigation, suggests that miRNA targets have a significantly reduced transcript abundance in prostate cancer, when compared with the combined pool of all mRNAs. The abnormal expression pattern of miRNA targets in human cancer could be a common feature of the human cancer transcriptome. Our study may help to shed new light on the functional roles of miRNAs in cancer transcriptomics.
Efficacy of chloroquine, amodiaquine and sulphadoxine-pyrimethamine for the treatment of uncomplicated falciparum malaria: revisiting molecular markers in an area of emerging AQ and SP resistance in Mali
Authors: Tekete Mamadou , Djimde Abdoulaye A , Beavogui Abdoul H , Maiga Hamma , Sagara Issaka , Fofana Bakary , Ouologuem Dinkorma , Dama Souleymane , Kone Aminatou , Dembele Demba , Wele Mamadou , Dicko Alassane , Doumbo Ogobara K 
Published: February 2009

Abstract

Background
To update the National Malaria Control Programme of Mali on the efficacy of chloroquine, amodiaquine and sulphadoxine-pyrimethamine in the treatment of uncomplicated falciparum malaria.

Methods
During the malaria transmission seasons of 2002 and 2003, 455 children – between six and 59 months of age, with uncomplicated malaria in Kolle, Mali, were randomly assigned to one of three treatment arms. In vivo outcomes were assessed using WHO standard protocols. Genotyping of msp1, msp2 and CA1 polymorphisms were used to distinguish reinfection from recrudescent parasites (molecular correction).

Results
Day 28 adequate clinical and parasitological responses (ACPR) were 14.1%, 62.3% and 88.9% in 2002 and 18.2%, 60% and 85.2% in 2003 for chloroquine, amodiaquine and sulphadoxine-pyrimethamine, respectively. After molecular correction, ACPRs (cACPR) were 63.2%, 88.5% and 98.0% in 2002 and 75.5%, 85.2% and 96.6% in 2003 for CQ, AQ and SP, respectively. Amodiaquine was the most effective on fever. Amodiaquine therapy selected molecular markers for chloroquine resistance, while in the sulphadoxine-pyrimethamine arm the level of dhfr triple mutant and dhfr/dhps quadruple mutant increased from 31.5% and 3.8% in 2002 to 42.9% and 8.9% in 2003, respectively. No infection with dhps 540E was found.

Conclusion
In this study, treatment with sulphadoxine-pyrimethamine emerged as the most efficacious on uncomplicated falciparum malaria followed by amodiaquine. The study demonstrated that sulphadoxine-pyrimethamine and amodiaquine were appropriate partner drugs that could be associated with artemisinin derivatives in an artemisinin-based combination therapy.
Necrotizing pneumonia and sepsis due to Clostridium perfringens: a case report
Authors: Palmacci Cristina , Antocicco Manuela , Bonomo Lorenzo , Maggi Fabio , Cocchi Alberto , Onder Graziano 
Published: February 2009

Abstract
Clostridia are uncommon causes of pleuropulmonary infection. Clostridial species infecting the pleuropulmonary structures characteristically cause a necrotizing pneumonia with involvement of the pleura. Most cases have iatrogenic causes usually due to invasive procedures into the pleural cavity, such as thoracentesis or thoracotomy, or penetrating chest injuries. Rarely clostridia pleuropulmonary infections are not related to these factors. The clinical course of pleuropulmonary clostridial infections can be very variable, but they may be rapid and fatal. We report a rare case of necrotizing pneumonia and sepsis due to Clostridium perfringens not related to iatrogenic causes or injuries in an 82 years old woman.
Hyperglycaemia results from beta-cell dysfunction in critically ill children with respiratory and cardiovascular failure: a prospective observational study
Authors: Preissig Catherine M , Rigby Mark R 
Published: February 2009

Abstract
Introduction
Hyperglycaemia is common in critical illness and associated with poor outcome. Glycaemic control using insulin may decrease morbidity and mortality. Many questions remain about the cause of critical illness hyperglycaemia (CIH). Our objective was to investigate the endocrinological basis of paediatric CIH.

Methods
C-peptide and blood glucose (BG) levels were assessed in 41 children aged 2 to 18 years old who were admitted to our paediatric intensive care unit (PICU). Patients who developed CIH, defined as persistent BG above 7.7 mmol/L, were treated with insulin infusion to achieve BG levels between 4.4 and 7.7 mmol/L. C-peptide levels were compared with respect to CIH development and degree of organ failure in all patients. Respiratory and cardiovascular failure were defined as need for mechanical ventilation and need for vasoactive infusions, respectively. Clinical and laboratory parameters, including c-peptide levels, were assessed.

Results
Of 41 children enrolled, 18 had respiratory failure only, 11 had both respiratory and cardiovascular failure, and 12 had neither respiratory or cardiovascular failure. Nine patients with respiratory failure only, 10 with both respiratory and cardiovascular failure, and none with no respiratory or cardiovascular failure developed CIH. Patients with CIH and respiratory and cardiovascular failure (n = 10) had very low c-peptide levels (4.4 ng/mL) despite significantly elevated mean BG levels (10.8 mmol/L), while those with CIH and respiratory failure only had very high c-peptide levels (11.5 ng/mL) with mean BG of 9.9 mmol/L. Low endogenous insulin production in those with respiratory and cardiovascular failure was associated with rapid onset of CIH, illness severity, higher insulin requirement and longer mechanical ventilation days, PICU length of stay and CIH duration.

Conclusions
Primary beta-cell dysfunction as defined by low endogenous c-peptide production appears to be prevalent in critically ill children with both respiratory and cardiovascular failure who develop CIH, whereas elevated insulin resistance appears to be the prominent cause of CIH in children with respiratory failure only. Our finding that beta-cell dysfunction is present in a subset of critically ill children with CIH challenges the assertion from adult studies that CIH is primarily the result of elevated insulin resistance.
Percussion and Cone Methods of Determining the Liquid Limit of Soils: Controlling Mechanisms
Authors: Sridharan A , Prakash K 
Published: February 2009

Abstract
The mechanisms controlling the liquid limit of montmorillonitic and kaolinitic soils are different. The observation that the liquid limits obtained by both the conventional percussion method and the cone penetration method differ quite appreciably from each other at low and high plasticity ranges indicates that the mechanisms dominating the two testing procedures are different. The analysis of the results obtained from the present experimental investigation, and the results available in the literature prove that the viscous shear resistance primarily controls the percussion method of testing, and that the frictional shear resistance dominates the cone method of testing. Since the viscous shear resistance is primarily due to the double-layer held water, which is characteristic of montmorillonitic soils, and the liquid limit of montmorillonitic soil is primarily governed by the diffuse double layer thickness, the percussion method is well suited to montmorillonitic soils. Likewise, as the interparticle frictional resistance is due to the mode of particle arrangement in addition to mineral frictional characteristics, and the same primarily controls the liquid limit of kaolinitic soils, the cone method suits kaolinitic soils better.
The Influence of Biofilm on the Mechanical Behavior of Sand
Authors: Perkins SW , Gyr P , James G 
Published: February 2009

Abstract
The growth of microbes on the surface of an object results in the formation of a biofilm, which in sand can lead to a reduction of hydraulic conductivity and can be used for groundwater containment and remediation. Sample preparation and testing techniques for triaxial and oedometer experiments were devised for the purpose of examining the influence of biofilm on the stress-strain-time properties of Ottawa sand. Results have shown that biofilm has a negligible influence on the strength and stiffness of the sand but increases time-dependent creep deformation. An elasto-viscoplastic constitutive model was calibrated for biofilm and non-biofilm sand and implemented into a finite-element code for the purpose of predicting creep deformation of a slope and a foundation resting on level ground. Numerical simulations showed that additional creep behavior of the biofilm sand had a negligible influence on the behavior of these geotechnical engineering facilities.
Dynamic Properties of Granulated Rubber/Sand Mixtures
Authors: Feng Z-Y , Sutter KG 
Published: February 2009

Abstract
Processed waste tires mixed with soils are applicable in lightweight fills for slopes, retaining walls, and embankments that may be subjected to seismic loads. Rubber's high damping capacity permits consideration of granulated rubber/soil mixtures as part of a damping system to reduce vibration. The dynamic properties of granulated rubber/soil mixtures are essential for the design of such systems. This research investigates the shear modulus and damping ratio of granulated rubber/sand mixtures using a torsional resonant column. Specimens were constructed using different percentages of granulated tire rubber and Ottawa sand at several different percentages. The maximum shear modulus and minimum damping ratio are presented with the percentage of granulated rubber. It is shown that reference strain can be used to normalize the shear modulus into a less scattered band for granulated rubber/sand mixtures. The normalized shear modulus reduction for 50% granulated rubber (by volumme) is close to a typical saturated cohesive soil. Empirical estimation of maximum shear modulus of soil/rubber mixtures can be achieved by treating the volume of rubber as voids.
A New Device for Measuring Permeability Under High Gradients and Sinusoidal Gradients
Authors: Khalifa M-AOA , Wahyudi I , Thomas P 
Published: February 2009

Abstract
This paper presents the design and testing procedures for a new type of permeameter that combines the methods of a constant-head permeameter for large hydraulic gradients (used to simulate hydraulic gradients in centrifuged geotechnical models) and a sinusoidal head permeameter (used to simulate internal flow in soils due to waves). The flow of permeant through a granular soil specimen is forced by a pump with a control servovalve used to regulate the flow rate according to the desired signal. The measurement instruments, which consist of temperature sensors, differential pressure transducers, flowmeters, and an electrical controller, are linked to a microcomputer and a data acquisition and control system that permits full automation of the tests.
Steady flow tests, carried out on fine sands with high hydraulic gradients, show that the flow is governed by Forchheimer's law. The analysis of the transient flow tests, carried out on fine sands, has shown that the classical Darcy's law is not valid when the material is subjected to a flow simulating a wave; a generalization of Darcy's law for this type of flow is proposed here.
Empirical Performance Classification for Cohesive Embankment Soils
Authors: White DJ , Bergeson KL 
Published: February 2009

Abstract
In response to recent evidence of poor highway embankment quality caused in part by improper soil identification and placement during construction, field-testing and laboratory analysis were conducted to develop a simple performance-based soil classification system that can be conducted in a field laboratory. Development of the Empirical Performance Classification (EPC) system is based on swell potential and frost susceptibility relationships of soils derived from liquid limit, plasticity index, and fines content (≤ 75 µm). From these parameters the EPC system is used to classify soils into one of three categories: select, suitable, or unsuitable. This paper presents the background for the development of this system and procedures for its use. A field trial in Iowa indicates that Iowa Department of Transportation field personnel can effectively use the EPC system to classify soils in the field and to link design with construction activities better. Increased field soil classification is expected to improve long-term performance of cohesive earth embankments.
Utilization of an Industrial Waste in Calcareous Expansive Clay Stabilization
Authors: Nalbantoglu Z , Gucbilmez E 
Published: February 2009

Abstract
The calcareous expansive soil in Cyprus has caused serious damage to structures. High-quality Soma fly ash admixture has shown tremendous potential as an economical method for the stabilization of the soil. Fly ash and lime-fly ash admixtures reduce the water absorption capacity and compressibility of the treated soils. Unlike some of the previously published research, an increase in hydraulic conductivity of the treated soils was obtained with an increase in percent fly ash and curing time. X-ray diffractograms indicate that pozzolanic reactions cause an alteration in the mineralogy of the treated soils, and new mineral formations with more stable silt-sand-like structures are produced. In the present study, an attempt has been made to use cation exchange capacity (CEC) values to substantiate the findings that, with increasing percentage of fly ash and curing time, soils become more granular in nature and show higher hydraulic conductivity values.
Evaluation of a Modified Soluble Sulfate Determination Method for Fine-Grained Cohesive Soils
Authors: Puppala AJ , Viyanant C , Kruzic AP , Perrin L 
Published: February 2009

Abstract
Soluble sulfate measurement in subgrade soils is an integral part of geotechnical investigations due primarily to sulfate-induced heave distress problems experienced by certain chemically treated sulfate soils. Sulfate measurements will assist engineers in the selection of appropriate soil stabilization methods in construction projects. There are no ASTM test methods that provide sulfate measurements in soils. Current methods including the University of Texas at Arlington (UTA) method, which are based on gravimetric procedures, often provide test results with high standard deviations. A modified UTA method, which was developed by addressing the limitations of the earlier methods, is presented in this paper. This procedure is evaluated for reproducible and reliable sulfate measurements in three artificial soils and one natural soil. The modified procedure provided reproducible sulfate measurements for all soils with coefficients of variations (COV) less than 10%. These results matched with ion chromatography measurements, which indicate that the modified method provided reliable measurements.
On the Identification of Critical State Lines for Sands
Authors: Klotz EU , Coop MR 
Published: February 2009

Abstract
New methods of geotechnical design in sands are often based on a state parameter type of approach, requiring the in situ state of the soil to be quantified relative to its critical state line. One difficulty in the application of these methods is then the correct identification of the location of this line, particularly at lower stress levels where sands strain soften and strains tend to localize within the sample. This paper examines the shearing behavior of two sands of diverse mineralogy by means of triaxial testing. The approach adopted has been to use existing techniques and apparatus that might reasonably be implemented in general practice. Recommendations are made as to the type of apparatus and test that should be used, and the corrections necessary to the data in order to identify as accurately as possible the critical states.
The Quality of Continuous Soil Samples
Authors: Long M 
Published: February 2009

AbstractThe quality of continuous soil samples from four typical Irish soft ground strata is studied. It was found that the MOSTAP® continuous specimens have lower initial moisture content and higher bulk density than block or tube samples. Test data from MOSTAP® samples underestimate 1D yield stress ratio, compression in the normally consolidated range and creep. Triaxial tests on the MOSTAP® specimens show erratic results. For the clays studied, they give lower undrained strength, a higher strain to failure, and a larger small strain stiffness than block samples. MOSTAP® specimen quality, however, improves with reducing soil sensitivity and increasing soil strength. These results are caused by the MOSTAP® sampler having an inferior cutting head geometry, leading to increased destructuring of the soils. In silt materials, the sampler penetration is partially drained, leading to densification of material, the effects being greatest for the MOSTAP® sampler. Recommendations are given for possible improvements to the sampler.
A Critical Assessment of the Moist Tamping Technique
Authors: Frost JD , Park J-Y 
Published: February 2009

Abstract
Current field sampling techniques are not readily able to produce high-quality undisturbed granular soil specimens for laboratory testing at an affordable cost. Accordingly, numerous specimen reconstitution methods have been developed for use in the laboratory. Among these methods, moist tamping has the advantage that it is relatively easy to control the global specimen density achieved, even for loose specimens, although unfortunately the method has also been qualitatively shown to yield less uniform specimens. This paper describes the findings of a study that critically assessed the moist tamping method by measuring the forces applied during the tamping process and investigated the uniformity of specimens prepared with the method by quantitatively analyzing both X-ray and optical images.