Physical Sciences and Mathematics Commons^™

On Dual Toric Complete Intersection Codes, Pinar Celebi Demiraslan, Ivan Soprunov

Mathematics and Statistics Faculty Publications

In this paper we study duality for evaluation codes on intersections of ℓ hypersurfaces with given ℓ-dimensional Newton polytopes, so called toric complete intersection codes. In particular, we give a condition for such a code to be quasi-self-dual. In the case of it reduces to a combinatorial condition on the Newton polygons. This allows us to give an explicit construction of dual and quasi-self-dual toric complete intersection codes. We provide a list of examples over and an algorithm for producing them.

Linear Operators That Preserve Graphical Properties Of Matrices: Isolation Numbers, Leroy B. Beasley, Seok-Zun Song, Young Bae Jun

Mathematics and Statistics Faculty Publications

Let A be a Boolean {0, 1} matrix. The isolation number of A is the maximum number of ones in A such that no two are in any row or any column (that is they are independent), and no two are in a 2 × 2 submatrix of all ones. The isolation number of A is a lower bound on the Boolean rank of A. A linear operator on the set of m × n Boolean matrices is a mapping which is additive and maps the zero matrix, O, to itself. A mapping strongly preserves a set, S, if it …

Prognostic Value Of Elevated Serum Ceruloplasmin Levels In Patients With Heart Failure, Muhammad Hammadah, Yiying Fan, Yuping Wu, Stanley L. Hazen, W.H. Wilson Tang

Mathematics and Statistics Faculty Publications

Background: Ceruloplasmin (Cp) is a copper-binding acute-phase protein that is increased in inflammatory states and deficient in Wilson's disease. Recent studies demonstrate that increased levels of Cp are associated with increased risk of developing heart failure. Our objective was to test the hypothesis that serum Cp provides incremental and independent prediction of survival in stable patients with heart failure. Methods and Results: We measured serum Cp levels in 890 patients with stable heart failure undergoing elective cardiac evaluation that included coronary angiography. We examined the role of Cp levels in predicting survival over 5 years of follow-up. Mean Cp level …

Γ-Butyrobetaine Is A Proatherogenic Intermediate In Gut Microbial Metabolism Of L-Carnitine To Tmao, Robert A. Koeth, Bruce S. Levison, Miranda K. Culley, Jennifer A. Buffa, Zeneng Wang, Jill C. Gregory, Elin Org, Yuping Wu, Lin Li, Jonathan D. Smith, W.H. Wilson Tang, Joseph A. Didonato, Aldons J. Lusis, Stanley L. Hazen

Mathematics and Statistics Faculty Publications

L-carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein, we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ∼1,000-fold higher than the formation of TMA. Moreover, we show that γBB is the major gut microbial metabolite formed from dietary L-carnitine in mice, is converted into TMA and TMAO in a gut microbiota-dependent manner (like dietary L-carnitine), and accelerates atherosclerosis. Gut microbial …

Prognostic Value Of Elevated Levels Of Intestinal Microbe-Generated Metabolite Trimethylamine-N-Oxide In Patients With Heart Failure: Refining The Gut Hypothesis, W.H. Wilson Tang, Zeneng Wang, Yiying Fan, Bruce Levison, Jennie E. Hazen, Lillian M. Donahue, Yuping Wu, Stanley L. Hazen

Mathematics and Statistics Faculty Publications

Background: Altered intestinal function is prevalent in patients with heart failure (HF), but its role in adverse outcomes is unclear. Objectives: This study investigated the potential pathophysiological contributions of intestinal microbiota in HF. Methods: We examined the relationship between fasting plasma trimethylamine-N-oxide (TMAO) and all-cause mortality over a 5-year follow-up in 720 patients with stable HF. Results:The median TMAO level was 5.0 μM, which was higher than in subjects without HF (3.5 μM; p < 0.001). There was modest but significant correlation between TMAO concentrations and B-type natriuretic peptide (BNP) levels (r = 0.23; p < 0.001). Higher plasma TMAO levels were associated with a 3.4-fold increased mortality risk. Following adjustments for traditional risk factors and BNP levels, elevated TMAO levels remained predictive of 5-year mortality risk (hazard ratio [HR]: 2.2; 95% CI: 1.42 to 3.43; p < 0.001), as well as following the addition of estimated glomerular filtration rate to the model (HR: 1.75; 95% CI: 1.07 to 2.86; p < 0.001). Conclusions: High TMAO levels were observed in patients with HF, and elevated TMAO levels portended higher long-term mortality risk independent of traditional risk factors and cardiorenal indexes.

Prognostic Value Of Estimated Functional Capacity Incremental To Cardiac Biomarkers In Stable Cardiac Patients, W.H. Wilson Tang, Eric J. Topol, Yiying Fan, Yuping Wu, Leslie Cho, Cindy Stevenson, Stephen G. Ellis, Stanley L. Hazen

Mathematics and Statistics Faculty Publications

Background: Few studies have investigated functional capacity self-assessment tools in either prediction of future major adverse cardiac outcomes beyond all-cause mortality or direct comparisons with clinically available biomarkers. Methods and Results: We estimated functional capacity using the Duke Activity Status Index (DASI) questionnaire in 8987 sequential stable patients without acute coronary syndrome who were undergoing elective diagnostic coronary angiography with 3-year follow-up of major adverse cardiac events (death, nonfatal myocardial infarction, or stroke). A low DASI score provided independent prediction of a 4.8-fold increase in future risk of incident major adverse cardiac events at 3 years (quartiles 1 versus 4 …

On The Structure Of Co-Kähler Manifolds, Giovanni Bazzoni, John Oprea

Mathematics and Statistics Faculty Publications

By the work of Li, a compact co-Kähler manifold M is a mapping torus Kφ, where K is a Kähler manifold and φ is a Hermitian isometry. We show here that there is always a finite cyclic cover M¯¯¯¯¯ of the form M¯¯¯¯¯≅K×S1, where ≅ is equivariant diffeomorphism with respect to an action of S1 on M and the action of S1 on K×S1 by translation on the second factor. Furthermore, the covering transformations act diagonally on S1,K and are translations on the S1 factor. In this way, we see that, up to a finite cover, all compact co-Kähler manifolds …

Diagnosis Of Infection After Splenectomy For Trauma Should Be Based On Lack Of Platelets Rather Than White Blood Cell Count, Aman Banerjee, Katherine B. Kelly, Hannah Y. Zhou, Shanteria D. Dixon, Ariadni Papana Dagiasis, Linda M. Quinn, Jeffrey A. Claridge

Mathematics and Statistics Faculty Publications

Background: There is a lack of evidence-based criteria to assist the diagnosis of infection following trauma splenectomy (TS). However, the literature suggests that white blood cell count (WBC) is associated with infection in patients who undergo TS. We sought to find whether there exist key differences in laboratory and clinical parameters that can assist the diagnosis of infection after TS. Methods: We evaluated all consecutive trauma patients who had undergone TS at a Level 1 trauma center from 2005 to 2011 for the development of infection. To do this, we compared the values of demographic, laboratory, and clinical variables of …

Synergistic Effects Of 3d Ecm And Chemogradients On Neurite Outgrowth And Guidance: A Simple Modeling And Microfluidic Framework, Parthasarathy Srinivasan, Ioannis K. Zervantonakis, Chandrasekhar R. Kothapalli

Mathematics and Statistics Faculty Publications

During nervous system development, numerous cues within the extracellular matrix microenvironment (ECM) guide the growing neurites along specific pathways to reach their intended targets. Neurite motility is controlled by extracellular signal sensing through the growth cone at the neurite tip, including chemoattractive and repulsive cues. However, it is difficult to regenerate and restore neurite tracts, lost or degraded due to an injury or disease, in the adult central nervous system. Thus, it is important to evaluate the dynamic interplay between ECM and the concentration gradients of these cues, which would elicit robust neuritogenesis. Such information is critical in understanding the …

Prognostic Value Of Choline And Betaine Depends On Intestinal Microbiota-Generated Metabolite Trimethylamine-N-Oxide, Zeneng Wang, W.H. Wilson Tang, Jennifer A. Buffa, Xiaoming Fu, Earl B. Britt, Robert A. Koeth, Bruce S. Levison, Yiying Fan, Yuping Wu, Stanley L. Hazen

Mathematics and Statistics Faculty Publications

Aims: Recent metabolomics and animal model studies show trimethylamine-N-oxide (TMAO), an intestinal microbiota-dependent metabolite formed from dietary trimethylamine-containing nutrients such as phosphatidylcholine (PC), choline, and carnitine, is linked to coronary artery disease pathogenesis. Our aim was to examine the prognostic value of systemic choline and betaine levels in stable cardiac patients. Methods and Results: We examined the relationship between fasting plasma choline and betaine levels and risk of major adverse cardiac events (MACE = death, myocardial infraction, stroke) in relation to TMAO over 3 years of follow-up in 3903 sequential stable subjects undergoing elective diagnostic coronary angiography. In our study …

Plasma Ceruloplasmin, A Regulator Of Nitric Oxide Activity, And Incident Cardiovascular Risk In Patients With Ckd, David J. Kennedy, Yiying Fan, Yuping Wu, Michael Pepoy, Stanley L. Hazen, W.H. Wilson Tang

Mathematics and Statistics Faculty Publications

Background and objectives: Increased serum levels of the acute-phase reactant ceruloplasmin predict adverse clinical outcomes in the setting of acute coronary syndromes and heart failure, but their role in patients with CKD is unclear. This study investigated the relationship of ceruloplasmin with clinical outcomes in CKD, especially with regard to traditional cardiac biomarkers. Design, setting, participants, & measurements: Serum ceruloplasmin levels in consecutive study participants with CKD (n=654; estimated GFR<60 ml/min per 1.73 m2) as well as a control group of non-CKD participants matched for age and sex (n=250) were measured. Study participants were enrolled during 2001–2006 from a population of patients presenting for elective diagnostic coronary angiography and prospectively followed for 3 years (median follow-up=1095 days) to determine incident major adverse cardiac events (defined as a composite of death, nonfatal myocardial infarction, and stroke). Results: Serum ceruloplasmin levels in CKD patients were elevated versus controls (median [interquartile range]; 25.5 [21.8–29.6] versus 22.7 [19.7–26.5] mg/dl; P<0.001) and associated with increased risk of future major adverse cardiac events (hazard ratio, 1.35; 95% confidence interval, 1.0 to 1.82; P=0.04). After adjusting for traditional risk factors, higher serum ceruloplasmin was still associated with higher risk of major adverse cardiac events at 3 years (hazard ratio, 1.61; 95% confidence interval, 1.15 to 2.25; P=0.01). Conclusion: In CKD patients, increased serum ceruloplasmin, a regulator of nitric oxide activity, is associated with increased risk of long-term adverse cardiovascular events, even after multivariable model adjustment for traditional clinical and biologic risk factors.

A Compartmentalized Mathematical Model Of The B1-Adrenergic Signaling System In Mouse Ventricular Myocytes, Vladimir E. Bondarenko

Mathematics and Statistics Faculty Publications

The b1-adrenergic signaling system plays an important role in the functioning of cardiac cells. Experimental data shows that the activation of this system produces inotropy, lusitropy, and chronotropy in the heart, such as increased magnitude and relaxation rates of [Ca2+]i transients and contraction force, and increased heart rhythm. However, excessive stimulation of b1-adrenergic receptors leads to heart dysfunction and heart failure. In this paper, a comprehensive, experimentally based mathematical model of the b1-adrenergic signaling system for mouse ventricular myocytes is developed, which includes major subcellular functional compartments (caveolae, extracaveolae, and cytosol). The model describes biochemical reactions that occur during stimulation …

An Abundant Dysfunctional Apolipoprotein A1 In Human Atheroma, Ying Huang, Joseph A. Didonato, Bruce S. Levison, Dave Schmitt, Lin Li, Yuping Wu, Jennifer Buffa, Timothy Kim, Gary S. Gerstenecker, Xiaodong Gu, Chandra S. Kadiyala, Zeneng Wang, Miranda K. Culley, Jennie E. Hazen, Anthony J. Didonato, Xiaoming Fu, Stela Z. Berisha, Daoquan Peng, Truc T. Nguyen, Shaohong Liang, Chia-Chi Chuang, Leslie Cho, Edward F. Plow, Paul L. Fox, Valentin Gogonea, W.H. Wilson Tang, John S. Parks, Edward A. Fisher, Jonathan D. Smith, Stanley L. Hazen

Mathematics and Statistics Faculty Publications

Recent studies have indicated that high-density lipoproteins (HDLs) and their major structural protein, apolipoprotein A1 (apoA1), recovered from human atheroma are dysfunctional and are extensively oxidized by myeloperoxidase (MPO). In vitro oxidation of either apoA1 or HDL particles by MPO impairs their cholesterol acceptor function. Here, using phage display affinity maturation, we developed a high-affinity monoclonal antibody that specifically recognizes both apoA1 and HDL that have been modified by the MPO-H2O2-Cl− system. An oxindolyl alanine (2-OH-Trp) moiety at Trp72 of apoA1 is the immunogenic epitope. Mutagenesis studies confirmed a critical role for apoA1 Trp72 in MPO-mediated inhibition of the ATP-binding …

Multi-Peak Solutions To Two Types Of Free Boundary Problems, Yi Li, Shuangjie Peng

Mathematics and Statistics Faculty Publications

We consider the existence of multi-peak solutions to two types of free boundary problems arising in confined plasma and steady vortex pair under conditions on the nonlinearity we believe to be almost optimal. Our results show that the “core” of the solution has multiple connected components, whose boundary called free boundary of the problems consists approximately of spheres which shrink to distinct single points as the parameter tends to zero.

Stability Of Traveling-Wave Solutions For A Schrodinger System With Power-Type Nonlinearities, Nghiem Nguyen, Rushun Tian, Zhi-Qiang Wang

Mathematics and Statistics Faculty Publications

In this article, we consider the Schrodinger system with powertype nonlinearities, (Formula presented) where j = 1,...,m, u_j are complex-valued functions of (x, t) 2 R^N+1, a, b are real numbers. It is shown that when b > 0, and a + (m - 1)b > 0, for a certain range of p, traveling-wave solutions of this system exist, and are orbitally stable.

A Shortcut For Multiple Testing On The Directed Acyclic Graph Of Gene Ontology, Garrett Saunders, John R. Stevens, S. Clay Isom

Mathematics and Statistics Faculty Publications

Background: Gene set testing has become an important analysis technique in high throughput microarray and next generation sequencing studies for uncovering patterns of differential expression of various biological processes. Often, the large number of gene sets that are tested simultaneously require some sort of multiplicity correction to account for the multiplicity effect. This work provides a substantial computational improvement to an existing familywise error rate controlling multiplicity approach (the Focus Level method) for gene set testing in high throughput microarray and next generation sequencing studies using Gene Ontology graphs, which we call the Short Focus Level.

Results: The Short Focus …

Statistical Genetics And Its Applications In Medical Studies, Ao Yuan, Wenqing He, Gengsheng Qin, Qizhai Li

Mathematics and Statistics Faculty Publications

No abstract provided.

On Coalescence Analysis Using Genealogy Rooted Trees, Ao Yuan, Gengsheng Qin, Wenqing He, Qizhai Li

Mathematics and Statistics Faculty Publications

No abstract provided.

3d Collagen Alignment Limits Protrusions To Enhance Breast Cancer Cell Persistence, Kristin M. Riching, Benjamin L. Cox, Max R. Salick, Carolyn Pehleke, Andrew S. Riching, Susan M. Ponik, Benjamin R. Bass, Wendy C. Crone, Yi Jiang, Alissa M. Weaver, Kevin W. Eliceiri, Patricia J. Keely

Mathematics and Statistics Faculty Publications

Patients with mammographically dense breast tissue have a greatly increased risk of developing breast cancer. Dense breast tissue contains more stromal collagen, which contributes to increased matrix stiffness and alters normal cellular responses. Stromal collagen within and surrounding mammary tumors is frequently aligned and reoriented perpendicular to the tumor boundary. We have shown that aligned collagen predicts poor outcome in breast cancer patients, and postulate this is because it facilitates invasion by providing tracks on which cells migrate out of the tumor. However, the mechanisms by which alignment may promote migration are not understood. Here, we investigated the contribution of …

Brain Control Of Functional Reach In Healthy Adults And Stroke Survivors, Janis J. Daly, Ken Hrovat, John Holcomb, Svetlana Pundik

Mathematics and Statistics Faculty Publications

Purpose: Recovery of the most basic shoulder-flexion/elbow-extension components of functional reach is critical for effective arm function following stroke. In order to understand the mechanisms of motor recovery, it is important to characterize the pattern of brain activation during the reach task. Methods: We evaluated 11 controls and 23 moderately to severely impaired chronic stroke survivors (>6 months), with impaired shoulder flexion and elbow extension. Measures were acquired for Arm Motor Ability Test (AMAT) and functional Magnetic Resonance Imaging (fMRI) during the basic shoulder/elbow reach. Results: First, in controls, lateralization of fMRI signal during the reach task was less …