Digital Commons Network^™

Wavelet-Based Functional Mixed Models To Characterize Population Heterogeneity In Accelerometer Profiles: A Case Study. , Jeffrey S. Morris, Cassandra Arroyo, Brent A. Coull, Louise M. Ryan, Steven L. Gortmaker

Jeffrey S. Morris

We present a case study illustrating the challenges of analyzing accelerometer data taken from a sample of children participating in an intervention study designed to increase physical activity. An accelerometer is a small device worn on the hip that records the minute-by-minute activity levels of the child throughout the day for each day it is worn. The resulting data are irregular functions characterized by many peaks representing short bursts of intense activity. We model these data using the wavelet-based functional mixed model. This approach incorporates multiple fixed effects and random effect functions of arbitrary form, the estimates of which are …

Alternative Probeset Definitions For Combining Microarray Data Across Studies Using Different Versions Of Affymetrix Oligonucleotide Arrays, Jeffrey S. Morris, Chunlei Wu, Kevin R. Coombes, Keith A. Baggerly, Jing Wang, Li Zhang

Jeffrey S. Morris

Many published microarray studies have small to moderate sample sizes, and thus have low statistical power to detect significant relationships between gene expression levels and outcomes of interest. By pooling data across multiple studies, however, we can gain power, enabling us to detect new relationships. This type of pooling is complicated by the fact that gene expression measurements from different microarray platforms are not directly comparable. In this chapter, we discuss two methods for combining information across different versions of Affymetrix oligonucleotide arrays. Each involves a new approach for combining probes on the array into probesets. The first approach involves …

Raphidophyceae [Chadefaud Ex Silva] Systematics And Rapid Identification: Sequence Analyses And Real–Time Pcr Assays, Torstein Tengs

Dr. Torstein Tengs

Species within the class Raphidophyceae were associated with fish kill events in Japanese, European, Canadian, and U.S. coastal waters. Fish mortality was attributable to gill damage with exposure to reactive oxygen species (peroxide, superoxide, and hydroxide radicals), neurotoxins, physical clogging, and hemolytic substances. Morphological identification of these organisms in environmental water samples is difficult, particularly when fixatives are used. Because of this difficulty and the continued global emergence of these species in coastal estuarine waters, we initiated the development and validation of a suite of real-time polymerase chain reaction (PCR) assays. Sequencing was used to generate complete data sets for …

Equal Performance Of Taqman, Mgb, Molecular Beacon, And Sybr Green-Based Detection Assays In Detection And Quantification Of Roundup Ready Soybean, Torstein Tengs

Dr. Torstein Tengs

We have tested and compared the performance of 12 different assays representing four different real-time polymerase chain reaction (PCR) chemistries in the context of genetically modified organism detection. Several different molecular beacon, SYBR Green, TaqMan, and MGB assays were designed for the event specific detection and quantification of the 3' integration junction of GTS 40-3-2 (Roundup Ready) soybean. Sensitivity as well as robustness in the presence of background DNA were tested. None of the PCR-based approaches appeared to be significantly better than any of the other, but the molecular beacon assays had the lowest efficiency and also seemed more sensitive …

Prepms: Tof Ms Data Graphical Preprocessing Tool, Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida

Jeffrey S. Morris

We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings experimentally determined to work well in most situations. These values can be changed by the user if desired. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection, and visual data quality assessment.

Qim Method Scores Quality, Shelf Life Of Pangasius Fillets, Huynh Nguyen Duy Bao

Huynh Nguyen Duy Bao

A Quality Index Method developed to assess the freshness of Pangasius hypophthalmus fillets stored on ice showed a high correlation between the index score and storage time. With cross referencing of total viable microbial count and ammonia content analysis, the shelf life of iced fillets was estimated at 12 days based on evaluation of eight sensory parameters.

An Anaerobic Methane Oxidizing Community Of Anme-1b Archaea In Hypersaline Gulf Of Mexico Sediments, Karen Lloyd, Laura Lapham, Andreas Teske

Karen Lloyd

Sediments overlying a brine pool methane seep in the Gulf of Mexico (Green Canyon 205) were analyzed using molecular and geochemical approaches to identify geochemical controls on microbial community composition and stratification. 16S rRNA gene and rRNA clone libraries, as well as mcrA gene clone libraries, showed that the archaeal community consists predominantly of ANME-1b methane oxidizers; no archaea of other ANME subgroups were found with general and group-specific PCR primers. The ANME-1b community was found in the sulfate-methane interface, where undersaturated methane concentrations of ca. 100 to 250 _M coexist with sulfate concentrations around 10 mM. Clone libraries of …

). Clonal Micropropagation Of Indian Gooseberry (Emblica Officinalis Gaertn)., Rajesh Pati

Rajesh Pati

No abstract provided.

Adding Ecological Considerations To Environmental Accounting, David A. Bainbridge

David A Bainbridge

Environmental accounting has often neglected ecological costs. These are essential to complete a true cost accounting. Ecological costs are often very large and long term and if they are ignored the costs/benefits of projects are incorrectly calculated.

The Transcriptome Of Human Oocytes, Jose Cibelli, Arif Kocabas, Javier Crosby, Pablo Ross, Hasan Otu, Zeki Beyhan, Zandan Can, Wau-Leong Tam, Guilherme Rosa, Robert Halgren, Bing Lim, Emilio Fernandez

Jose Cibelli

The identification of genes and deduced pathways from the mature human oocyte can help us better understand oogenesis, folliculogenesis, fertilization, and embryonic development. Human metaphase II oocytes were used within minutes after removal from the ovary, and its transcriptome was compared with a reference sample consisting of a mixture of total RNA from 10 different normal human tissues not including the ovary. RNA amplification was performed by using a unique protocol. Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays were used for hybridizations. Compared with reference samples, there were 5,331 transcripts significantly up-regulated and 7,074 transcripts significantly down-regulated in the …

Effect Of Sugar, Pectin And Acid Balance On The Quality Characteristics Of Pineapple (Ananas Comosus) Jam., Emmanuel Ohene Afoakwa, Dorinda Nartey, Joseph Ashong, George Annor

Joseph Okai Ashong

Investigations were conducted on the effects of sugar concentration (0%, 50%, and 100%), pH balance (3.0, 3.2, and 3.5) and high methoxy pectin concentration (0%, 0.5%, and 1.0%) on the chemical, physico-chemical characteristic of pineapple jams using standard analytical methods. Inclusion of 50% sugar was observed to improve the colour of the jam as well as the texture, gel set and solid content. The low calorie jams had unacceptable texture, colour, gel set and total soluble solids content. The jams of this formulation were too soft, and could not hold their form. Addition of 100% sugar concentration did not improve …

The Elimination Of Madagascar’S Vanilla Marketing Board, Ten Years On, Laure C. Dutoit, Olivier Cadot, Jaime De Melo

Olivier Cadot

This paper explores how the elimination of Madagascar’s Vanilla Marketing Board (VMB) in 1993 affected prices paid to farmers, incentives, and regional indicators of poverty and inequality. After steadily losing market share, Madagascar has been able to regain some of the lost ground since the mid-1990s. Margins between FOB and farmgate prices have narrowed down and analysis of changes in poverty and inequality suggests some positive impact in regions where vanilla is grown, though it is difficult to control for other intervening factors. A counterfactual analysis based on a model of Cournot competition between vanilla traders suggests that whatever limited …

Heterotachy Processes In Rhodophyte-Derived Secondhand Plastid Genes: Implications For Addressing The Origin And Evolution Of Dinoflagellate Plastids, Torstein Tengs

Dr. Torstein Tengs

Serial transfer of plastids from one eukaryotic host to another is the key process involved in evolution of secondhand plastids. Such transfers drastically change the environment of the plastids and hence the selection regimes, presumably leading to changes over time in the characteristics of plastid gene evolution and to misleading phylogenetic inferences. About half of the dinoflagellate protists species are photosynthetic and unique in harboring a diversity of plastids acquired from a wide range of eukaryotic algae. They are therefore ideal for studying evolutionary processes of plastids gained through secondary and tertiary endosymbioses. In the light of these processes, we …

Sensitive Mutation Detection In Heterogeneous Cancer Specimens By Massively Parallel Picoliter Reactor Sequencing, Torstein Tengs

Dr. Torstein Tengs

The sensitivity of conventional DNA sequencing in tumor biopsies is limited by stromal contamination and by genetic heterogeneity within the cancer. Here, we show that microreactor-based pyrosequencing can detect rare cancer-associated sequence variations by independent and parallel sampling of multiple representatives of a given DNA fragment. This technology can thereby facilitate accurate molecular diagnosis of heterogeneous cancer specimens and enable patient selection for targeted cancer therapies.

Some Statistical Issues In Microarray Gene Expression Data, Matthew S. Mayo, Byron J. Gajewski, Jeffrey S. Morris

Jeffrey S. Morris

In this paper we discuss some of the statistical issues that should be considered when conducting experiments involving microarray gene expression data. We discuss statistical issues related to preprocessing the data as well as the analysis of the data. Analysis of the data is discussed in three contexts: class comparison, class prediction and class discovery. We also review the methods used in two studies that are using microarray gene expression to assess the effect of exposure to radiofrequency (RF) fields on gene expression. Our intent is to provide a guide for radiation researchers when conducting studies involving microarray gene expression …

Diverse Mechanisms Of Antiepileptic Drugs In The Development Pipeline, Michael A. Rogawski

Michael A. Rogawski

There is a remarkable array of new chemical entities in the current antiepileptic drug (AED) development pipeline. In some cases, the compounds were synthesized in an attempt improve upon the activity of marketed AEDs. In other cases, the discovery of antiepileptic potential was largely serendipitous. Entry into the pipeline begins with the demonstration of activity in one or more animal screening models. Results from testing in a panel of such models provide a basis to differentiate agents and may offer clues as to the mechanism. Target activity may then be defined through cell-based studies, often years after the initial identification …

Probability Of Real -Time Detection Vs Probability Of Infection For Aerosolized Biowarfare Agents: A Model Study., Alexander G. Sabelnikov, Vladimir Zhukov, C Ruth Kempf

Alexander G Sabelnikov

No abstract provided.

Shrinkage Estimation For Sage Data Using A Mixture Dirichlet Prior, Jeffrey S. Morris, Keith A. Baggerly, Kevin R. Coombes

Jeffrey S. Morris

Serial Analysis of Gene Expression (SAGE) is a technique for estimating the gene expression profile of a biological sample. Any efficient inference in SAGE must be based upon efficient estimates of these gene expression profiles, which consist of the estimated relative abundances for each mRNA species present in the sample. The data from SAGE experiments are counts for each observed mRNA species, and can be modeled using a multinomial distribution with two characteristics: skewness in the distribution of relative abundances and small sample size relative to the dimension. As a result of these characteristics, a given SAGE sample will fail …

An Introduction To High-Throughput Bioinformatics Data, Keith A. Baggerly, Kevin R. Coombes, Jeffrey S. Morris

Jeffrey S. Morris

High throughput biological assays supply thousands of measurements per sample, and the sheer amount of related data increases the need for better models to enhance inference. Such models, however, are more effective if they take into account the idiosyncracies associated with the specific methods of measurement: where the numbers come from. We illustrate this point by describing three different measurement platforms: microarrays, serial analysis of gene expression (SAGE), and proteomic mass spectrometry.

Bayesian Mixture Models For Gene Expression And Protein Profiles, Michele Guindani, Kim-Anh Do, Peter Mueller, Jeffrey S. Morris

Jeffrey S. Morris

We review the use of semi-parametric mixture models for Bayesian inference in high throughput genomic data. We discuss three specific approaches for microarray data, for protein mass spectrometry experiments, and for SAGE data. For the microarray data and the protein mass spectrometry we assume group comparison experiments, i.e., experiments that seek to identify genes and proteins that are differentially expressed across two biologic conditions of interest. For the SAGE data example we consider inference for a single biologic sample.

Analysis Of Mass Spectrometry Data Using Bayesian Wavelet-Based Functional Mixed Models, Jeffrey S. Morris, Philip J. Brown, Keith A. Baggerly, Kevin R. Coombes

Jeffrey S. Morris

In this chapter, we demonstrate how to analyze MALDI-TOF/SELDITOF mass spectrometry data using the wavelet-based functional mixed model introduced by Morris and Carroll (2006), which generalizes the linear mixed models to the case of functional data. This approach models each spectrum as a function, and is very general, accommodating a broad class of experimental designs and allowing one to model nonparametric functional effects for various factors, which can be conditions of interest (e.g. cancer/normal) or experimental factors (blocking factors). Inference on these functional effects allows us to identify protein peaks related to various outcomes of interest, including dichotomous outcomes, categorical …

Production Of A Completely Organic Fertilizer Economically And Testing Its Effect On The Morphology Of Plants, Dominique Frances Hoover, Akash Prabhu

Dominique Frances Hoover Ms.

No abstract provided.

Survey Of The Illinois Endangered Kankakee Mallow, Iliamna Remota, In Kankakee County, April L. Mcdonnell, Henry R. Owen, Sean C. Jones, Vincent P. Gutowski, John E. Ebinger

Henry R. Owen

Iliamna remota Greene (Malvaceae), endemic only to Langham Island in the Kankakee River, Kankakee County, Illinois, is a state endangered species. During the present study, the size of the population was determined, the habitat structure in and around the individual colonies analyzed, and management recommendation made to potentially increase the size of the population. During the summer of 2005, the I remota population consisted of 1,074 stems in 12 colonies, located along the northwest side of the island. In late June, flowering appeared to be prolific, where means and standard deviations of floral buds and open flowers were 1.6 :t …

Element Levels In Snakes In South Carolina: Differences Between A Control Site And Exposed Site On The Savannah River Site, J. Burger, S. Murray, K. F. Gaines, James M. Novak, T. Punshon, C. Dixon, M. Gochfeld

James M. Novak

Levels of 18 elements, including lead, mercury, selenium, and uranium, were examined in three species of snakes from an exposed and reference site on the Department of Energy’s Savannah River Site in South Carolina. We tested the hypotheses that there were no differences as a function of species, and there were no difference between the exposed and control site for blood and muscle (tail) samples for banded water snake (Nerodia fasciata), brown water snake (N. taxispilota) and cottonmouth (Akistrodon piscivorous). The banded water snakes collected were significantly smaller than the other two species. For blood, there were significant species differences …

The Effects Of Some Methacrylate Monomers Used As Liquid Component On Tensile And Flexural Strengths Of A Poly (Methyl Methacrylate) Denture Base Resin., Selda Keskin

No abstract provided.

Mental Retardation: A Mri Study Of 146 Brazilian Children, Armando F. Rocha, Cláudia C. Leite, Fábio T. Rocha

Armando F Rocha

We report results of a magnetic ressonance imaging (MRI) study of 146 Brazilian children, whose intelligence quotient scored less than 70. 50% of MRI examinations did not exhibit any signal of structural lesion (N group), whereas a focal thinning at the junction of the body and splenium of the corpus callosum; ventricular asymmetry; periventricular leukomalacia; gliosis and arachnoid cysts were among the most frequent findings in the remaining of subjects (L group). Maternal stress and altered blood pre ss u re were the most frequent findings in the pre-natal history of both N and L children. Familial antecedents of mental …

Acorn Use As Food, David A. Bainbridge

David A Bainbridge

The acorns from oaks (Quercus) and tan oaks (Lithocarpus) have been used as food for many thousands of years. They occur in the archaeological record of the early town sites in the Zagros Mountains, at Catal Hüyük (6000 BC), and oak trees were carefully inventoried by the Assyrians during the reign of Sargon II. In Europe, Asia, North Africa, the Mid-East, and North America, acorns were once a staple food. They are still a commercial food crop in several countries. Acorns are still harvested and used in several areas of the United States, most notably Southern Arizona and California. There …

A Group Of Dinoflagellates Similar To Pfiesteria As Defined By Morphology And Genetic Analysis, Torstein Tengs

Dr. Torstein Tengs

Eight novel pfiesteria-similar dinoflagellates are described that form a genetically well-defined group with distinct morphological features, and are capable of feeding myzocytotically on cryptophytes and other algae. Taxonomically, there was concordance between the genetic analysis and plate tabulation features among these taxa. It is suggested that these dinoflagellates are important grazers of other phytoplankton in the environment, and their total ecological significance has been underestimated.

Variation In Shoot Anatomy And Rooting Behaviour Of Stem Cuttings In Relation To Age Of Donor Plants In Teak (Tectona Grandis Linn. F.), Azamal Husen Dr., Mohinder Pal

Dr. Azamal Husen

No abstract provided.

Identifying Placebo Effects With Data From Clinical Trials, Anup Malani

Anup Malani

A medical treatment is said to have placebo effects if patients who are optimistic about the treatment respond better to the treatment. This paper proposes a simple test for placebo effects. Instead of comparing the treatment and control arms of a single trial, one should compare the treatment arms of two trials with different probabilities of assignment to treatment. If there are placebo effects, patients in the higher-probability trial will experience better outcomes simply because they believe that there is a greater chance of receiving treatment. This paper finds evidence of placebo effects in trials of antiulcer and cholesterol-lowering drugs.