TREMSUCS-TCGA - an integrated workflow for the identification of biomarkers for treatment success.

Many publicly available databases provide disease related data, that makes it possible to link genomic data to medical and meta-data. The cancer genome atlas (TCGA), for example, compiles tens of thousand of datasets covering a wide array of cancer types. Here we introduce an interactive and highly automatized TCGA-based workflow that links and analyses epigenomic and transcriptomic data with treatment and survival data in order to identify possible biomarkers that indicate treatment success.

Harmonization of experimental procedures to assess mitochondrial respiration in human permeabilized skeletal muscle fibers.

Aim: High-resolution respirometry in human permeabilized muscle fibers is extensively used for analysis of mitochondrial adaptions to nutrition and exercise interventions, and is linked to athletic performance. However, the lack of standardization of experimental conditions limits quantitative inter- and intra-laboratory comparisons.

Methods: In our study, an international team of investigators measured mitochondrial respiration of permeabilized muscle fibers obtained from three biopsies (vastus lateralis) from the same healthy volunteer to avoid inter-individual variability.

PET-BIDS, an extension to the brain imaging data structure for positron emission tomography.

The Brain Imaging Data Structure (BIDS) is a standard for organizing and describing neuroimaging datasets, serving not only to facilitate the process of data sharing and aggregation, but also to simplify the application and development of new methods and software for working with neuroimaging data. Here, we present an extension of BIDS to include positron emission tomography (PET) data, also known as PET-BIDS, and share several open-access datasets curated following PET-BIDS along with tools for conversion, validation and analysis of PET-BIDS datasets.

SMORE: Synteny Modulator of Repetitive Elements.

Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation.

Similarity-Based Segmentation of Multi-Dimensional Signals.

The segmentation of time series and genomic data is a common problem in computational biology. With increasingly complex measurement procedures individual data points are often not just numbers or simple vectors in which all components are of the same kind. Analysis methods that capitalize on slopes in a single real-valued data track or that make explicit use of the vectorial nature of the data are not applicable in such scenaria.

Phylogenetic distribution of plant snoRNA families.

Background: Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs.

Fluorescence excitation-emission matrix spectroscopy as a tool for determining quality of sparkling wines.

Browning in sparkling wines was assessed by the use of excitation-emission fluorescence spectroscopy combined with PARAllel FACtor analysis (PARAFAC). Four different cava sparkling wines were monitored during an accelerated browning process and subsequently storage. Fluorescence changes observed during the accelerated browning process were monitored and compared with other conventional parameters: absorbance at 420nm (A420) and the content of 5-hydroxymethyl-2-furfural (5-HMF).

Conservation and losses of non-coding RNAs in avian genomes.

Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase.

Periodic solutions and refractory periods in the soliton theory for nerves and the locust femoral nerve.

Close to melting transitions it is possible to propagate solitary electromechanical pulses which reflect many of the experimental features of the nerve pulse including mechanical dislocations and reversible heat production. Here we show that one also obtains the possibility of periodic pulse generation when the constraint for the nerve is the conservation of the overall length of the nerve. This condition generates an undershoot beneath the baseline ('hyperpolarization') and a 'refractory period', i.

Relationship between tumor response and the ratio of nucleotide triphosphates to inorganic-phosphate in small-cell lung-cancer xenografts.

We examined whether grossly similar tumor responses, obtained by different therapies, induce similar patterns of change in the ratios of nucleotide triphosphate (NTP) to inorganic phosphate (P-i) in two human tumor lines, derived from the tumor of the same patient. The tumor responses were induced by doxorubicin 10 mg/kg i.p.

Proliferating cell nuclear antigen (pcna) and C-erbb-2 oncoprotein in breast-carcinoma with correlations to histopathological parameters and prognosis.

Overexpression of PCNA (more than 25% positive tumour cells) and positivity of c-erbB-2 oncoprotein were immunohistochemically demonstrated in 490 formalin-fixed and paraffin-embedded breast carcinomas. Overexpression of PCNA and c-erbB-2 correlated with large tumour size, presence of lymph node metastases, high histological grade (poor differentiation), and absence of steriod hormone receptors features indicating an aggressive phenotype. In univariate analysis overexpression of PCNA correlated with poor overall survival (p<0.

Anorexia in patients with cancer with special references on its association with early changes in food-intake behavior chemotherapeutic treatment and adjuvant enteral nutrition (review).

Anorexia defined as decreased appetite resulting in fatigue, change of body image and weight loss is stated to be fundamental to the syndrome of cancer cachexia. Weight loss is the most apparent symptom of anorexia and cachexia, and occurs quite frequently in patients with cancer. Interest in the pathogenetic mechanisms, is due to the strong association between weight loss and lower duality and quantity of life.

The prognostic-significance of cathepsin-d in breast carcinomas - an immunohistochemical study.

Cathepsin D, a lysosomal protease, was examined by immunohistochemistry in 481 breast carcinomas. The immunoreactivity for cathepsin D was registered in the tumour cells, in the surrounding stroma, and in the macrophages and correlated with clinicopathological parameters. In univariate analysis of survival data, less than 25% positive tumour cells, any positivity in the stroma, and moderate or strong positivity in the macrophages were poor prognostic parameters.