3,193 research outputs found
SU86.86 cells exhibit phenotypic and genotypic changes following selection by IH.
No full text<p>SU86.86 cells were treated with IH for 50 cycles, had clonal populations raised, and grown in normoxia for 2 months. A significant decrease in expression of E-cadherin (A) and p53 (B) was detected by quantitative Real-Time PCR. IH-selected SU86.86 clones also exhibited an increase in resistance to etoposide (C) and hypoxia (D).Results of selection of RKO cells following IH-selection (E-H). We do not detect any changes in p53 or E-cadherin expression within clones of RKO IH-selected (E,F). Furthermore, these cells did not exhibit resistance to etoposide (G), nor hypoxia (H).</p
Differential protein levels and phenotypes are exhibited among MCF10A cells following selection through IH.
No full text<p>(A) Analysis of protein levels was performed using the Reverse Phase Protein Array (RPPA) on the parental MCF10A line, passaged control clone 7, IH-selected clone 4, and IH-selected clone 9. Each clone was submitted in duplicate. Hierarchical clustering of significant (FDR ≤ 0.05) protein markers in control versus IH-selected samples is shown. The clustering was carried out with Euclidean distance metric with average linkage, and the data was median normalized and log2 transformed. The clustering was arbitrarily stopped at 2 and 5 groups for the samples and features respectively. (B) Western blotting analysis of p53 and E-cadherin protein. p53 protein is reduced by in IH-selected clones. E-cadherin is completely lost following selection by IH, and N-cadherin protein is detectable, indicating EMT in IH-selected clones. (C) Quantitative RT-PCR was performed on DNA levels of the <i>P53</i> and <i>E-CAD</i> loci. A 0.5 fold reduction in the number of copies of <i>P53</i> and <i>E-CAD</i> indicates a loss of one allele of each. (D) Western blotting against HIF-1α and GLUT-1 indicates constitutive stabilization of HIF-1α and its downstream effector GLUT-1 in IH-selected cells. MCF10A cells cultured in hypoxia are used as a positive control.</p
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.
No full textMalaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome
Selection of MCF10A cells by intermittent hypoxia (IH) induces drug resistance and reduced expression of p53 and E-cadherin.
No full text<p>(A) Multiple intermittent hypoxia regimens were tested at 1%O<sub>2</sub> and 0.2% O<sub>2</sub> over 6 days. Factor survival is expressed as compared to cells grown in parallel in normoxia (21%O<sub>2</sub>). MCF10A cells undergoing repetitive cycles of 16 hours hypoxia followed by 8 hrs reoxygenation exhibited the most cell death. (B) MCF10A cells were cultured in 50 cycles of IH in the selective regimen described in (A), and individual cells were isolated to be raised as clones, and then passaged for 2 months in normoxia. These clonal populations were tested for etoposide resistance. Heterogeneity in the IH-selected clones was detected, while a significant overall increase in etoposide resistance was measured. (C) MCF10A IH-selected clones 4 and 9 were further tested for resistance to multiple cytotoxic conditions, including treatment to the microtubule stabilizing docetaxel, the folate metabolism inhibitor methotrexate, as well as hypoxia and reduction of growth factors. Intermittent hypoxia exhibited increased survival to all of these conditions except for survival to growth factor removal. (D,E) Intermittent hypoxia exhibits changes in the expression of p53 and E-cadherin. Quantitative Real-Time PCR was performed on each IH-selected and passage control clone. Reduced <i>p53</i> and E-cadherin mRNA expression levels were detected in IH-selected control clones. Factor expression is relative to the average of control clones.</p
Operating Speed and Geometry Relationships for Rural Single Carriageways in the UK
No full textThe aim of this study was to find an up to date operating speed model for rural single carriageways (two-lane highways) in the United Kingdom, as part of wider research into the consistency of highway alignment. A series of speed surveys were carried out in the North East of England. A novel method of estimating horizontal curvature details from digital mapping was developed for this study. Other geometric features of the survey sites were measured on site using appropriate electronic and manual methods. Analysis of the spot speed distributions confirmed the findings of previous research, following a normal distribution in the majority of cases. Significant differences were found between the mean and operating speeds in the two directions of flow. Further analysis looked at the differences between speeds on the inside and outside of curves. Single and multiple regression analyses were used to examine the speed data and the various geometric parameters of tangents and curves to find suitable operating speed models. The best predictive models for curves were found to rely mainly on the radius of the curve. On tangents the speed was mainly dependent on the length of the tangent
Analysis of Accident Rates and Geometric Consistency Measures on Sections of Rural Single Carriageway.
No full textGeometric consistency is becoming a useful technique, with research being carried out in various countries to develop predictive models to improve rural road safety. The main aim of this research is to develop reliable accident prediction models for rural single carriageways in the UK using highway geometric design consistency measures. This paper describes a research project that is being carried out using data from two counties in the north east of England. In order to collect the relevant data, a novel method of estimating horizontal curvature details from digital mapping was developed for this study, as no as built drawings available for such roads. After that, roads under study were divided into sections according to certain criteria. Traffic flows and accident data for each road section were obtained for the 5 year period 2000-2004. Accidents were located in the correct element (e.g. curve or tangent) for each road section. As operating speed (V85th percentile) was needed in order to apply the some of the consistency measures, several single and multiple operating speed regression models were developed for both horizontal curves and tangents. As a step towards achieving the main goal of this project which is to develop several accident prediction models, a set of consistency measures over entire road sections were defined. A bivariate correlation analysis between accident rates and these measures have been carried out. Many consistency measures were found to have an association with accident rates especially in the case of single vehicle accidents. Applying univariate regression has shown that some relationships do exist, but that further work is required using multivariate analysis. This work is now being out, using appropriate statistical techniques including artificial neural networks
Details of the significant protein markers with FDR and fold change (log of Control to IH-selected group).
No full text<p>Details of the significant protein markers with FDR and fold change (log of Control to IH-selected group).</p
Exploring the Relationship between the Geometric Design Consistency and Safety in Rural Single Carriageways in the UK
No full textExploring the factors that may affect road safety and trying to modify these factors for safety improvements has been, for many years, a high priority for highway authorities. One of the factors that is believed to have a major effect in road safety is the geometric design consistency, especially for single rural carriageways. Rural single carriageways, in most highway networks, represent an important component and also exhibit more accidents than other roads. Although the concept of highway design consistency emerged more than ten years ago in North America and some European Countries, no recent research appears to have been done to date in the UK. The goal of this research is to establish the nature of the relationship between consistency measures and geometric characteristics of roads in the UK, as these relationships have been established in the North America and some European countries, as well as to explore the relationship between the geometric design consistency measures and road safety for UK roads
Operating Speed Behaviour Models for Single Rural Carriageways - Case Study of North East of England
No full textImproving road safety is a high priority for highway authorities. It is believed that geometric design consistency may affect road safety on rural single carriageways, which exhibit higher accident rates than other rural roads. This research aims to study the geometric consistency and safety of rural single carriageways, many of which follow historic alignments, and are not designed to modern standards. This paper investigates the operating speed and geometry relationships for rural single carriageways using speed data collected for curves and tangents in two counties in the North East of England. Accurate operating speed models are needed to calculate the measures of Geometric Design Consistency. They include models for curves, straights and acceleration/dec eleration behaviour prior to or following the curves/ straights. A series of speed surveys were carried out in the North East of England. A novel method of estimating horizontal curvature details from digital mapping was developed for this study. Other geometric features of the survey sites were measured on site using appropriate electronic and manual methods. Analysis of the spot speed distributions confirmed the findings of previous research, following a normal distribution in the majority of cases. Significant differences were found between the mean and operating speeds in the two directions of flow. Further analysis looked at the differences between speeds on the inside and outside of curves. Single and multiple regression analysis were used to examine the speed data and the various geometric parameters of tangents and curves to find suitable operating speed models. The best predictive models for curves were found to rely mainly on the radius of the curve. On tangents the speed was mainly dependant on the length of the tangent
(A) Soft agar colony formation assays were performed on each clone as a measure of cell-adhesion growth. IH-selected clones demonstrated an increase in the number of colonies relative to passage control clones. Metastatic MDA-MB-231 cells were seeded as a positive control. (B) Passage control MCF01A clones (top) and IH-selected clones (bottom) were imaged using brightfield microscopy. While control clones exhibited smooth borders indicative of an epithelial phenotype, IH-selected cells migrated apart from adjacent cells, indicating an increase in migration as well as EMT. (C) As a measure of migratory capacity, passage control MCF10A clones (in grey) and IH-selected MCF10A (in black) were seeded within an xCELLIGENCE CIM plate, which measures in real time the number of cells passing through a barrier from a low-serum well to high-serum well. Measurements taken over the span of 24 hours indicates IH-selected clones have increased migratory rates (D) Proliferation rates of each of the fo
No full text<p>(A) Soft agar colony formation assays were performed on each clone as a measure of cell-adhesion growth. IH-selected clones demonstrated an increase in the number of colonies relative to passage control clones. Metastatic MDA-MB-231 cells were seeded as a positive control. (B) Passage control MCF01A clones (top) and IH-selected clones (bottom) were imaged using brightfield microscopy. While control clones exhibited smooth borders indicative of an epithelial phenotype, IH-selected cells migrated apart from adjacent cells, indicating an increase in migration as well as EMT. (C) As a measure of migratory capacity, passage control MCF10A clones (in grey) and IH-selected MCF10A (in black) were seeded within an xCELLIGENCE CIM plate, which measures in real time the number of cells passing through a barrier from a low-serum well to high-serum well. Measurements taken over the span of 24 hours indicates IH-selected clones have increased migratory rates (D) Proliferation rates of each of the four clones. Cell counts were performed daily. IH-selected clones exhibited reduced proliferation relative to passage control clones. (E) Oxygen consumption and proton production (a proxy for glycolysis) were measured for each clone with the Seahorse XF Analyzer. The ratio of oxygen consumption to proton production was increased in IH-selected clones.</p
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