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A prey species using crypsis to avoid predators has the opportunity to evolve polymorphic crypsis when it is being exposed to two (or more) habitats with different backgrounds. Here, we investigate when this phenomenon can occur, in a simulation study with a sexually reproducing prey and a predator that can learn to find hiding prey, represented by an artificial neural network. Initially, the prey
Background. Artificial neural networks have successfully been applied for automated interpretation of myocardial perfusion images. So far the networks have used data from the myocardial perfusion images only. The purpose of this study was to investigate whether the automated interpretation of myocardial perfusion images with the use of artificial neural networks was improved if clinical data were
To investigate the phenotype associated with estrogen receptor alpha (ER) expression in breast carcinoma, gene expression profiles of 58 node-negative breast carcinomas discordant for ER status were determined using DNA microarray technology. Using artificial neural networks as well as standard hierarchical clustering techniques, the tumors could be classified according to ER status, and a list of
Background: The availability of high throughput methods for measurement of mRNA concentrations makes the reliability of conclusions drawn from the data and global quality control of samples and hybridization important issues. We address these issues by an information theoretic approach, applied to discretized expression values in replicated gene expression data. Results: Our approach yields a quan
In order to identify biological processes relevant for cell death and survival in the brain following stroke, the postischemic brain transcriptome was studied by a large-scale cDNA array analysis of three peri-infarct brain regions at eight time points during the first 24 h of reperfusion following middle cerebral artery occlusion in the rat. K-means cluster analysis revealed two distinct biphasic
We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree distributions, we find that the networks are dynamically stable. Furthermore, for architectures with few inputs per node, the dynamics of the networks is close to critical. In addition, the fraction of gene
The driving force behind oncoproteomics is to identify protein signatures that are associated with a particular malignancy. Here, we have used a recombinant scFv antibody microarray in an attempt to classify sera derived from pancreatic adenocarcinoma patients versus healthy subjects. Based on analysis of nonfractionated, directly labeled, whole human serum proteomes we have identified a protein s
A number of studies have implicated a role for the cell surface glycoprotein CD44 in several biologic events, such as lymphopoiesis, homing, lymphocyte activation, and apoptosis. We have earlier reported that signaling via CD44 on naive B cells in addition to B-cell receptor (BCR) and CD40 engagement generated a germinal center-like phenotype. To further characterize the global role of CD44 in B d
Pathway-specific therapy is the future of cancer management. The oncogenic phosphatidylinositol 3-kinase (P13K) pathway is frequently activated in solid tumors; however, currently, no reliable test for P13K pathway activation exists for human tumors. Taking advantage of the observation that loss of PTEN, the negative regulator of P13K, results in robust activation of this pathway, we developed and
Array Close Information Database is an online database for information about microarray cDNA clones. For each clone, the database contents include assigned UniGene cluster(s), location in the full-length transcript, assigned gene ontology terms and position in the genome assembly.
in search for a strawberry (Fragaria ananassa) with low allergen content, we determined the proteomic variation within and between different varieties. Proteomics data were generated by DIGE and proteins identified with MALDI-MS/MS. The amount of the strawberry allergen Fra a 1 varied between different strawberry varieties (CV = 39%). The variation was at the same level, or even slightly larger, d
We describe an approach to screen large sets of MALDI-MS mass spectra for protein isoforms separated on two-dimensional electrophoresis gels. Mass spectra are matched against each other by utilizing extracted peak mass lists and hierarchical clustering. The output is presented as dendrograms in which protein isoforms cluster together. Clustering could be applied to mass spectra from different samp
Some clinical results indicate that somatostatin (sms) might be useful in the treatment of advanced prostate cancer (HRPC). Because of its transient in vivo half-life only more stable derivatives of sms are of interest in this context. Recent studies have shown that natural sms can be conjugated to a carbohydrate (smsdx) with preservation of sms-like effects on the prostatic tumor cell proteome. T
BioArray Software Environment (BASE) is a web-based software package for storing, searching, and analyzing locally generated microarray data and information surrounding microarray production. The workflow begins in sample management and, optionally, microtiter plate tracking and ends in visualization and analysis of entire experiments. The relative ease with which new analysis plug-ins can be adde
ProDaC (Proteomics Data Collection), a Coordination Action within the 6th EU framework programme, was created to support the collection, distribution and public availability of data from proteomics experiments. Within the consortium standards are created and maintained enabling an extensive data collection within the proteomics community. Important elements of ProDaC are workshops held twice a yea
The prediction of transcription factor binding sites in genomic sequences is in principle very useful to identify upstream regulatory factors. However, when applying this concept to genomes of multicellular organisms such as mammals, one has to deal with a large number of false positive predictions since many transcription factor genes are only expressed in specific tissues or cell types. We devel
Abstract in UndeterminedDifferential in-gel electrophoresis (DIGE) experiments allow three protein samples to be run per gel. The three samples are labeled with the spectrally resolvable fluorescent dyes, Cy2, Cy3, and Cy5, respectively. Here, we show that protein-specific dye effects exist, and we present a linear mixed model for analysis of DIGE data which takes dye effects into account. A Java
Background: Tumour hypoxia is a common characteristic of many solid human tumours, and is associated with a poor prognosis in various types of cancer. Metabolic changes occur when cells are exposed to low oxygen pressure; however, little is known about the mechanisms underlying malignant transformation and/or progression caused by hypoxia. Materials and Methods: We monitored global gene expression
Proteome analysis involves many steps that generate large quantities of data in different formats. This creates a need for automatic data merging and extraction of important features from data. Furthermore, metadata need to be collected and reported to enable critical evaluation of results. Many data analysis tools are developed locally in research laboratories and are nontrivial to adapt for othe
Of increasing interest in the field of protein modelling and simulation is the effects of crowding. In a living cell, large molecules can take up 30% of the cell plasma volume, and affects the folding and dynamics of proteins. Computer simulations have so far focused mainly on simple spherical crowders, but recent simulations with protein crowders have shown effects beyond what can be replicated u
