A Comparative Classification Analysis of Abdominal Aortic Aneurysms by Machine Learning Algorithms.

The objective of this work was to perform image-based classification of abdominal aortic aneurysms (AAA) based on their demographic, geometric, and biomechanical attributes. We retrospectively reviewed existing demographics and abdominal computed tomography angiography images of 100 asymptomatic and 50 symptomatic AAA patients who received an elective or emergent repair, respectively, within 1-6 months of their last follow up. An in-house script developed within the MATLAB computational platform was used to segment the clinical images, calculate 53 descriptors of AAA geometry, and generate volume meshes suitable for finite element analysis (FEA).

Phasic Dopamine Transmission Reflects Initiation Vigor and Exerted Effort in an Action- and Region-Specific Manner.

Unlabelled: Initiating a reward-seeking behavior involves deciding on an action, how fast to initiate the action (initiation vigor), as well as how much effort to exert. These processes are thought to involve the mesolimbic dopamine system. Dopamine levels in the ventral striatum rise before initiating a reliably reinforced behavior.

Transcriptional and translational heterogeneity among neonatal mouse spermatogonia.

Spermatogonial stem cells (SSCs) are a subset of undifferentiated spermatogonia responsible for ongoing spermatogenesis in mammalian testes. Spermatogonial stem cells arise from morphologically homogeneous prospermatogonia, but growing evidence suggests that only a subset of prospermatogonia develops into the foundational SSC pool. This predicts that subtypes of undifferentiated spermatogonia with discrete mRNA and protein signatures should be distinguishable in neonatal testes.

Food restriction increases glutamate receptor-mediated burst firing of dopamine neurons.

Restriction of food intake increases the acquisition of drug abuse behavior and enhances the reinforcing efficacy of those drugs. However, the neurophysiological mechanisms responsible for the interactions between feeding state and drug use are largely unknown. Here we show that chronic mild food restriction increases the burst firing of dopamine neurons in the substantia nigra.

Before It Gets Started: Regulating Translation at the 5' UTR.

Translation regulation plays important roles in both normal physiological conditions and diseases states. This regulation requires cis-regulatory elements located mostly in 5' and 3' UTRs and trans-regulatory factors (e.g.

Enriching for correct prediction of biological processes using a combination of diverse classifiers.

Background: Machine learning models (classifiers) for classifying genes to biological processes each have their own unique characteristics in what genes can be classified and to what biological processes. No single learning model is qualitatively superior to any other model and overall precision for each model tends to be low. The classification results for each classifier can be complementary and synergistic suggesting the benefit of a combination of algorithms, but often the prediction probability outputs of various learning models are neither comparable nor compatible for combining.

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line.

Transcription, mRNA decay, translation and protein degradation are essential processes during eukaryotic gene expression, but their relative global contributions to steady-state protein concentrations in multi-cellular eukaryotes are largely unknown. Using measurements of absolute protein and mRNA abundances in cellular lysate from the human Daoy medulloblastoma cell line, we quantitatively evaluate the impact of mRNA concentration and sequence features implicated in translation and protein degradation on protein expression. Sequence features related to translation and protein degradation have an impact similar to that of mRNA abundance, and their combined contribution explains two-thirds of protein abundance variation.

The effect of gonadectomy and estradiol on sensitivity to oxidative stress.

The sexual dimorphism of life span and caloric restriction effects in numerous species suggest that estradiol (E2) is protective against oxidative damage. The only direct test of E2's protective effect in mice against in vivo oxidative stress to date may have been confounded by E2's direct chemical action as an antioxidant because it was administered at very high dosages. Therefore, we have identified a low yet physiologically effective dose of E2.

Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes.

Musashi1 (Msi1) is a highly conserved RNA-binding protein with pivotal functions in stem cell maintenance, nervous system development, and tumorigenesis. Despite its importance, only three direct mRNA targets have been characterized so far: m-numb, CDKN1A, and c-mos. Msi1 has been shown to affect their translation by binding to short elements located in the 3'-untranslated region.

Over-represented sequences located on 3' UTRs are potentially involved in regulatory functions.

Eukaryotic gene expression must be coordinated for the proper functioning of biological processes. This coordination can be achieved both at the transcriptional and post-transcriptional levels. In both cases, regulatory sequences placed at either promoter regions or on UTRs function as markers recognized by regulators that can then activate or repress different groups of genes according to necessity.

The origin of chromosome imbalances in neuroblastoma.

Many recurrent large-scale chromosome abnormalities associated with poor clinical outcomes have been identified in neuroblastoma, a pediatric tumor that accounts for 15% of childhood cancer deaths. We have previously used high-resolution oligonucleotide array comparative genomic hybridization to map 461 chromosome breakpoints leading to large-scale chromosome imbalances in 56 primary neuroblastoma tumors and cell lines. Here, we analyze the distribution of DNA sequence elements and genomic landmarks found within these breakpoint intervals and in 15,800 randomly generated intervals of similar size.

Gene function classification using NCI-60 cell line gene expression profiles.

Gene expression patterns from NCI's panel of 60 cell lines were used to train a Neural Network model for classifying genes to pathways. The model assigns probabilities to each gene for each of the 21 modeled pathways assigned by the Kyoto Encyclopedia of Genes and Genomes. Cross-validation of the model showed that 10 of the 21 pathways exhibited good performance in statistical significance and accuracy.