Early oxygen levels contribute to brain injury in extremely preterm infants.

Background: Extremely low gestational age newborns (ELGANs) are at risk of neurodevelopmental impairments that may originate in early NICU care. We hypothesized that early oxygen saturations (SpO), arterial pO levels, and supplemental oxygen (FiO) would associate with later neuroanatomic changes.

Methods: SpO, arterial blood gases, and FiO from 73 ELGANs (GA 26.

Reliability of temperature signal in various climate indicators from northern Europe.

We collected relevant observational and measured annual-resolution time series dealing with climate in northern Europe, focusing in Finland. We analysed these series for the reliability of their temperature signal at annual and seasonal resolutions. Importantly, we analysed all of the indicators within the same statistical framework, which allows for their meaningful comparison.

Newtonian boreal forest ecology: The Scots pine ecosystem as an example.

Isaac Newton's approach to developing theories in his book Principia Mathematica proceeds in four steps. First, he defines various concepts, second, he formulates axioms utilising the concepts, third, he mathematically analyses the behaviour of the system defined by the concepts and axioms obtaining predictions and fourth, he tests the predictions with measurements. In this study, we formulated our theory of boreal forest ecosystems, called NewtonForest, following the four steps introduced by Newton.

Homozygous deletions of cadherin genes in chondrosarcoma-an array comparative genomic hybridization study.

Chondrosarcoma is a malignant bone tumor that is often resistant to chemotherapy and radiotherapy. We applied high resolution oligonucleotide array comparative genomic hybridization to 46 tumor specimens from 44 patients with chondrosarcoma and identified several genes with potential importance for the development of chondrosarcoma. Several homozygous deletions were detected.

Prognostic classification of patients with acute lymphoblastic leukemia by using gene copy number profiles identified from array-based comparative genomic hybridization data.

The development of risk-adapted therapy has improved the treatment results of acute lymphoblastic leukemia (ALL) especially in children. However, more accurate risk classifiers are warranted. In this study we aimed at defining a prognostic classifier based on DNA copy number alterations of adolescent and young adult (AYA) (10-25 yrs) ALL patients (n=60) determined by microarray CGH and the relapse status of the patients.

Focal 9p instability in hematologic neoplasias revealed by comparative genomic hybridization and single-nucleotide polymorphism microarray analyses.

Copy number losses in chromosome arm 9p are well-known aberrations in malignancies, including leukemias. The CDKN2A gene is suggested to play a key role in these aberrations. In this study overviewing 9p losses in hematologic neoplasias, we introduce the term focal 9p instability to indicate multiple areas of copy number loss or homozygous loss within a larger heterozygous one in 9p.

Genomic profiles associated with early micrometastasis in lung cancer: relevance of 4q deletion.

Purpose: Bone marrow is a common homing organ for early disseminated tumor cells (DTC) and their presence can predict the subsequent occurrence of overt metastasis and survival in lung cancer. It is still unclear whether the shedding of DTC from the primary tumor is a random process or a selective release driven by a specific genomic pattern.

Experimental Design: DTCs were identified in bone marrow from lung cancer patients by an immunocytochemical cytokeratin assay.

Pathways affected by asbestos exposure in normal and tumour tissue of lung cancer patients.

Background: Studies on asbestos-induced tumourigenesis have indicated the role of, e.g., reactive oxygen/nitrogen species, mitochondria, as well as NF-kappaB and MAPK signalling pathways.

Integrated gene copy number and expression microarray analysis of gastric cancer highlights potential target genes.

We performed an integrated array comparative genomic hybridization (aCGH) and expression microarray analysis of 8 normal gastric tissues and 38 primary tumors, including 25 intestinal and 13 diffuse gastric adenocarcinomas to identify genes whose expression is deregulated in association with copy number alteration. Our aim was also to identify molecular genetic alterations that are specific to particular clinicopathological characteristics of gastric cancer. Distinct molecular genetic profiles were identified for intestinal and diffuse gastric cancers and for tumors obtained from 2 different locations of the stomach.

Classification of human cancers based on DNA copy number amplification modeling.

Background: DNA amplifications alter gene dosage in cancer genomes by multiplying the gene copy number. Amplifications are quintessential in a considerable number of advanced cancers of various anatomical locations. The aims of this study were to classify human cancers based on their amplification patterns, explore the biological and clinical fundamentals behind their amplification-pattern based classification, and understand the characteristics in human genomic architecture that associate with amplification mechanisms.

Aberrations of chromosome 19 in asbestos-associated lung cancer and in asbestos-induced micronuclei of bronchial epithelial cells in vitro.

Exposure to asbestos is known to induce lung cancer, and our previous studies have suggested that specific chromosomal regions, such as 19p13, are preferentially aberrant in lung tumours of asbestos-exposed patients. Here, we further examined the association between the 19p region and exposure to asbestos using array comparative genomic hybridization and fluorescence in situ hybridization (FISH) in lung tumours and FISH characterization of asbestos-induced micronuclei (MN) in human bronchial epithelial BEAS 2B cells in vitro. We detected an increased number of 19p losses in the tumours of asbestos-exposed patients in comparison with tumours from non-exposed subjects with similar distribution of tumour histology in both groups (13/33; 39% versus 3/25; 12%, P = 0.

Microarray image segmentation using additional dye--an experimental study.

Unlabelled: The DNA microarray technique allows monitoring the expression levels of thousands of genes simultaneously. A single DNA microarray experiment involves a number of error-prone manual and automated processes, which influence the results and have an impact on the subsequent stages of analysis. Typical problems of arrays are pinning errors while probe printing and the corruption of spots by noise patches.

Gene expression profiles in asbestos-exposed epithelial and mesothelial lung cell lines.

Background: Asbestos has been shown to cause chromosomal damage and DNA aberrations. Exposure to asbestos causes many lung diseases e.g.

Predictive value of histopathologic parameters in early squamous cell carcinoma of oral tongue.

The clinical course of early squamous cell carcinoma of oral tongue (OTSCC) is unpredictable and various histopathologic parameters of the primary tumour have been suggested as prognostic factors to be used in clinical decision-making. We reviewed clinicopathologic data of 73 patients diagnosed with Stage I-II OTSCC. Predictive value of pathological T-stage, depth of infiltration, grade, and mode of invasion with respect to local recurrences, occult cervical metastases, and disease specific survival (DSS) was analysed.

Identification of specific gene copy number changes in asbestos-related lung cancer.

Asbestos is a well-known lung cancer-causing mineral fiber. In vitro and in vivo experiments have shown that asbestos can cause chromosomal damage and aberrations. Lung tumors, in general, have several recurrently amplified and deleted chromosomal regions.

Are N and S deposition altering the mineral composition of Norway spruce and Scots pine needles in Finland?

Data from a large-scale foliar survey were used to calculate the extent to which N and S deposition determined the mineral composition of Scots pine and Norway spruce needles in Finland. Foliar data were available from 367 needle samples collected on 36 plots sampled almost annually between 1987 and 2000. A literature study of controlled experiments revealed that acidifying deposition mediates increasing N and S concentrations, and decreasing Mg:N and Ca:Al ratios in the needles.

Data integration and visualization system for enabling conceptual biology.

Motivation: Integration of heterogeneous data in life sciences is a growing and recognized challenge. The problem is not only to enable the study of such data within the context of a biological question but also more fundamentally, how to represent the available knowledge and make it accessible for mining.

Results: Our integration approach is based on the premise that relationships between biological entities can be represented as a complex network.

Caveolins as tumour markers in lung cancer detected by combined use of cDNA and tissue microarrays.

To identify new potential diagnostic markers for lung cancer, the expression profiles of 37 lung tumours were analysed using cDNA arrays. Seven samples were from small-cell lung cancer (SCLC), two from large-cell neuroendocrine tumours (LCNEC), and 28 from other non-small-cell lung cancers (mainly squamous cell cancer and adenocarcinoma). Principal component analysis and the permutation test were used to detect differences in the gene expression profiles and a set of genes was found that distinguished high-grade neuroendocrine carcinomas (SCLC and LCNEC) from other lung cancers.

Differentially expressed genes in nonsmall cell lung cancer: expression profiling of cancer-related genes in squamous cell lung cancer.

The expression patterns of cancer-related genes in 13 cases of squamous cell lung cancer (SCC) were characterized and compared with those in normal lung tissue and 13 adenocarcinomas (AC), the other major type of nonsmall cell lung cancer (NSCLC). cDNA array was used to screen the gene expression levels and the array results were verified using a real-time reverse-transcriptase-polymerase chain reaction (RT-PCR). Thirty-nine percent of the 25 most upregulated and the 25 most downregulated genes were common to SCC and AC.

Evaluation of forest nutrition based on large-scale foliar surveys: are nutrition profiles the way of the future?

This paper introduces the use of nutrition profiles as a first step in the development of a concept that is suitable for evaluating forest nutrition on the basis of large-scale foliar surveys. Nutrition profiles of a tree or stand were defined as the nutrient status, which accounts for all element concentrations, contents and interactions between two or more elements. Therefore a nutrition profile overcomes the shortcomings associated with the commonly used concepts for evaluating forest nutrition.

Investigatory and analytical approaches to differential gene expression profiling in mantle cell lymphoma.

Mantle cell lymphoma (MCL) is a non-Hodgkin's lymphoma of B-cell lineage. The blastoid variant of MCL, characterized by high mitotic rate, is clinically more aggressive than common MCL. We used the cDNA array technology to examine the gene expression profiles of both blastoid variant and common MCL.

Identification of differentially expressed genes in pulmonary adenocarcinoma by using cDNA array.

No clear patterns in molecular changes underlying the malignant processes in lung cancer of different histological types have been found so far. To identify critical genes in lung cancer progression we compared the expression profile of cancer related genes in 14 pulmonary adenocarcinoma patients with normal lung tissue by using the cDNA array technique. Principal component analyses (PCA) and permutation test were used to detect the differentially expressed genes.