Life Sciences Commons^™

An Ensemble Learning Approach To Reverse-Engineering Transcriptional Regulatory Networks From Time-Series Gene Expression Data, Jianhua Ruan, Youping Deng, Edward J. Perkins, Weixiong Zhang

Faculty Publications

Background

One of the most challenging tasks in the post-genomic era is to reconstruct the transcriptional regulatory networks. The goal is to reveal, for each gene that responds to a certain biological event, which transcription factors affect its expression, and how a set of transcription factors coordinate to accomplish temporal and spatial specific regulations.

Results

Here we propose a supervised machine learning approach to address these questions. We focus our study on the gene transcriptional regulation of the cell cycle in the budding yeast, thanks to the large amount of data available and relatively well-understood biology, although the main ideas …

Impacts Of Marine Docks On Eelgrass In New England: A Spreadsheet-Based Model For Managers And Planners, David M. Burdick, Frederick T. Short, Gregg Moore

Faculty Publications

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Survey Of Blueberry (Vaccinium Spp.) Problems In The Gulf South, Melinda A. Miller-Butler, Kenneth J. Curry, Barbara J. Smith, Jeffrey S. Braswell

Faculty Publications

The blueberry (Vaccinium) industry in Mississippi has been steadily increasing since the early 1980s, but some plants in older fields are now in decline. The root rot pathogen, Phytophthora cinnamomi, is endemic in the southeastern United States and has caused severe losses to blueberries in North Carolina and Arkansas. Because the warm, humid climate of Mississippi, with periods of high precipitation, provides a favorable environment for Phytophthora root rot disease, it was suspected to be the cause of plant decline in older blueberry fields. Members of the Gulf South Blueberry Growers Association were mailed surveys to determine …

Seal Bounties In Maine And Massachusetts, 1888 To 1962, Barbarai Lelli, David Harris Ph.D, Aboueissa Abouel-Makarim

Faculty Publications

Maine and Massachusetts paid bounties on seals during the 19th and 20th centuries. To determine the number of seals killed for bounty, we examined historical records of bounty claims, and used geographic information systems and multiple linear regression to find predictors of places where large numbers of bounties were paid. We found records of 24,831 bounties paid in Maine (1891-1945) and 15,690 in Massachusetts (1888-1962), Considering possible fraud, missing data, and seals struck and lost, this suggests that 72,284 to 135,498 seals were killed in the bounty hunt, probably enough to account for regional declines in seal populations. Larger numbers …

Subcellular Localization Of Marine Bacterial Alkaline Phosphatases, H. Luo, Ronald Benner, R. A. Long, Jianjun Hu

Faculty Publications

Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate utilization in the ocean. The subcellular localization of APases has significant ecological implications for marine biota but is largely unknown. The extensive metagenomic sequence databases from the Global Ocean Sampling Expedition provide an opportunity to address this question. A bioinformatics pipeline was developed to identify marine bacterial APases from the metagenomic databases, and a consensus classification algorithm was designed to predict their subcellular localizations. We identified 3,733 bacterial APase sequences (including PhoA, PhoD, and PhoX) and found that cytoplasmic (41%) and extracellular (30%) APases exceed their periplasmic (17%), outer membrane (12%), …

Position Of The American Dietetic Association: Vegetarian Diets, Winston J. Craig, Ann Reed Mangels

Faculty Publications

It is the position of the American Dietetic Association that appropriately planned vegetarian diets, including total vegetarian or vegan diets, are healthful, nutritionally adequate, and may provide health benefits in the prevention and treatment of certain diseases. Well-planned vegetarian diets are appropriate for individuals during all stages of the life cycle, including pregnancy, lactation, infancy, childhood, and adolescence, and for athletes. A vegetarian diet is defined as one that does not include meat (including fowl) or seafood, or products containing those foods. This article reviews the current data related to key nutrients for vegetarians including protein, n-3 fatty acids, iron, …

The Metal Chelators, Trientine And Citrate, Inhibit The Development Of Cardiac Pathology In The Zucker Diabetic Rat, John W. Baynes, David B. Murray

Faculty Publications

Purpose. The objective of this study was to determine the efficacy of dietary supplementation with the metal chelators, trientine or citric acid, in preventing the development of cardiomyopathy in the Zucker diabetic rat.

Hypothesis. We hypothesized that dietary chelators would attenuate metal-catalyzed oxidative stress and damage in tissues and protect against pathological changes in ventricular structure and function in type II diabetes.

Methods. Animals (10 weeks old) included lean control (LC, fa/+), untreated Zucker diabetic fatty (ZDF, fa/fa), and ZDF rats treated with either trientine (triethylenetetramine) or citrate at 20 mg/d in drinking water, starting …

Effects Of Light And Group Size On The Activity Of Wood Frog Tadpoles (Rana Sylvatica) And Their Response To A Shadow Stimulus, K. V. Mcclure, J. W. Mora, Geoffrey R. Smith

Faculty Publications

No abstract provided.

Within-Pond Oviposition Site Selection In The Wood Frog (Rana Sylvatica), A. A. Brindle, S. B. Karr, Geoffrey R. Smith, Jessica E. Rettig

Faculty Publications

No abstract provided.

The Short-Term Effect Of Whole Body Vibration Training On Sprint Start Performance In Collegiate Athletes, J. Brent Feland, J. Ty Hopkins, Iain Hunter, Brad Roberts

Faculty Publications

Whole body vibration (WBV) is characterized by a vibratory stimulus emitted throughout the body through the use of a vibrating platform on which the subject stands. Studies have shown over 30% increases in maximal explosive strength such as maximal speed biceps curl as well as increases in maximum dynamic force such as maximal sitting bench pull as the result of vibration. The purpose of this study was to investigate the effects of short term whole-body vibration on sprint starts among collegiate track athletes. On the first day eleven subjects were randomly assigned to either a non-vibration or vibration group for …

Neurophysiological Reflex Mechanisms’ Lack Of Contribution To The Success Of Pnf Stretches, J. Brent Feland, Sterling C. Hilton, J. Ty Hopkins, Iain Hunter, Ulrike H. Mitchell, J. William Myrer

Faculty Publications

Background and Purpose: Proprioceptive neuromuscular facilitation (PNF) stretches are widely used in athletics and rehabilitation. Although it has been shown that they produce better range-of-motion (ROM) increases than the slow or static stretch, the mechanisms responsible remain an enigma. This study was conducted to determine whether the previously proposed neurophysiological mechanisms of reciprocal inhibition and autogenic inhibition are responsible for the success of PNF stretches. In addition, the authors assessed the existence of the phenomenon of successive induction because it is used to strengthen reciprocal inhibition. Methods: Eighteen subjects 17–44 y performed the PNF stretches contract–relax (CR) and contract–relax, agonist …

Optimization Of A Convective Air Flow Solar Food Dryer, Jonathan K. Russon, Michael L. Dunn, Frost M. Steele

Faculty Publications

A solar food dryer, previously developed for personal and small community use, was the object of this optimization study. Based on previous research of convective solar food dehydrators, several dryer parameters were identified for this study. Chimney height and dryer product load were two factors tested in a central composite experimental design. Dryer product load was found to produce a maximum efficiency of the dryer when fifteen product-filled trays were inserted in the dryer. Maximum efficiency was observed at the maximum chimney height tested. Post-optimization configuration compared with pre-optimization configuration resulted in a 40% increase in final dry product production …

High-Throughput Next-Generation Sequencing Technologies Foster New Cutting-Edge Computing Techniques In Bioinformatics, Mary Qu Yang, Brian D. Athey, Hamid R. Arabnia, Andrew H. Sung, Qingzhong Liu, Jack Y. Yang, Jinghe Mao, Youping Deng

Faculty Publications

The advent of high-throughput next generation sequencing technologies have fostered enormous potential applications of supercomputing techniques in genome sequencing, epi-genetics, metagenomics, personalized medicine, discovery of non-coding RNAs and protein-binding sites. To this end, the 2008 International Conference on Bioinformatics and Computational Biology (Biocomp) - 2008 World Congress on Computer Science, Computer Engineering and Applied Computing (Worldcomp) was designed to promote synergistic inter/multidisciplinary research and education in response to the current research trends and advances. The conference attracted more than two thousand scientists, medical doctors, engineers, professors and students gathered at Las Vegas, Nevada, USA during July 14-17 and received great …

The Malina Oceanographic Expedition: How Do Changes In Ice Cover, Permafrost And Uv Radiation Impact On Biodiversity And Biogeochemical Fluxes In The Arctic Ocean?, Phillippe Massicotte, Rainer Amon, David Antoine, Philippe Archambault, Sergio Balzano, Simon Bélanger, Ronald Benner, Dominique Boeuf, Annick Bricaud, Flavienne Bruyant, Gwenaëlle Chaillou, Malik Malik, Bruno Charrière, Jing Chen, Hervé Claustre, Pierre Coupel, Nicole Delsaut, David Doxaran, Et. Al.

Faculty Publications

The MALINA oceanographic campaign was conducted during summer 2009 to investigate the carbon stocks and the processes controlling the carbon fluxes in the Mackenzie River estuary and the Beaufort Sea. During the campaign, an extensive suite of physical, chemical and biological variables was measured across seven shelf–basin transects (south-north) to capture the meridional gradient between the estuary and the open ocean. Key variables such as temperature, absolute salinity, radiance, irradiance, nutrient concentrations, chlorophyll-a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, and carbon stocks and fluxes were routinely measured onboard the Canadian research icebreaker CCGS Amundsen and from a barge …

Integrative Disease Classification Based On Cross-Platform Microarray Data, C.-C. Liu, Jianjun Hu, M. Kalakrishnan, H. Huang, X. J. Zhou

Faculty Publications

Background

Disease classification has been an important application of microarray technology. However, most microarray-based classifiers can only handle data generated within the same study, since microarray data generated by different laboratories or with different platforms can not be compared directly due to systematic variations. This issue has severely limited the practical use of microarray-based disease classification.

Results

In this study, we tested the feasibility of disease classification by integrating the large amount of heterogeneous microarray datasets from the public microarray repositories. Cross-platform data compatibility is created by deriving expression log-rank ratios within datasets. One may then compare vectors of log-rank …

Using A Mathematical Model Of Cadherin-Based Adhesion To Understand The Function Of The Actin Cytoskeleton, J. C. Dallon, Elijah Newren, Marc Hansen

Faculty Publications

The actin cytoskeleton plays a role in cell-cell adhesion but its specific function is not clear. Actin might anchor cadherins or drive membrane protrusions in order to facilitate cell-cell adhesion. Using a mathematical model of the forces involved in cadherin-based adhesion we investigate its possible functions. The immersed boundary method is used to model the cell membrane and cortex with cadherin binding forces added as linear springs. The simulations indicate that cells in suspension can develop normal cell-cell contacts without actin-based cadherin anchoring or membrane protrusions. The cadherins can be fixed in the membrane or free to move and the …

Topographic Effects On The Path And Evolution Of Loop Current Eddies, Kyung Hoon Hyun, Patrick J. Hogan

Faculty Publications

Eddy-topography (ET) interactions are important in determining the path and evolution of oceanic eddies, including Loop Current Eddies (LCE) in the Gulf of Mexico (GOM). We use the Hybrid Coordinate Ocean Model and satellite altimetry data to investigate the ET interactions and the impact on LCE pathway evolution in the GOM. Satellite altimetry reveals that LCEs translate dominantly westward in the central GOM and strongly collide and reflect against topography near the continental slope in the northern and western GOM. The result is the frequent generation of an anticyclone-cyclone (AC) pair in conjunction with the LCEs. In the absence of …

The Role Of Msa In Staphylococcus Aureus Biofilm Formation, Karthik Sambanthamoorthy, Antony Schwartz, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Background

Staphylococcus aureus is an important pathogen that forms biofilms. The global regulator sarA is essential for biofilm formation. Since the modulator of sarA (msa) is required for full expression of sarA and regulates several virulence factors, we examined the capacity of the msa mutant to form biofilm.

Results

We found that mutation of msa results in reduced expression of sarA in biofilm and that the msa mutant formed a weak and unstable biofilm. The msa mutant is able to adhere to surfaces and begins to form biofilm but fails to mature indicating that the defect of the …

Biological Invasions And Biocultural Diversity: Linking Ecological And Cultural Systems, Jeanine Pfeiffer, Robert Voeks

Faculty Publications

Study of the ecological and economic effects of invasive species has paralleled their progressively pervasive influence worldwide, yet their cultural impacts remain largely unexamined and therefore unrecognized. Unlike biological systems, where the ecological consequences of biological invasions are primarily negative, from an ethnoscientific standpoint, invasive species' impacts on cultural systems span a range of effects. Biological invasions affect cultural groups in myriad, often unpredictable and at times contradictory ways. This review groups case studies into a conceptual matrix suggesting three categorically different cultural impacts of invasive species. Culturally impoverishing invasive species precipitate the loss or replacement of culturally important native …

Gene Order Phylogeny Of The Genus Prochlorococcus, Haiwei Luo, Jian Shi, William Arndt, Jijun Tang, Robert Friedman

Faculty Publications

Background
Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria.

Methodology/Principal Findings
Orthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based …

Using Sport Science To Improve Coaching: A Case Study Of The American Record Holder In The Women’S Hammer Throw, Iain Hunter, Erin Gilreath, Larry W. Judge

Faculty Publications

Conclusions from biomechanical data can make a significant difference in the performance of athletes in the hammer throw if properly understood by coaches. By utilizing this scientific approach to the hammer throw event, the throws coach will be able to determine more accurate adjustments and devise training stimuli to better accommodate the athlete. In this case study, we have attempted to bridge the gap between the researcher and the coach in our approach to teaching the hammer throw, by integrating biomechanical analysis. We have employed the use of video analysis as an essential part of our coaching/teaching system. This USATF …

Leucon (Crymoleucon) Rossi, A New Species (Crustacea: Cumacea: Leuconidae) From The Shelf Waters Of The Ross Sea (Antarctica), With A Key To The Genus Leucon South Of 60°S, Peter Rehm, Richard W. Heard

Faculty Publications

A new leuconid cumacean, Leucon (Crymoleucon) rossi n. sp., is described from depths of 84 to 458 m in the Ross Sea off the Victoria Land coast. Leucon rossi n. sp. is distinguished from other members of the genus by a combination of characters including 1) a blunt, horizontally directed pseudorostrum) Without a distinctly protruding siphon; 2) strongly developed antennal notch; 3) entire dorsomedian margin of carapace appearing serrate, armed with 14 to 19 anteriorly Curved spines in female (up to 21 in subadult males); 4) a small, but distinct, spine behind the frontal lobe; and 5) the uropodal peduncle …

A Simple, Anatomically Based Correction To The Conventional Ankle Joint Center, Dustin A. Bruening, Ashlie N. Crewe, Frank L. Buczek

Faculty Publications

Background

Conventional motion analysis studies define the ankle joint center as the midpoint between the most medial and lateral aspects of the malleoli, yet research points toward a more distal joint center location. The purpose of this study was to develop and evaluate an anatomically based correction that would move the conventional ankle joint center to a more accurate location.

Methods

Lower extremity radiographs from 30 pediatric patients were analyzed retrospectively. An offset between the conventional and more accurate ankle joint centers was measured and correlated to other common anatomical measures based on conventional skin mounted marker positions. The best …

Timing Of Supplementation Of Selenium And Isoflavones Determines Prostate Cancer Risk Factor Reduction In Rats, Merrill J. Christensen, Jessica R. Tolman, Edwin D. Lephart, Dennis L. Eggett, Kenneth Setchell

Faculty Publications

High dietary intake of selenium or isoflavones reduces risk factors for prostate cancer. We tested whether combined supplementation of these two dietary components would reduce prostate cancer risk factors in rats more than supplementation of each component individually. Methods Male Noble rat pups were exposed from conception to diets containing an adequate (0.33-0.45 mg/kg diet) or high (3.33-3.45 mg/kg) concentration of selenium as Se-methylselenocysteine and a low (10 mg/kg) or high (600 mg/kg) level of isoflavones in a 2 x 2 factorial design. Pups consumed their respective diets until sacrifice at 35, 100, or 200 days. Male Noble rat breeders, …

Improving Reversal Median Computation Using Commuting Reversals And Cycle Information, William Arndt, Jijun Tang

Faculty Publications

In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods for reconstructing phylogeny from genome rearrangements include distance-based methods, MCMC methods, and direct optimization methods. The latter, pioneered by Sankoff and extended with the software suites GRAPPA and MGR, is the most accurate approach, but is very limited due to the difficulty of its scoring procedure—it must solve multiple instances of the reversal median problem to compute the score of a given tree. The reversal median problem is known to be NP-hard and all …

Multi-Break Rearrangements And Breakpoint Re-Uses: From Circular To Linear Genomes, Max A. Alekseyev

Faculty Publications

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Alekseyev and Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion …

Infant-Feeding Practices Of Low-Income Vietnamese American Women, Yashmi Mistry, Marjorie Freedman, Kathleen Sweeney, Clarie Hollenbeck

Faculty Publications

Healthy People 2010 breastfeeding goals include 50% exclusive breastfeeding at 6 months. In California, US, Santa Clara County Women, Infants, and Children (SCCWIC) data indicated Asian participants had low (5.6%) 6-month breastfeeding rates. To examine infant-feeding practices, Vietnamese breastfeeding peer counselors surveyed 133 Vietnamese SCCWIC participants (≥ 18 years old, nonpregnant, < 28 months postpartum) using a structured questionnaire regarding intentions, attitudes, and subjective norms toward breastfeeding. Results indicated that 75% initiated breastfeeding in the hospital (33% exclusively, 42% partially), and 25% exclusively formula fed. At survey time, 49% had terminated breastfeeding (average duration 4.4 months). Feeding intentions during pregnancy predicted feeding method used (P < .001). Most prenatal advice was from SCCWIC employees, friends, and doctors who supported breastfeeding. Most postnatal advice was from nurses who supported breastfeeding and bottle-feeding equally. Stronger control beliefs, peer counseling, and education were correlated with breastfeeding (P < .001). Improved postdelivery hospital advice may further increase breastfeeding initiation and duration.

Commercial Evaluation Of A Continuous Micronutrient Fortification Process For Nixtamal Tortillas, Michael L. Dunn, Sergio O. Serna-Saldivar, Diana Sanchez-Hernandez, Robert W. Griffin

Faculty Publications

The corn tortilla plays an integral role in the Mexican diet and is an ideal vehicle for micronutrient fortification. Approximately 60% of corn tortillas in Mexico are produced from nixtamal, with the remainder prepared from masa flour. A process for continuous fortification of nixtamal tortillas was evaluated in two commercial mills in Mexico. A commercial powder dosifier was used to add micronutrient premix containing iron, zinc, folic acid, niacin, riboflavin, and thiamin to nixtamal (1 g/kg) as it was milled. After training and preliminary sampling, mills produced fortified tortillas unassisted for four weeks. Masa flow rates over a four-day period …

A Competitive Hybridization Model Predicts Probe Signal Intensity On High Density Dna Microarrays, Shuzhao Li, Alex Pozhitkov, Marius Brouwer

Faculty Publications

A central, unresolved problem of DNA microarray technology is the interpretation of different signal intensities from multiple probes targeting the same transcript. We propose a competitive hybridization model for DNA microarray hybridization. Our model uses a probe-specific dissociation constant that is computed with current nearest neighbor model and existing parameters, and only four global parameters that are fitted to Affymetrix Latin Square data. This model can successfully predict signal intensities of individual probes, therefore makes it possible to quantify the absolute concentration of targets. Our results offer critical insights into the design and data interpretation of DNA microarrays.

Calculating Expected Dna Remnants From Ancient Founding Events In Human Population Genetics, Nathan C. Sheffield, Keith A. Crandall, Andrew Stacey

Faculty Publications

Background- Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations. Results- We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current …