A System for Induction of Oblique Decision Trees

This article describes a new system for induction of oblique decision trees. This system, OC1, combines deterministic hill-climbing with two forms of randomization to find a good oblique split (in the form of a hyperplane) at each node of a decision tree. Oblique decision tree methods are tuned especially for domains in which the attributes are numeric, although they can be adapted to symbolic or mixed symbolic/numeric attributes. We present extensive empirical studies, using both real and artificial data, that analyze OC1's ability to construct oblique trees that are smaller and more accurate than their axis-parallel counterparts. We also examine the benefits of randomization for the construction of oblique decision trees.Comment: See http://www.jair.org/ for an online appendix and other files accompanying this articl

Early Life Stress as an Influence on Limbic Epilepsy: An Hypothesis Whose Time has Come?

The pathogenesis of mesial temporal lobe epilepsy (MTLE), the most prevalent form of refractory focal epilepsy in adults, is thought to begin in early life, even though seizures may not commence until adolescence or adulthood. Amongst the range of early life factors implicated in MTLE causation (febrile seizures, traumatic brain injury, etc.), stress may be one important contributor. Early life stress is an a priori agent deserving study because of the large amount of neuroscientific data showing enduring effects on structure and function in hippocampus and amygdala, the key structures involved in MTLE. An emerging body of evidence directly tests hypotheses concerning early life stress and limbic epilepsy: early life stressors, such as maternal separation, have been shown to aggravate epileptogenesis in both status epilepticus and kindling models of limbic epilepsy. In addition to elucidating its influence on limbic epileptogenesis itself, the study of early life stress has the potential to shed light on the psychiatric disorder that accompanies MTLE. For many years, psychiatric comorbidity was viewed as an effect of epilepsy, mediated psychologically and/or neurobiologically. An alternative – or complementary – perspective is that of shared causation. Early life stress, implicated in the pathogenesis of several psychiatric disorders, may be one such causal factor. This paper aims to critically review the body of experimental evidence linking early life stress and epilepsy; to discuss the direct studies examining early life stress effects in current models of limbic seizures/epilepsy; and to suggest priorities for future research

Hawkeye: An interactive visual analytics tool for genome assemblies

Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye. © 2007 Schatz et al.; licensee BioMed Central Ltd

Re-Assembly of the Genome of Francisella tularensis Subsp. holarctica OSU18

Francisella tularensis is a highly infectious human intracellular pathogen that is the causative agent of tularemia. It occurs in several major subtypes, including the live vaccine strain holarctica (type B). F. tularensis is classified as category A biodefense agent in part because a relatively small number of organisms can cause severe illness. Three complete genomes of subspecies holarctica have been sequenced and deposited in public archives, of which OSU18 was the first and the only strain for which a scientific publication has appeared [1]. We re-assembled the OSU18 strain using both de novo and comparative assembly techniques, and found that the published sequence has two large inversion mis-assemblies. We generated a corrected assembly of the entire genome along with detailed information on the placement of individual reads within the assembly. This assembly will provide a more accurate basis for future comparative studies of this pathogen

Left ventricular assist device as bridge to heart transplantation - lessons learned with the MicroMed DeBakey axial blood flow pump

Objective: The MicroMed DeBakey left ventricular assist device (LVAD) axial blood flow pump was used as bridge to heart transplantation (HTx) in patients with terminal heart failure. The aim was to evaluate this novel mechanical circulatory support system in regard to overall outcome. Methods: Prospective study in 15 HTx candidates (mean age 40±7 years) with terminal heart failure and maximal medical treatment due to ischemic cardiomyopathy (CMP, n=5), dilated CMP (n=3), restrictive CMP (n=2), unclassified CMP (n=1), metabolic CMP (n=1), valvular CMP (n=1) and congenital CMP (n=2). All patients were implanted with a MicroMed DeBakey LVAD. A rescue procedure was necessary in eight critical patients, while seven underwent elective LVAD implantation. Procedures were performed via median sternotomy, in normotherm femoro-femoral CPB (mean duration 59±1 min). Oral Marcoumar© (INR 2.0-3.0) and Aspirin© (100 mg daily) were started as soon as possible. Patients were discharged into a specialized rehabilitation clinic from which it was possible to release them home after a few weeks. Results: Successful implantation and discharge from ICU (mean stay 10±7 days) was possible in 11 patients. Seven were transplanted (mean support 50.7 days) and one is awaiting HTx (support >310 days) in the comfort of his home (NYHA I). Survival was 100% among the transplanted patients. Of the seven elective implants, five, and of the eight rescue procedures three patients underwent successful HTx. Four patients died early, while three patients died late on pump support due to intracranial hemorrhage (n=2, 73 and 76 days) and chest infection (n=1, 124 days). All survivors were discharged from hospital, with significant decrease in NYHA class (mean 3.8-2.4 (n=11)). Treadmill testing showed increased exercise tolerance, from 35 to 71 W (n=4). Plasma BNP values (mean 950-162 ng/l (n=4)) and pulmonary resistance (mean 316-194.5 dyne s/cm5 (n=3)) decreased significantly during LVAD support. Conclusions: The MicroMed DeBakey LVAD is simple to implant; outpatient treatment is safe and efficient. Patients' condition and pulmonary resistances normalize within 6 weeks, making previously considered inoperable patients amenable for HTx. HTx can be performed in low-risk situation, allowing better donor-recipient matching and improving overall outcom

Nucleotide Frequencies in Human Genome and Fibonacci Numbers

This work presents a mathematical model that establishes an interesting connection between nucleotide frequencies in human single-stranded DNA and the famous Fibonacci's numbers. The model relies on two assumptions. First, Chargaff's second parity rule should be valid, and, second, the nucleotide frequencies should approach limit values when the number of bases is sufficiently large. Under these two hypotheses, it is possible to predict the human nucleotide frequencies with accuracy. It is noteworthy, that the predicted values are solutions of an optimization problem, which is commonplace in many nature's phenomena.Comment: 12 pages, 2 figure