An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads

BACKGROUND: Next generation sequencing technologies have greatly advanced many research areas of the biomedical sciences through their capability to generate massive amounts of genetic information at unprecedented rates. The advent of next generation sequencing has led to the development of numerous computational tools to analyze and assemble the millions to billions of short sequencing reads produced by these technologies. While these tools filled an important gap, current approaches for storing, processing, and analyzing short read datasets generally have remained simple and lack the complexity needed to efficiently model the produced reads and assemble them correctly. RESULTS: Previously, we presented an overlap graph coarsening scheme for modeling read overlap relationships on multiple levels. Most current read assembly and analysis approaches use a single graph or set of clusters to represent the relationships among a read dataset. Instead, we use a series of graphs to represent the reads and their overlap relationships across a spectrum of information granularity. At each information level our algorithm is capable of generating clusters of reads from the reduced graph, forming an integrated graph modeling and clustering approach for read analysis and assembly. Previously we applied our algorithm to simulated and real 454 datasets to assess its ability to efficiently model and cluster next generation sequencing data. In this paper we extend our algorithm to large simulated and real Illumina datasets to demonstrate that our algorithm is practical for both sequencing technologies. CONCLUSIONS: Our overlap graph theoretic algorithm is able to model next generation sequencing reads at various levels of granularity through the process of graph coarsening. Additionally, our model allows for efficient representation of the read overlap relationships, is scalable for large datasets, and is practical for both Illumina and 454 sequencing technologies

A long-term "memory" of HIF induction in response to chronic mild decreased oxygen after oxygen normalization

Background Endothelial dysfunction (ED) is functionally characterized by decreased vasorelaxation, increased thrombosis, increased inflammation, and altered angiogenic potential, has been intimately associated with the progression and severity of cardiovascular disease. Patients with compromised cardiac function oftentimes have a state of chronic mild decreased oxygen at the level of the vasculature and organs, which has been shown to exacerbate ED. Hypoxia inducible factor (HIF) is a transcription factor complex shown to be the master regulator of the cellular response to decreased oxygen levels and many HIF target genes have been shown to be associated with ED. Methods Human endothelial and aortic smooth muscle cells were exposed either to A) normoxia (21% O2) for three weeks, or to B) mild decreased oxygen (15% O2) for three weeks to mimic blood oxygen levels in patients with heart failure, or to C) mild decreased oxygen for two weeks followed by one week of normoxia ("memory" treatment). Levels of HIF signaling genes (HIF-1α, HIF-2α, VEGF, BNIP3, GLUT-1, PAI-1 and iNOS) were measured both at the protein and mRNA levels. Results It was found that chronic exposure to mild decreased oxygen resulted in significantly increased HIF signaling. There was also a "memory" of HIF-1α and HIF target gene induction when oxygen levels were normalized for one week, and this "memory" could be interrupted by adding a small molecule HIF inhibitor to the last week of normalized oxygen. Finally, levels of ubiquitylated HIF-1α were reduced in response to chronic mild decreased oxygen and were not full restored after oxygen normalization. Conclusion These data suggest that HIF signaling may be contributing to the pathogenesis of endothelial dysfunction and that normalization of oxygen levels may not be enough to reduce vascular stress

Achlioptas processes are not always self-averaging

We consider a class of percolation models, called Achlioptas processes, discussed in [Science 323, 1453 (2009)] and [Science 333, 322 (2011)]. For these the evolution of the order parameter (the rescaled size of the largest connected component) has been the main focus of research in recent years. We show that, in striking contrast to `classical' models, self-averaging is not a universal feature of these new percolation models: there are natural Achlioptas processes whose order parameter has random fluctuations that do not disappear in the thermodynamic limit.Comment: 4 pages, 3 figures. Revised and expanded. Title change

Going Beyond Promoting: Preparing Students to Creatively Solve Future Problems

While we cannot know what problems the future will bring, we can be almost certain that solving them will require creativity. In this article we describe how our course, a first-year undergraduate mathematics course, supports creative problem solving. Creative problem solving cannot be learned through a single experience, so we provide our students with a blend of experiences. We discuss how the course structure enables creative problem solving through class instruction, during class activities, during out of class assessments, and during in class assessments. We believe this course structure increases student comfort with solving open-ended and ill-defined problems similar to what they will encounter in the real world

Co-expression of CD56 and CD30 in lymphomas with primary presentation in the skin: clinicopathologic, immunohistochemical and molecular analyses of seven cases

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74772/1/j.1600-0560.2000.027008392.x.pd

A five-year observance of changes in the cardiovascular risk profile in 505 HIV-positive individuals

Purpose: Since the introduction of antiretroviral therapy (ART) and the extension of life expectancy, HIV-infected persons have shown an increasing number of cardiovascular events. The reduction of cardiovascular risk factors becomes a new challenge in HIV care. One of the main objectives of the HIV&HEART study is to examine the development of cardiovascular risk factors and treatment of cardiovascular diseases. Methods: This study is an on-going, prospective, regional multicentre trial that was conducted to analyse the frequency and clinical course of cardiac disorders as well as cardiovascular risk factors in HIV-infected patients. 505 HIV-infected outpatients were recruited at baseline (BL) and re-examined during 5-year follow up (5YFU). Results: 84% of 505 eligible HIV-infected patients were male. The average age was 44.3±9.5 years at BL. The proportion of ART-treated patients increased from 85.7% at BL to 96.4% at 5YFU. During the 5-year observation period mean cardiovascular risk detected by Framingham score increased from 6% at BL to 10% at 5YFU. Even after adjusting for age there was a difference in the Framingham score of 2%. Between BL and 5YFU systolic blood pressure increased from 128.4±19.8 mmHg to 138.3±19.9 mmHg in spite of an intensified use of antihypertensive drugs, from 11.9% at BL to 24.0% at 5YFU. The rate of participants with adiposity, characterised by a BMI>30, increased from 7.9% at BL to 11.2% at 5YFU. Lipid-lowering therapy was applied in 10.3% of the patients at BL and in 13.9% at 5YFU. Triglycerides (TAG)≥200 mg/dl reduced from 38.9% at BL to 36.8% at 5YFU; in contrast cholesterol values≥200 mg/dl elevated from 57.8% to 61.8%. The same trend was observed in HDL≤40 mg/dl. Here we found a change from 29.2% versus 31.3%. Doing regular sports elevated from 1.9% to 3.3%. The count of smokers increased for 2.8% and also mean pack-years changes from 24 to 26.5 pack-years. Conclusion: During a 5-year period the cardiovascular risk in Framingham score increased disproportionately high in this HIV-infected cohort even after adjusting for age. There was an increasing blood pressure although an elevated use of antihypertensive therapy. There was also a tendency of elevating BMI and an increasing trend in smoking behavior. As protective facts, we found a tendency in doing sports and a decreasing TAG value during intensifying lipid-lowering therapy. Cardiovascular risk was increasing, in spite of interventions

Pathways Regulating Spheroid Formation of Human Follicular Thyroid Cancer Cells under Simulated Microgravity Conditions: A Genetic Approach

Microgravity induces three-dimensional (3D) growth in numerous cell types. Despite substantial efforts to clarify the underlying mechanisms for spheroid formation, the precise molecular pathways are still not known. The principal aim of this paper is to compare static 1g-control cells with spheroid forming (MCS) and spheroid non-forming (AD) thyroid cancer cells cultured in the same flask under simulated microgravity conditions. We investigated the morphology and gene expression patterns in human follicular thyroid cancer cells (UCLA RO82-W-1 cell line) after a 24 h-exposure on the Random Positioning Machine (RPM) and focused on 3D growth signaling processes. After 24 h, spheroid formation was observed in RPM-cultures together with alterations in the F-actin cytoskeleton. qPCR indicated more changes in gene expression in MCS than in AD cells. Of the 24 genes analyzed VEGFA, VEGFD, MSN, and MMP3 were upregulated in MCS compared to 1g-controls, whereas ACTB, ACTA2, KRT8, TUBB, EZR, RDX, PRKCA, CAV1, MMP9, PAI1, CTGF, MCP1 were downregulated. A pathway analysis revealed that the upregulated genes code for proteins, which promote 3D growth (angiogenesis) and prevent excessive accumulation of extracellular proteins, while genes coding for structural proteins are downregulated. Pathways regulating the strength/rigidity of cytoskeletal proteins, the amount of extracellular proteins, and 3D growth may be involved in MCS formation

Genetic and metabolic predictors of chemosensitivity in oligodendroglial neoplasms

The −1p/−19q genotype predicts chemosensitivity in oligodendroglial neoplasms, but some with intact 1p/19q also respond and not all with 1p/19q loss derive durable benefit from chemotherapy. We have evaluated the predictive and prognostic significance of pretherapy 201Tl and 18F-FDG SPECT and genotype in 38 primary and 10 recurrent oligodendroglial neoplasms following PCV chemotherapy. 1p/19q loss was seen in 8/15 OII, 6/15 OAII, 7/7 OIII, 3/11 OAIII and was associated with response (Fisher-Exact: P=0.000) and prolonged progression-free (log-rank: P=0.002) and overall survival (OS) (log-rank: P=0.0048). Response was unrelated to metabolism, with tumours with high or low metabolism showing response. Increased 18F-FDG or 201Tl uptake predicted shorter progression-free survival (PFS) in the series (log-rank: 201Tl P=0.0097, 18F-FDG P=0.0170) and in cases with or without the −1p/−19q genotype. Elevated metabolism was associated with shorter OS in cases with intact 1p/19q (log-rank: 18F-FDG P=0.0077; 201Tl P=0.0004) and shorter PFS in responders (log-rank: 18F-FDG P=0.005; 201Tl P=0.0132). 201Tl uptake and 1p/19q loss were independent predictors of survival in multivariate analysis. In this initial study, 201Tl and 18F-FDG uptake did not predict response to PCV, but may be associated with poor survival following therapy irrespective of genotype. This may be clinically useful warranting further study

Acute Disseminated Encephalomyelitis with Seizures and Myocarditis: A Fatal Triad.

Autoimmune pathology of acute disseminated encephalomyelitis (ADEM) is generally restricted to the brain. Our objective is to expand the phenotype of ADEM. A four-year-old girl was admitted to the pediatric emergency room of a university medical center five days after a common upper respiratory tract infection. Acute symptoms were fever, leg pain, and headaches. She developed meningeal signs, and her level of consciousness dropped rapidly. Epileptic seizure activity started, and she became comatose, requiring intubation and mechanical ventilation. Serial brain magnetic resonance imaging (MRI) illustrated the fulminant development of ADEM. Treatment escalation with high-dose corticosteroids, immunoglobulins, and plasma exchange did not lead to clinical improvement. On day ten, the patient developed treatment-refractory cardiogenic shock and passed away. The postmortem assessment confirmed ADEM and revealed acute lymphocytic myocarditis, likely explaining the acute cardiac failure. Human metapneumovirus and picornavirus were detected in the tracheal secrete by PCR. Data sources-medical chart of the patient. This case is consistent with evidence from experimental findings of an association of ADEM with myocarditis as a postinfectious systemic autoimmune response, with life-threatening involvement of the brain and heart