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Full-Text Articles in Life Sciences

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 Dec 2006

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 Dec 2006

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 ...


Physical And Structural Basis For The Strong Interactions Of The -Impy- Central Pairing Motif In The Polyamide F-Impyim, K. Buchmueller, S. Bailey, D. Matthews, Z. Taherbhai, J. Register, Z. Davis, Chrystal Bruce, C. O'Hare, J. Hartley, M. Lee Nov 2006

Physical And Structural Basis For The Strong Interactions Of The -Impy- Central Pairing Motif In The Polyamide F-Impyim, K. Buchmueller, S. Bailey, D. Matthews, Z. Taherbhai, J. Register, Z. Davis, Chrystal Bruce, C. O'Hare, J. Hartley, M. Lee

Chrystal D. Bruce

The polyamide f-ImPyIm has a higher affinity for its cognate DNA than either the parent analogue, distamycin A (10-fold), or the structural isomer, f-PyImIm (250-fold), has for its respective cognate DNA sequence. These findings have led to the formulation of a two-letter polyamide “language” in which the -ImPy- central pairings associate more strongly with Watson−Crick DNA than -PyPy-, -PyIm-, and -ImIm-. Herein, we further characterize f-ImPyIm and f-PyImIm, and we report thermodynamic and structural differences between -ImPy- (f-ImPyIm) and -PyIm- (f-PyImIm) central pairings. DNase I footprinting studies confirmed that f-ImPyIm is a stronger binder than distamycin A and f-PyImIm ...


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 Nov 2006

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.


The Importance Of Emerging Biobased Industries To Engineering And Technology, Kurt A. Rosentrater, R. Balamuralikrishma Oct 2006

The Importance Of Emerging Biobased Industries To Engineering And Technology, Kurt A. Rosentrater, R. Balamuralikrishma

Kurt A. Rosentrater

Our society has developed an insatiable demand for energy and material goods. Historically, these needs have been met primarily by fossil fuels and other non-renewable raw materials. As environmental concerns grow, however, renewable resources are gaining increased attention. This paper examines the emergence and importance that biobased industries are increasingly beginning to play. A biobased enterprise, similar in concept to a traditional refinery or factory, utilizes conversion technologies to produce various products. These operations are rapidly increasing both in number as well as in capacity throughout this country, and are poised to add significantly to the nation’s energy and ...


Analytical And Experimental Studies Of Properties Of Ethanol Coproduct-Filled Plastics, Robert Tatara, Andrew Otieno, Srikrishna Suraparaju, Kurt A. Rosentrater Oct 2006

Analytical And Experimental Studies Of Properties Of Ethanol Coproduct-Filled Plastics, Robert Tatara, Andrew Otieno, Srikrishna Suraparaju, Kurt A. Rosentrater

Kurt A. Rosentrater

As the renewable fuels industry continues to grow, the quantity of resulting byproducts has expanded in tandem. Currently, these materials are primarily used for animal feed, but at some point will saturate the animal feeds market. Thus, it is necessary to investigate alternative methods and applications by which these coproducts can be utilized. One potential application for these process residues involves plastics manufacturing. Due, in part, to the increasing cost of resins and conventional fillers, alternate fillers have been increasingly sought. Many of these include biological materials such as grasses, bamboo, starch, chicken feathers, soy protein, and cellulose. Not only ...


The Localized Dynamics Of A Ca2+Channel (30-Minute Talk), Borbala Mazzag, Christoper Tignanelli, Gregory D. Smith Aug 2006

The Localized Dynamics Of A Ca2+Channel (30-Minute Talk), Borbala Mazzag, Christoper Tignanelli, Gregory D. Smith

Borbala Mazzag

No abstract provided.


How Earth Remote Sensing From The International Space Station Complements Current Satellite‐Based Sensors, Jennifer Gebelein, Dean Eppler Jul 2006

How Earth Remote Sensing From The International Space Station Complements Current Satellite‐Based Sensors, Jennifer Gebelein, Dean Eppler

Jennifer Gebelein

The International Space Station (ISS) will provide an Earth‐and space‐observing platform that will support sensors built by 16 different countries and deliver data and images for local, regional and global research. When complete, it will be an exceptional platform for conducting remote sensing of the Earth, astrophysics, and space physics research programmes. Additionally, the ISS will operate as a testbed for engineering studies and complex technological developments that will benefit future Earth‐observing capabilities. ...


The Global Relevance Of Bio-Based Industries To Engineering And Technology Education, Kurt A. Rosentrater, Radha Balamuralikrishma Jun 2006

The Global Relevance Of Bio-Based Industries To Engineering And Technology Education, Kurt A. Rosentrater, Radha Balamuralikrishma

Kurt A. Rosentrater

The society in which we live has developed an insatiable demand for energy and material goods. In particular, recent data reveals that the aggressive pursuit of improved standards of living in the highly populated countries of India and China has contributed to increased demand for fossil fuels, which has exacerbated the recent spike in energy costs. Historically, these needs have been met primarily by fossil fuels and other non-renewable raw materials. As environmental concerns grow, however, renewable resources are gaining increased attention. This paper examines the emergence and importance that bio-based industries are increasingly beginning to play. A bio-based enterprise ...


Bi-Level Clustering Of Mixed Categorical And Numerical Biomedical Data, Bill Andreopoulos, Aijun An, Xiaogang Wang Jun 2006

Bi-Level Clustering Of Mixed Categorical And Numerical Biomedical Data, Bill Andreopoulos, Aijun An, Xiaogang Wang

William B. Andreopoulos

Biomedical data sets often have mixed categorical and numerical types, where the former represent semantic information on the objects and the latter represent experimental results. We present the BILCOM algorithm for |Bi-Level Clustering of Mixed categorical and numerical data types|. BILCOM performs a pseudo-Bayesian process, where the prior is categorical clustering. BILCOM partitions biomedical data sets of mixed types, such as hepatitis, thyroid disease and yeast gene expression data with Gene Ontology annotations, more accurately than if using one type alone.


Some Statistical Issues In Microarray Gene Expression Data, Matthew S. Mayo, Byron J. Gajewski, Jeffrey S. Morris Jun 2006

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 ...


Homeland Security: Engaging The Frontlines - Symposium Proceedings, George H. Baker, Cheryl J. Elliott Apr 2006

Homeland Security: Engaging The Frontlines - Symposium Proceedings, George H. Baker, Cheryl J. Elliott

George H Baker

The rise of the American homeland security endeavor under the leadership of the new Department of Homeland Security has been heralded by several major national strategy documents. These documents have served to organize efforts at top levels within the government and industry. However, the national strategy guidance is not getting to many organizations and people at the grass-roots level who can make the most difference in preventing attacks, protecting systems, and recovering from catastrophic events, viz. the general citizenry, private infrastructure owners, and local governments. To better understand grass-roots issues and solutions, James Madison University, in cooperation with the Federal ...


Biochemical Characterization Of The Major Sorghum Grain Peroxidase, Mamoudou H. Dicko, Harry Gruppen, Riet Hilhorst, Alphons G. J. Voragen, Willen W. H. Van Berkel Apr 2006

Biochemical Characterization Of The Major Sorghum Grain Peroxidase, Mamoudou H. Dicko, Harry Gruppen, Riet Hilhorst, Alphons G. J. Voragen, Willen W. H. Van Berkel

Pr. Mamoudou H. DICKO, PhD

The major cationic peroxidase in sorghum grain (SPC4) , which is ubiquitously present in all sorghum varieties was purified to apparent homogeneity, and found to be a highly basic protein (pI #1;11). MS analysis showed that SPC4 consists of two glycoforms with molecular masses of 34227 and 35629 Da and it contains a type-b heme. Chemical deglycosylation allowed to estimate sugar contents of 3.0% and 6.7% (w ⁄ w) in glycoform I and II, respectively, and a mass of the apoprotein of 33 246 Da. High performance anion exchange chromatography allowed to determine the carbohydrate constituents of the polysaccharide ...


Shrinkage Estimation For Sage Data Using A Mixture Dirichlet Prior, Jeffrey S. Morris, Keith A. Baggerly, Kevin R. Coombes Mar 2006

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 Mar 2006

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 Mar 2006

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 Mar 2006

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 ...


Model For Assembly And Gelation Of Four-Armed Dna Dendrimers, Francis Starr, Francesco Sciortino Jan 2006

Model For Assembly And Gelation Of Four-Armed Dna Dendrimers, Francis Starr, Francesco Sciortino

Francis Starr

No abstract provided.


Dna Damage Responses In Progeroid Syndromes Arise From Defective Maturation Of Prelamin A, Michael Sinensky, Y. Liu, A. Rusinol, Y. Wang, Y. Zou Jan 2006

Dna Damage Responses In Progeroid Syndromes Arise From Defective Maturation Of Prelamin A, Michael Sinensky, Y. Liu, A. Rusinol, Y. Wang, Y. Zou

Michael Sinensky

The genetic diseases Hutchinson-Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) arise from accumulation of farnesylated prelamin A because of defects in the lamin A maturation pathway. Both of these diseases exhibit symptoms that can be viewed as accelerated aging. The mechanism by which accumulation of farnesylated prelamin A leads to these accelerated aging phenotypes is not understood. Here we present evidence that in HGPS and RD fibroblasts, DNA damage checkpoints are persistently activated because of the compromise in genomic integrity. Inactivation of checkpoint kinases Ataxia-telangiectasia-mutated (ATM) and ATR (ATM- and Rad3-related) in these patient cells can partially overcome their ...


Farnesylated Lamins, Progeroid Syndromes And Farnesyl Transferase Inhibitors, Michael Sinensky, A. E. Rusinol Jan 2006

Farnesylated Lamins, Progeroid Syndromes And Farnesyl Transferase Inhibitors, Michael Sinensky, A. E. Rusinol

Michael Sinensky

Three mammalian nuclear lamin proteins, lamin B1, lamin B2 and the lamin A precursor, prelamin A, undergo canonical farnesylation and processing at CAAX motifs. In the case of prelamin A, there is an additional farnesylation-dependent endoproteolysis, which is defective in two congenital diseases: Hutchinson-Gilford progeria (HGPS) and restrictive dermopathy (RD). These two diseases arise respectively from defects in the prelamin A substrate and the enzyme (ZmpSte24) that processes it. Recent work has shed light on the roles of the lamin proteins and the enzymes involved in their farnesylation-dependent maturation. Other experimental work, including mouse model studies, have examined the possibility ...


On The Robustness Of Robustness Checks Of The Environmental Kuznets Curve, Marzio Galeotti, Matteo Manera, Alessandro Lanza Jan 2006

On The Robustness Of Robustness Checks Of The Environmental Kuznets Curve, Marzio Galeotti, Matteo Manera, Alessandro Lanza

Matteo Manera

Since its first inception in the debate on the relationship between environment and growth in 1992, the Environmental Kuznets Curve has been subject of continuous and intense scrutiny. The literature can be roughly divided in two historical phases. Initially, after the seminal contributions, additional work aimed to extend the investigation to new pollutants and to verify the existence of an inverted-U shape as well as assessing the value of the turning point. The following phase focused instead on the robustness of the empirical relationship, particularly with respect to the omission of relevant explanatory variables other than GDP, alternative datasets, functional ...


Expanding The Role Of Systems Modeling: Considering Byproduct Generation From Biofuel Production, Kurt A. Rosentrater Jan 2006

Expanding The Role Of Systems Modeling: Considering Byproduct Generation From Biofuel Production, Kurt A. Rosentrater

Kurt A. Rosentrater

The bioethanol industry has been experiencing rapid growth over the past several years, and is expected to continue to increase production for the foreseeable future. A vital component to the success of this industry is the sales and marketing of processing residues, which are primarily sold as dried distillers grains with solubles (DDGS). Systems modeling, a technique that has been used to predict future demand for bioethanol, can also be used to determine potential byproduct generation rates. This paper discusses the development of one such model, and presents predicted generation of DDGS as well as carbon dioxide emissions from this ...


Renewable Energy Alternatives—A Growing Opportunity For Engineering And Technology Education, Kurt A. Rosentrater Jan 2006

Renewable Energy Alternatives—A Growing Opportunity For Engineering And Technology Education, Kurt A. Rosentrater

Kurt A. Rosentrater

A hallmark of the United States’ economic growth is an ever-increasing demand for energy, which has traditionally been met primarily by combusting the hydrocarbons found in fossil fuels. As national security and environmental concerns grow, renewable energy resources are gaining increased attention. Unfortunately, there is currently a dearth of renewable energy coverage in engineering and technology curricula. The objectives of this paper are to examine historical energy data for both traditional as well as alternative energy sources, and to motivate educators to address this gap. Even with the progressive developments of non-traditional energy sources over the years, the U.S ...


Incorporating Targeted Grazing Into Farming Systems, Andrew W. Lenssen, Patrick Hatfield, Hayes Goosey, Sue Blodgett Jan 2006

Incorporating Targeted Grazing Into Farming Systems, Andrew W. Lenssen, Patrick Hatfield, Hayes Goosey, Sue Blodgett

Andrew W. Lenssen

When incorporating targeted grazing into farming systems, livestock producers and farm operators need assurance that the benefits from their activities are worth their investments. This chapter will focus on how integrating grazing, particularly with sheep and goats, into farming systems can offer those benefits. The concepts are not new. Cropping systems were once integrated with livestock production: Livestock gained forage value from crop aftermath, crops were grown to sustain livestock, and livestock were used as implements to produce crops. Today, few cropping systems include livestock. Sheep and goats are traditionally produced on rangelands or pasture forages and supplemented during winter ...


Channel-Reach Morphology Dependence On Energy, Scale, And Hydroclimatic Processes With Implications For Prediction Using Geospatial Data, Alejandro N. Flores, Brian P. Bledsoe, Christopher O. Cuhaciyan, Ellen E. Wohl Jan 2006

Channel-Reach Morphology Dependence On Energy, Scale, And Hydroclimatic Processes With Implications For Prediction Using Geospatial Data, Alejandro N. Flores, Brian P. Bledsoe, Christopher O. Cuhaciyan, Ellen E. Wohl

Alejandro N. Flores

Channel types found in mountain drainages occupy characteristic but intergrading ranges of bed slope that reflect a dynamic balance between erosive energy and channel boundary resistance. Using a classification and regression tree (CART) modeling approach, we demonstrate that drainage area scaling of channel slopes provides better discrimination of these forms than slope alone among supply- and capacity-limited sites. Analysis of 270 stream reaches in the western United States exhibiting four common mountain channel types reveals that these types exist within relatively discrete ranges of an index of specific stream power. We also demonstrate associations among regional interannual precipitation variability, discharge ...


Functional Connectivity In A Baseline Resting-State Network In Autism, Vladimir Cherkassky, Rajesh Kana, Timothy Keller, Marcel Just Dec 2005

Functional Connectivity In A Baseline Resting-State Network In Autism, Vladimir Cherkassky, Rajesh Kana, Timothy Keller, Marcel Just

Marcel Adam Just

No abstract provided.


Comparison Of Virulence Gene Profiles Between Escherichia Coli Strains Isolated From Healthy And Diarrheic Swine, Mark Wilson, Karl A Bettelheim, X Y Wu, S Driesen, James Chin, Toni Chapman, I Barchia, D Trott Dec 2005

Comparison Of Virulence Gene Profiles Between Escherichia Coli Strains Isolated From Healthy And Diarrheic Swine, Mark Wilson, Karl A Bettelheim, X Y Wu, S Driesen, James Chin, Toni Chapman, I Barchia, D Trott

Mark R Wilson

No abstract provided.


Head Tilt-Translation Combinations Distinguished At The Level Of Neurons, Jan E. Holly, Sarah E. Pierce, Gin Mccollum Dec 2005

Head Tilt-Translation Combinations Distinguished At The Level Of Neurons, Jan E. Holly, Sarah E. Pierce, Gin Mccollum

Gin McCollum

Angular and linear accelerations of the head occur throughout everyday life, whether from external forces such as in a vehicle or from volitional head movements. The relative timing of the angular and linear components of motion differs depending on the movement. The inner ear detects the angular and linear components with its semicircular canals and otolith organs, respectively, and secondary neurons in the vestibular nuclei receive input from these vestibular organs. Many secondary neurons receive both angular and linear input. Linear information alone does not distinguish between translational linear acceleration and angular tilt, with its gravity-induced change in the linear ...


Brain Correlates Of Discourse Processing: An Fmri Investigation Of Irony And Conventional Metaphor Comprehension, Zohar Eviatar, Marcel Adam Just Dec 2005

Brain Correlates Of Discourse Processing: An Fmri Investigation Of Irony And Conventional Metaphor Comprehension, Zohar Eviatar, Marcel Adam Just

Marcel Adam Just

No abstract provided.


Nmr Investigations Of Natural Organic Matter In Forest Ecosystems, Chris E. Johnson Dec 2005

Nmr Investigations Of Natural Organic Matter In Forest Ecosystems, Chris E. Johnson

Chris E Johnson

No abstract provided.