A Family of Quasisymmetry Models

We present a one-parameter family of models for square contingency tables that interpolates between the classical quasisymmetry model and its Pearsonian analogue. Algebraically, this corresponds to deformations of toric ideals associated with graphs. Our discussion of the statistical issues centers around maximum likelihood estimation.Comment: 17 pages, 10 figure

The prognostic value of electroencephalography in epilepsy: a long-term follow-up study

Predicting the evolution of epilepsy is of obvious importance for patients and their families. Value of electroencephalography (EEG) is extensively used in the diagnosis of epilepsy yet its role as a prognostication method remains unclear. The aim of the present retrospective study is to investigate the relationship between serial EEG recordings and long-term clinical and social outcomes in a cohort of patients with epilepsy. Thirty-nine epileptic patients were monitored clinically and with repeat EEG recordings for more than 15 years. All patients who initially had epileptiform discharges ended up with poor or moderate seizure control whereas more than half of the patients with normal initial recordings had good clinical outcomes and satisfactory social adjustment. Deterioration of the recordings over time was associated with unfavourable results in a significant proportion of patients (90 %), while stable or improved EEG findings predicted a favourable outcome. It is concluded that serial EEG recordings can be used in the prognostic evaluation of epilepsy

Design and validation of an open-source modular Microplate Photoirradiation System for high-throughput photobiology experiments

Research in photobiology is currently limited by a lack of devices capable of delivering precise and tunable irradiation to cells in a high-throughput format. This limits researchers to using expensive commercially available or custom-built light sources which make it difficult to replicate, standardize, optimize, and scale experiments. Here we present an open-source Microplate Photoirradiation System (MPS) developed to enable high-throughput light experiments in standard 96 and 24-well microplates for a variety of applications in photobiology research. This open-source system features 96 independently controlled LEDs (4 LEDs per well in 24-well), Wi-Fi connected control and programmable graphical user interface (GUI) for control and programming, automated calibration GUI, and modular control and LED boards for maximum flexibility. A web-based GUI generates light program files containing irradiation parameters for groups of LEDs. These parameters are then uploaded wirelessly, stored and used on the MPS to run photoirradiation experiments inside any incubator. A rapid and semi-quantitative porphyrin metabolism assay was also developed to validate the system in wild-type fibroblasts. Protoporphyrin IX (PpIX) fluorescence accumulation was induced by incubation with 5-aminolevulinic acid (ALA), a photosensitization method leveraged clinically to destroy malignant cell types in a process termed photodynamic therapy (PDT), and cells were irradiated with 405nm light with varying irradiance, duration and pulsation parameters. Immediately after light treatment with the MPS, subsequent photobleaching was measured in live, adherent cells in both 96-well and a 24-well microplates using a microplate reader. Results demonstrate the utility and reliability of the Microplate Photoirradiation System to irradiate cells with precise irradiance and timing parameters in order to measure PpIx photobleaching kinetics in live adherent cells and perform comparable experiments with both 24 and 96 well microplate formats. The high-throughput capability of the MPS enabled measurement of enough irradiance conditions in a single microplate to fit PpIX fluorescence to a bioexponential decay model of photobleaching, as well as reveal a dependency of photobleaching on duty-cycle-but not frequency-in a pulsed irradiance regimen.We thank the Graduate School of Biological Sciences and the Black Family Stem Cell Institute at Icahn School of Medicine for providing financial support for the project. Chris Merck is affiliated with his own LLC (Merck Engineering LLC). Merck Engineering LLC did not contribute funding to the development of the MPS or its biological validation and has no pecuniary interest in this study. Chris Merck worked as a volunteer collaborator not representing any company or institution. Merck Engineering LLC did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific role of this author is articulated in the 'author contributions' section

Families of Generalized Quasisymmetry Models: A <i>ϕ</i>-Divergence Approach

The quasisymmetry (QS) model for square contingency tables is revisited, highlighting properties and features on the basis of its alternative definitions. More parsimonious QS-type models, such as the ordinal QS model for ordinal classification variables and models based on association models (AMs) with homogeneous row and column scores, are discussed. All these models are linked to the local odds ratios (LOR). QS-type models and AMs were extended in the literature for generalized odds ratios other than LOR. Furthermore, in an information-theoretic context, they are expressed as distance models from a parsimonious reference model (the complete symmetry for QS and the independence for AMs), while they satisfy closeness properties with respect to Kullback–Leibler (KL) divergence. Replacing the KL by ϕ divergence, flexible classes of QS-type models for LOR, AMs for LOR, and AMs for generalized odds ratios were generated. However, special QS-type models that are based on homogeneous AMs for LOR have not been extended to ϕ-divergence-based classes so far, or the QS-type models for generalized odds ratios. In this work, we develop these missing extensions, and discuss QS-type models and their generalizations in depth. These flexible families enrich the modeling options, leading to models of better fit and sound interpretation, as illustrated by representative examples

ϕ-Divergence in Contingency Table Analysis

The ϕ -divergence association models for two-way contingency tables is a family of models that includes the association and correlation models as special cases. We present this family of models, discussing its features and demonstrating the role of ϕ -divergence in building this family. The most parsimonious member of this family, the model of ϕ -scaled uniform local association, is considered in detail. It is implemented and representative examples are commented on