Extensions of D-optimal Minimal Designs for Symmetric Mixture Models.

The purpose of mixture experiments is to explore the optimum blends of mixture components, which will provide desirable response characteristics in finished products. D-optimal minimal designs have been considered for a variety of mixture models, including Scheffé\u27s linear, quadratic, and cubic models. Usually, these D-optimal designs are minimally supported since they have just as many design points as the number of parameters. Thus, they lack the degrees of freedom to perform the Lack of Fit tests. Also, the majority of the design points in D-optimal minimal designs are on the boundary: vertices, edges, or faces of the design simplex. IN THIS PAPER EXTENSIONS OF THE D-OPTIMAL MINIMAL DESIGNS ARE DEVELOPED FOR A GENERAL MIXTURE MODEL TO ALLOW ADDITIONAL INTERIOR POINTS IN THE DESIGN SPACE TO ENABLE PREDICTION OF THE ENTIRE RESPONSE SURFACE: Also a new strategy for adding multiple interior points for symmetric mixture models is proposed. We compare the proposed designs with Cornell (1986) two ten-point designs for the Lack of Fit test by simulations

Statistics of Tumor Micro-environment

Introduction: Immune cells play a prominent role in keeping tumors suppressed, but how the distribution of these immune cells within a tumor’s microenvironment remains poorly understood. The long-term goal of this project is to study how statistical spatial distributions of different immune cells is associated with clinical outcome. The first objective is developing an algorithm for identifying different types of immune cells. Methods: The data motivating this project includes spatial localization information (x-y coordinates) and expression levels of immune cell CD markers quantified by immunofluorescence immunohistochemistry (IF-IHC) in ~1,500 cases of invasive breast cancer. Using expression levels of CD markers in cancer cells (viewed as background noise), we compute upper nonparametric tolerance limits for CD expression in cancer cells. The stroma cells with CD expression above this tolerance limit are considered to be immune cells of the corresponding CD marker type. Results: We have developed a Python program allowing us to quickly process a dataset of x-y coordinates of various cells that took up IHC stain, and creates a dataset of coordinates that are true immune cells. We have additionally analyzed multiple parameters for the development of a tolerance interval and concluded that a combination of 95%-confidence 99%-content allows for a minuscule chance of including the stroma cells that are not immune while maintaining enough data for analysis. Exploratory analysis of spatial point patterns of identified immune cell populations and their association with progression-free survival is in progress. Discussion: We have developed an algorithm for the identification of different types of immune cells associated with type-specific CD markers quantified using IF-IHC. These tools enable further studies of spatial arrangement of immune cells in the tumor tissue and relating them to clinical outcome

Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types.

Isoforms of human miRNAs (isomiRs) are constitutively expressed with tissue- and disease-subtype-dependencies. We studied 10 271 tumor datasets from The Cancer Genome Atlas (TCGA) to evaluate whether isomiRs can distinguish amongst 32 TCGA cancers. Unlike previous approaches, we built a classifier that relied solely on \u27binarized\u27 isomiR profiles: each isomiR is simply labeled as \u27present\u27 or \u27absent\u27. The resulting classifier successfully labeled tumor datasets with an average sensitivity of 90% and a false discovery rate (FDR) of 3%, surpassing the performance of expression-based classification. The classifier maintained its power even after a 15× reduction in the number of isomiRs that were used for training. Notably, the classifier could correctly predict the cancer type in non-TCGA datasets from diverse platforms. Our analysis revealed that the most discriminatory isomiRs happen to also be differentially expressed between normal tissue and cancer. Even so, we find that these highly discriminating isomiRs have not been attracting the most research attention in the literature. Given their ability to successfully classify datasets from 32 cancers, isomiRs and our resulting \u27Pan-cancer Atlas\u27 of isomiR expression could serve as a suitable framework to explore novel cancer biomarkers

Pathologic evaluation of tumor-associated macrophage density and vessel inflammation in invasive breast carcinomas

Tumor-associated macrophages (TAMs) are major constituents of the tumor microenvironment in solid tumors and have been implicated as mediators of tumor progression, invasion and metastasis. Correspondingly, accumulation of TAMs is associated with unfavorable clinical outcomes in numerous types of solid tumors. E-selectin is a hallmark of inflammation and a key adhesion molecule that accommodates the initial contact of circulating immune cells with the inflamed vessel surface. Currently, the association between E-selectin and TAMs is not fully elucidated; therefore, the present study investigated the association between vessel inflammation, TAM infiltration, and clinical outcome in breast cancer. A total of 53 procedure-naïve invasive breast cancer cases were immunohistochemically analyzed for the presence of cluster of differentiation (CD)68+ TAMs, E-selectin+ vessels and tumor inflammation. The association between CD68 and E-selectin expression, and tumor inflammation as well as overall survival was evaluated using Kaplan-Meier survival curves and multivariable Cox\u27s proportional hazards regression analysis. The abundance of TAMs was identified to be positively associated with tumor inflammation, estrogen receptor and E-selectin expression levels. A greater prevalence of TAMs and tumor inflammation was significantly associated with shorter overall survival times. E-selectin expression levels were significantly higher in tumor vessels among elderly patients, but were not associated with overall survival. The abundance of TAMs was associated with the presence of E-selectin-expressing inflamed tumor vessels and tumor inflammation, as well as overall survival in patients with invasive breast carcinoma. © 2017, Spandidos Publications. All rights reserved

Long-term effect of antiepileptic drug switch on serum lipids and C-reactive protein.

BACKGROUND: Prior studies have shown that switching patients from inducing antiepileptic drugs (AEDs) to lamotrigine, levetiracetam, or topiramate reduces serum lipids and C-reactive protein (CRP). These studies were all of short duration, and some drugs, such as zonisamide, have not been investigated. METHODS: We recruited 41 patients taking phenytoin or carbamazepine who were being switched to zonisamide, lamotrigine, or levetiracetam. We measured serum lipids and CRP before the switch, \u3e6weeks after, and \u3e6months after. An untreated control group (n=14) underwent similar measurement. We combined these data with those of our previous investigation (n=34 patients and 16 controls) of a very similar design. RESULTS: There were no differences in outcome measures between the two inducing AEDs nor among the three noninducing AEDs. Total cholesterol (TC), atherogenic lipids, and CRP were higher under inducer treatment than in controls. All measures were elevated under inducer treatment relative to noninducer treatment, including TC (24mg/dL higher, 95% CI: 17.5-29.9, p CONCLUSIONS: We demonstrate that switching from inducing to noninducing AEDs produces an enduring reduction in serum lipids and CRP. These results provide further evidence that inducing AEDs may be associated with elevated vascular disease risk. These are the first vascular risk marker data in patients taking zonisamide, which shows a profile similar to that of other noninducing AEDs

Drug Interaction Study Of Apixaban With Cyclosporine Or Tacrolimus: Results From A Phase 1, Randomized, Open-Label, Crossover Study In Healthy Volunteers

BACKGROUND Solid organ transplant recipients commonly require anticoagulation. Apixaban (APX) is principally metabolized by CYP3A4, undergoes direct intestinal excretion, and is a substrate to P-glycoprotein (P-gp) and Breast Cancer Resistance Protein (BCRP) transporters. We examined the potential drug interaction between cyclosporine (CsA) and tacrolimus (Tac) [combined inhibitors of CYP3A4, P-gp and, BCRP] with APX.https://jdc.jefferson.edu/petposters/1005/thumbnail.jp

Tumor Epithelial Cell Matrix Metalloproteinase 9 (MMP-9) is a Prognostic Marker in Colorectal Cancer

Presented at American Association Cancer Research in 2008 Zuzga D.S., Gibbons A.V., Li P., Lubbe W.J., Chervoneva I., Pitari G.M. “Tumor epithelial cell MMP-9 is a prognostic marker in colorectal cancer”. In: American Association for Cancer Research Special Conference, Molecular Diagnostics in Cancer Therapeutic Development: Proceedings; 2008 Sept 22-25; Philadelphia, PA. Abstract A40. Colorectal cancer is the second leading cause of cancer-related mortality indeveloped nations. Mortality from colon cancer largely reflects metastasis, thespread of the disease to distant sites. Early diagnosis of pre-metastatic diseaseand accurate stratification of patients with metastasis is pivotal to decreasemortality rates from colon cancer by effectively administering surgery alone orwith chemotherapy. However, specific pathological markers of colorectal cancermetastasis have not emerged. Matrix metalloproteinase 9 (MMP-9) is a keyregulator of metastasis and a therapeutic target in colon cancer. Here, MMP-9overexpression in pure tumor epithelial, but nor stromal, cell populations frompatients was associated with metastatic colorectal cancer progression as definedby RT-PCR and confirmed by immunostaining. Thus, tumors with increasedMMP-9 expression compared to matched normal adjacent tissues alwaysexhibited metastatic dissemination. In particular, MMP-9 overexpression in tumorepithelial cells, compared to normal epithelial cells, specifically predicted lymphnode involvement. Importantly, patients with relative increase of MMP-9 levels intumor epithelial cells were characterized by more advanced disease stages, withsignificantly higher proportion of regional lymph nodes harboring metastasis,compared to patients with a relative decrease in MMP-9 expression. Together,these observations suggest tumor epithelial cell MMP-9 is a novel prognosticmarker that may be exploited for more efficient disease stage stratification andtherapeutic regimen selection in patients with colorectal cancer

Reversibility of Apixaban Anticoagulation with a Four-Factor Prothrombin Complex Concentrate in Healthy Volunteers.

It was hypothesized that the four-factor prothrombin complex concentrate (4F-PCC) Kcentra 25 unit/kg would reverse impairment of thrombin generation in healthy volunteers dosed with apixaban to steady state. In this randomized, two-period crossover, assessor-blinded trial, 12 healthy subjects received 5 mg apixaban every 12 h. Three h after the fifth dose, four-factor prothrombin complex concentrate (4F-PCC) 25 unit/kg or saline were infused. Serial blood samples were assessed for thrombin generation using PPP-reagent and PPP-reagent low, anti-Xa, PT, and PTT assays. Geometric mean ratio was calculated at 30 min postinfusion, and at 24, 48, and 72 h. Peak thrombin generation was 76% higher at 30 min postinfusion with 4F-PCC (p = 0.025). The difference declined to 24% at 24 h and resolved by 48 h. Other thrombin generation parameters were also partially normalized. There was no difference between 4F-PCC and saline in anti-Xa assessment at 30 min or later time points

Bimodal coupling of ripples and slower oscillations during sleep in patients with focal epilepsy.

OBJECTIVE: Differentiating pathologic and physiologic high-frequency oscillations (HFOs) is challenging. In patients with focal epilepsy, HFOs occur during the transitional periods between the up and down state of slow waves. The preferred phase angles of this form of phase-event amplitude coupling are bimodally distributed, and the ripples (80-150 Hz) that occur during the up-down transition more often occur in the seizure-onset zone (SOZ). We investigated if bimodal ripple coupling was also evident for faster sleep oscillations, and could identify the SOZ. METHODS: Using an automated ripple detector, we identified ripple events in 40-60 min intracranial electroencephalography (iEEG) recordings from 23 patients with medically refractory mesial temporal lobe or neocortical epilepsy. The detector quantified epochs of sleep oscillations and computed instantaneous phase. We utilized a ripple phasor transform, ripple-triggered averaging, and circular statistics to investigate phase event-amplitude coupling. RESULTS: We found that at some individual recording sites, ripple event amplitude was coupled with the sleep oscillatory phase and the preferred phase angles exhibited two distinct clusters (p \u3c 0.05). The distribution of the pooled mean preferred phase angle, defined by combining the means from each cluster at each individual recording site, also exhibited two distinct clusters (p \u3c 0.05). Based on the range of preferred phase angles defined by these two clusters, we partitioned each ripple event at each recording site into two groups: depth iEEG peak-trough and trough-peak. The mean ripple rates of the two groups in the SOZ and non-SOZ (NSOZ) were compared. We found that in the frontal (spindle, p = 0.009; theta, p = 0.006, slow, p = 0.004) and parietal lobe (theta, p = 0.007, delta, p = 0.002, slow, p = 0.001) the SOZ incidence rate for the ripples occurring during the trough-peak transition was significantly increased. SIGNIFICANCE: Phase-event amplitude coupling between ripples and sleep oscillations may be useful to distinguish pathologic and physiologic events in patients with frontal and parietal SOZ