53 research outputs found
Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae
Uncovering interactions between genes, gene networks, is important to increase our understanding of intrinsic cellular processes and responses to external stimuli such as drugs. Gene networks can be computationally inferred from repeated measurements of gene expression, using algorithms, which assume that each gene is controlled by only a small number of other proteins. Here, by extending the transcription network with cofactors (defined from protein-protein binding data) as active regulators, we identified the effective gene network, providing evidence of in-hubs in the gene regulatory networks of yeast. Then, using the notion that in-hub genes will be differentially expressed over several experimental conditions, we designed an algorithm, the HubDetector, enabling identification of in-hubs directly from gene expression data. Applying the HubDetector to 488 genome-wide expression profiles from two independent datasets, we identified putative in-hubs overlapping significantly with in-hubs in the effective gene network
Scale Stain: Multi-Resolution Feature Enhancement in Pathology Visualization
Digital whole-slide images of pathological tissue samples have recently
become feasible for use within routine diagnostic practice. These gigapixel
sized images enable pathologists to perform reviews using computer workstations
instead of microscopes. Existing workstations visualize scanned images by
providing a zoomable image space that reproduces the capabilities of the
microscope. This paper presents a novel visualization approach that enables
filtering of the scale-space according to color preference. The visualization
method reveals diagnostically important patterns that are otherwise not
visible. The paper demonstrates how this approach has been implemented into a
fully functional prototype that lets the user navigate the visualization
parameter space in real time. The prototype was evaluated for two common
clinical tasks with eight pathologists in a within-subjects study. The data
reveal that task efficiency increased by 15% using the prototype, with
maintained accuracy. By analyzing behavioral strategies, it was possible to
conclude that efficiency gain was caused by a reduction of the panning needed
to perform systematic search of the images. The prototype system was well
received by the pathologists who did not detect any risks that would hinder use
in clinical routine
Towards Grading Gleason Score using Generically Trained Deep convolutional Neural Networks
We developed an automatic algorithm with the purpose to assist pathologists to report Gleason score on malignant prostatic adenocarcinoma specimen. In order to detect and classify the cancerous tissue, a deep convolutional neural network that had been pre-trained on a large set of photographic images was used. A specific aim was to support intuitive interaction with the result, to let pathologists adjust and correct the output. Therefore, we have designed an algorithm that makes a spatial classification of the whole slide into the same growth patterns as pathologists do. The 22-layer network was cut at an earlier layer and the output from that layer was used to train both a random forest classifier and a support vector machines classifier. At a specific layer a small patch of the image was used to calculate a feature vector and an image is represented by a number of those vectors. We have classified both the individual patches and the entire images. The classification results were compared for different scales of the images and feature vectors from two different layers from the network. Testing was made on a dataset consisting of 213 images, all containing a single class, benign tissue or Gleason score 3-5. Using 10-fold cross validation the accuracy per patch was 81 %. For whole images, the accuracy was increased to 89 %
Revisorns roll och uppgift i en föränderlig social kontext
Uppsatsens syfte är att belysa hur revisorns roll och uppgift kan påverkas av förändringar i den sociala kontexten, och vad detta kan få för konsekvenser för revisorsbranschen. Uppsatsen utgår från en fenomenologisk vetenskapsansats, då det är ett fenomen som studeras. Syftet med studien är att bidra med kunskap som inte var känd förut, och därav har ett kvalitativt metodperspektiv valts. Undersökningsansatsen är huvudsakligen induktiv, men även abduktiva inslag förekommer i studien. Referensramen omfattar en genomgång av relevant litteratur för problemområdet. Teorier om social ordning, oberoende och förtroende studeras. Det empiriska materialet utgörs av en fallstudie baserad på nio personliga intervjuer med revisorer. Studien har resulterat i ett praktiskt och ett teoretiskt bidrag. Det praktiska bidraget består av att fem teorier formuleras, som sedan ska kunna testas genom hypotesprövning. Hypotesprövning faller emellertid utanför ramarna för denna uppsats. Det teoretiska bidraget utgörs av en modell som visar hur revisorns roll och uppgift påverkas av och interagerar med den sociala ordningen och revisorns trovärdighet. Denna interaktion och utveckling sker i ett sammanhang som utgör revisorns sociala kontext
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Multi-Organ Expression Profiling Uncovers a Gene Module in Coronary Artery Disease Involving Transendothelial Migration of Leukocytes and LIM Domain Binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) Study
Environmental exposures filtered through the genetic make-up of each individual alter the transcriptional repertoire in organs central to metabolic homeostasis, thereby affecting arterial lipid accumulation, inflammation, and the development of coronary artery disease (CAD). The primary aim of the Stockholm Atherosclerosis Gene Expression (STAGE) study was to determine whether there are functionally associated genes (rather than individual genes) important for CAD development. To this end, two-way clustering was used on 278 transcriptional profiles of liver, skeletal muscle, and visceral fat (n = 66/tissue) and atherosclerotic and unaffected arterial wall (n = 40/tissue) isolated from CAD patients during coronary artery bypass surgery. The first step, across all mRNA signals (n = 15,042/12,621 RefSeqs/genes) in each tissue, resulted in a total of 60 tissue clusters (n = 3958 genes). In the second step (performed within tissue clusters), one atherosclerotic lesion (n = 49/48) and one visceral fat (n = 59) cluster segregated the patients into two groups that differed in the extent of coronary stenosis (P = 0.008 and P = 0.00015). The associations of these clusters with coronary atherosclerosis were validated by analyzing carotid atherosclerosis expression profiles. Remarkably, in one cluster (n = 55/54) relating to carotid stenosis (P = 0.04), 27 genes in the two clusters relating to coronary stenosis were confirmed (n = 16/17, P<10). Genes in the transendothelial migration of leukocytes (TEML) pathway were overrepresented in all three clusters, referred to as the atherosclerosis module (A-module). In a second validation step, using three independent cohorts, the A-module was found to be genetically enriched with CAD risk by 1.8-fold (P<0.004). The transcription co-factor LIM domain binding 2 (LDB2) was identified as a potential high-hierarchy regulator of the A-module, a notion supported by subnetwork analysis, by cellular and lesion expression of LDB2, and by the expression of 13 TEML genes in Ldb2–deficient arterial wall. Thus, the A-module appears to be important for atherosclerosis development and, together with LDB2, merits further attention in CAD research
Transcriptional Profiling Uncovers a Network of Cholesterol-Responsive Atherosclerosis Target Genes
Despite the well-documented effects of plasma lipid lowering regimes halting atherosclerosis lesion development and reducing morbidity and mortality of coronary artery disease and stroke, the transcriptional response in the atherosclerotic lesion mediating these beneficial effects has not yet been carefully investigated. We performed transcriptional profiling at 10-week intervals in atherosclerosis-prone mice with human-like hypercholesterolemia and a genetic switch to lower plasma lipoproteins (Ldlr−/−Apo100/100 Mttpflox/flox Mx1-Cre). Atherosclerotic lesions progressed slowly at first, then expanded rapidly, and plateaued after advanced lesions formed. Analysis of lesion expression profiles indicated that accumulation of lipid-poor macrophages reached a point that led to the rapid expansion phase with accelerated foam-cell formation and inflammation, an interpretation supported by lesion histology. Genetic lowering of plasma cholesterol (e.g., lipoproteins) at this point all together prevented the formation of advanced plaques and parallel transcriptional profiling of the atherosclerotic arterial wall identified 37 cholesterol-responsive genes mediating this effect. Validation by siRNA-inhibition in macrophages incubated with acetylated-LDL revealed a network of eight cholesterol-responsive atherosclerosis genes regulating cholesterol-ester accumulation. Taken together, we have identified a network of atherosclerosis genes that in response to plasma cholesterol-lowering prevents the formation of advanced plaques. This network should be of interest for the development of novel atherosclerosis therapies
Carotid Plaque Age Is a Feature of Plaque Stability Inversely Related to Levels of Plasma Insulin
C-declination curve (a result of the atomic bomb tests in the
1950s and 1960s) to determine the average biological age of carotid
plaques.C
content by accelerator mass spectrometry. The average plaque age (i.e.
formation time) was 9.6±3.3 years. All but two plaques had formed
within 5–15 years before surgery. Plaque age was not associated with
the chronological ages of the patients but was inversely related to plasma
insulin levels (p = 0.0014). Most plaques were
echo-lucent rather than echo-rich (2.24±0.97, range 1–5).
However, plaques in the lowest tercile of plaque age (most recently formed)
were characterized by further instability with a higher content of lipids
and macrophages (67.8±12.4 vs. 50.4±6.2,
p = 0.00005; 57.6±26.1 vs. 39.8±25.7,
p<0.0005, respectively), less collagen (45.3±6.1 vs.
51.1±9.8, p<0.05), and fewer smooth muscle cells (130±31
vs. 141±21, p<0.05) than plaques in the highest tercile.
Microarray analysis of plaques in the lowest tercile also showed increased
activity of genes involved in immune responses and oxidative
phosphorylation.C, can improve our understanding of carotid
plaque stability and therefore risk for clinical complications. Our results
also suggest that levels of plasma insulin might be involved in determining
carotid plaque age
Multi-Organ Expression Profiling Uncovers a Gene Module in Coronary Artery Disease Involving Transendothelial Migration of Leukocytes and LIM Domain Binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) Study
Environmental exposures filtered through the genetic make-up of each individual alter the transcriptional repertoire in organs central to metabolic homeostasis, thereby affecting arterial lipid accumulation, inflammation, and the development of coronary artery disease (CAD). The primary aim of the Stockholm Atherosclerosis Gene Expression (STAGE) study was to determine whether there are functionally associated genes (rather than individual genes) important for CAD development. To this end, two-way clustering was used on 278 transcriptional profiles of liver, skeletal muscle, and visceral fat (n = 66/tissue) and atherosclerotic and unaffected arterial wall (n = 40/tissue) isolated from CAD patients during coronary artery bypass surgery. The first step, across all mRNA signals (n = 15,042/12,621 RefSeqs/genes) in each tissue, resulted in a total of 60 tissue clusters (n = 3958 genes). In the second step (performed within tissue clusters), one atherosclerotic lesion (n = 49/48) and one visceral fat (n = 59) cluster segregated the patients into two groups that differed in the extent of coronary stenosis (P = 0.008 and P = 0.00015). The associations of these clusters with coronary atherosclerosis were validated by analyzing carotid atherosclerosis expression profiles. Remarkably, in one cluster (n = 55/54) relating to carotid stenosis (P = 0.04), 27 genes in the two clusters relating to coronary stenosis were confirmed (n = 16/17, P<10−27and−30). Genes in the transendothelial migration of leukocytes (TEML) pathway were overrepresented in all three clusters, referred to as the atherosclerosis module (A-module). In a second validation step, using three independent cohorts, the A-module was found to be genetically enriched with CAD risk by 1.8-fold (P<0.004). The transcription co-factor LIM domain binding 2 (LDB2) was identified as a potential high-hierarchy regulator of the A-module, a notion supported by subnetwork analysis, by cellular and lesion expression of LDB2, and by the expression of 13 TEML genes in Ldb2–deficient arterial wall. Thus, the A-module appears to be important for atherosclerosis development and, together with LDB2, merits further attention in CAD research
Asthmatics Exhibit Altered Oxylipin Profiles Compared to Healthy Individuals after Subway Air Exposure
Asthma is a chronic inflammatory lung disease that causes significant morbidity and mortality worldwide. Air pollutants such as particulate matter (PM) and oxidants are important factors in causing exacerbations in asthmatics, and the source and composition of pollutants greatly affects pathological implications.This randomized crossover study investigated responses of the respiratory system to Stockholm subway air in asthmatics and healthy individuals. Eicosanoids and other oxylipins were quantified in the distal lung to provide a measure of shifts in lipid mediators in association with exposure to subway air relative to ambient air.Sixty-four oxylipins representing the cyclooxygenase (COX), lipoxygenase (LOX) and cytochrome P450 (CYP) metabolic pathways were screened using liquid chromatography-tandem mass spectrometry (LC-MS/MS) of bronchoalveolar lavage (BAL)-fluid. Validations through immunocytochemistry staining of BAL-cells were performed for 15-LOX-1, COX-1, COX-2 and peroxisome proliferator-activated receptor gamma (PPARγ). Multivariate statistics were employed to interrogate acquired oxylipin and immunocytochemistry data in combination with patient clinical information.Asthmatics and healthy individuals exhibited divergent oxylipin profiles following exposure to ambient and subway air. Significant changes were observed in 8 metabolites of linoleic- and α-linolenic acid synthesized via the 15-LOX pathway, and of the COX product prostaglandin E(2) (PGE(2)). Oxylipin levels were increased in healthy individuals following exposure to subway air, whereas asthmatics evidenced decreases or no change.Several of the altered oxylipins have known or suspected bronchoprotective or anti-inflammatory effects, suggesting a possible reduced anti-inflammatory response in asthmatics following exposure to subway air. These observations may have ramifications for sensitive subpopulations in urban areas
Gene networks and modules in atherosclerosis
In this thesis we are using global gene expression profiles to unravel
functional gene networks and modules. The focus is atherosclerosis, a
disease with manifestations in the artery wall where deposits of lipids
accumulate and trigger immune responses causing the development of
plaques, which upon rupture can lead to a myocardial infarction or
stroke. Atherosclerosis is a complex disease influenced by energy
metabolism in multiple organs and by several genetic and environmental
risk factors. To meet this complexity, we believe the most appropriate
approach is to identify gene networks and modules in patients suffering
coronary artery disease as well as a relevant mouse model with human-like
dyslipidemia prone to atherosclerosis development.
First, we investigate structural properties of the regulatory gene
network in yeast, integrating protein protein interactions with the
transcription network resulting in an estimate the effective gene network
underlying gene expression data. In this effective gene network, we show
evidence of in-hubs and provide a method for predicting in-hubs directly
from gene expression data.
In the second study, we used the Ldlr−/− Apob100/100 Mttpflox/flox
Mx1-Cre mouse model to study atherosclerosis development and how this
development is effected by plasma cholesterollowering. This mouse model
has a lipid profile similar to human hyperlipidemia and develops
atherosclerosis on a chow diet. Moreover, it contains a genetic switch
(Mttpflox/flox Mx1-Cre) to turn off the VLDL synthesis in the liver and
lowering plasma cholesterol by > 80%. Atherosclerotic lesions progressed
slowly at first, then expanded rapidly, and plateaued after advanced
lesions formed. Analysis of lesion expression profiles indicated
lipid-poor macrophages accumulated prior the rapid expansion of the
plaques. When macrophage concentration reached a critical point it was
followed by a rapid expansion phase with accelerated foam-cell formation
and inflammation, an interpretation also supported by lesion histology. A
network of 8 cholesterol-responsive atherosclerosis genes was identified
as central to the rapid expansion of the plaques.
Third, in the Stockholm Atherosclerosis Gene Expression (STAGE) study,
including 124 well-characterized patients undergoing coronary artery
bypass surgery, we measured and analyzed 278 expression profiles from the
liver, skeletal muscle, mediastinal fat, and aortic lesion
(atherosclerotic artery expression with unaffected arterial wall
expression subtracted). Clustering of these gene expression
profiles performed separately in each organ generated a total of 60
clusters. Two clusters, in aortic lesion (n = 49) and fat (n = 59),
related to degree of atherosclerosis. Remarkably, in a validation cohort
27 genes were replicated in a cluster (n =55) also related to the degree
of atherosclerosis. In all three clusters relating to atherosclerosis
(i.e., the atherosclerosis module), genes in the transendothelial
migration of leukocyte pathway (TEML) were overrepresented and the
transcription co-factor LIM-domain binding 2 (LDB2) expressed in lesion
macrophages and endothelial cells was identified as a potential regulator
of this module.
In the last study, we first identified 2457 cholesterol-responsive genes
in the atherosclerotic arterial wall by lowering plasma cholesterol at
10-weeks intervals during atherosclerosis development using the mouse
model of Study II. To prioritize the most atherosclerosis-relevant genes
among these 2457, we used a list of 1259 genes active during
atherogenesis (Study II) together with three global gene networks
generated from human atherosclerosis gene expression profiles in study
III, public literature mining, and protein-protein interaction data.
Using an integrative network approach to identify genes neighboring any
of 68 atherosclerosis seed genes, we identified 35 cholesterol-responsive
genes that were believed to be highly relevant to atherosclerosis. Taken
together, this thesis provides evidence that systems biological analysis
of global gene expression profiles isolated from a wide range of
biological specimens can be used to infer functional interactions of
genes in modules or networks. The content and architecture of these
modules and networks can be used to improve our understanding how complex
disorders like atherosclerosis develop
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