Life Sciences Commons^™

An Efficient Algorithm For Biomarker Identification, Jiang Li, Rick Mckenzie, Lisa Cazares, Richard Drake, John Semmens

Electrical & Computer Engineering Faculty Publications

No abstract provided.

Optimum Stand Density Of Spring Triticale For Grain Yield And Alfalfa Establishment, Lance R. Gibson, Jeremy W. Singer, Ronald Vos, Brock C. Blaser

Faculty Work Comprehensive List

Triticale (×Triticosecale Wittmack) has potential as a feed crop in the north central United States and could also function as a companion crop for alfalfa (Medicago sativa L.) establishment. The objectives of this research were to assess the suitability of a short-statured spring triticale as a companion crop and determine optimum triticale seeding rates for grain yield and alfalfa establishment. Spring triticale ‘Trimark 37812’ and alfalfa were grown in companion at Ames and Sioux Center, IA during 2004 and 2005. Triticale was seeded at 198, 297, 396, 495, and 594 pure live seeds (PLS) m⁻² and alfalfa …

Rates Of Carbonate Dissolution In Permeable Sediments Estimated From Porewater Profiles: The Role Of Sea Grasses, David J. Burdige, Richard C. Zimmerman, Xinping Hu

OES Faculty Publications

In this study we estimate sediment carbonate dissolution rates for sandy sea grass sediments on the Bahamas Bank using an inverse pore-water advection/diffusion/reaction model constrained by field observations. This model accounts for sea grass O₂ input to these sediments, and also parameterizes pore-water advection through these permeable sediments as a nonlocal exchange process. The resulting rates of carbonate dissolution are positively correlated with sea grass density, and are comparable with previous rate estimates for Florida Bay sediments. In contrast, the advective uptake of O₂ by these sediments decreased with increasing sea grass density. This suggests that the competing …

The Use Of Extractable Lipofuscin For Age Determination Of Crustaceans: Reply To Sheehy (2008), H. Rodger Harvey, David H. Secor, Se-Jong Ju

OES Faculty Publications

The heterogeneous mixture of metabolic by-products termed lipofuscin (LF) or age pigments has long been known to accumulate in post mitotic cells with increasing age. In crustaceans several approaches have been developed over the years to track LF accumulation and provide a proxy for chronological age. Histological approaches have been traditionally used for LF determination of crustaceans (e.g. Sheehy et al. 1994, Mar Biol 121:237-245), but over the last decade extraction approaches for neural tissues have been introduced (Ju et al. 1999, Mar Ecol Prog Ser 185:171-179) and tested (Ju et al. 2001, Mar Ecol Prog Ser 224:197-205; 2003, Fish …

Melody Recognition At Fast And Slow Tempos: Effects Of Age, Experience, And Familiarity, W. Jay Dowling, James C. Bartlett, Andrea R. Halpern, Melinda W. Andrews

Faculty Journal Articles

Eighty-one listeners defined by three age ranges (18–30, 31–59, and over 60 years) and three levels of musical experience performed an immediate recognition task requiring the detection of alterations in melodies. On each trial, a brief melody was presented, followed 5 sec later by a test stimulus that either was identical to the target or had two pitches changed, for a same–different judgment. Each melody pair was presented at 0.6 note/sec, 3.0 notes/sec, or 6.0 notes/sec. Performance was better with familiar melodies than with unfamiliar melodies. Overall performance declined slightly with age and improved substantially with increasing experience, in agreement …

Effects Of Timbre And Tempo Change On Memory For Music, Andrea R. Halpern, Daniel Mullensiefen

Faculty Journal Articles

We investigated the effects of different encoding tasks and of manipulations of two supposedly surface parameters of music on implicit and explicit memory for tunes. In two experiments, participants were first asked to either categorize instrument or judge familiarity of 40 unfamiliar short tunes. Subsequently, participants were asked to give explicit and implicit memory ratings for a list of 80 tunes, which included 40 previously heard. Half of the 40 previously heard tunes differed in timbre (Experiment 1) or tempo (Experiment 2) in comparison with the first exposure. A third experiment compared similarity ratings of the tunes that varied in …

I Know What I Like: Stability Of Aesthetic Preference In Alzheimer's Disease, Andrea R. Halpern, Jenny Ly, Seth Elkin-Franklin, Margaret G. O'Connor

Faculty Journal Articles

Two studies explored the stability of art preference in patients with Alzheimer’s disease and age-matched control participants. Preferences for three different styles of paintings, displayed on art postcards, were examined over two sessions. Preference for specific paintings differed among individuals but AD and non-AD groups maintained about the same stability in terms of preference judgments across two weeks, even though the AD patients did not have explicit memory for the paintings. We conclude that aesthetic responses can be preserved in the face of cognitive decline. This should encourage caregivers and family to engage in arts appreciation activities with patients, and …

Differential Dynamic Properties Of Scleroderma Fibroblasts In Response To Perturbation Of Environmental Stimuli, Xiaodong Zhou

Faculty, Staff and Student Publications

Diseases are believed to arise from dysregulation of biological systems (pathways) perturbed by environmental triggers. Biological systems as a whole are not just the sum of their components, rather ever-changing, complex and dynamic systems over time in response to internal and external perturbation. In the past, biologists have mainly focused on studying either functions of isolated genes or steady-states of small biological pathways. However, it is systems dynamics that play an essential role in giving rise to cellular function/dysfunction which cause diseases, such as growth, differentiation, division and apoptosis. Biological phenomena of the entire organism are not only determined by …

Multifactor Effects And Evidence Of Potential Interaction Between Complement Factor H Y402h And Loc387715 A69s In Age-Related Macular Degeneration, Petri V. Tommila, Jukka A. Moilanen, Tapani Palosaari, Kai Kaarniranta, Seppo Meri, Ilkka R. Immonen, Irma E. Järvelä

Faculty, Staff and Student Publications

BACKGROUND: Variants in the complement cascade genes and the LOC387715/HTRA1, have been widely reported to associate with age-related macular degeneration (AMD), the most common cause of visual impairment in industrialized countries. METHODS/PRINCIPAL FINDINGS: We investigated the association between the LOC387715 A69S and complement component C3 R102G risk alleles in the Finnish case-control material and found a significant association with both variants (OR 2.98, p = 3.75 x 10(-9); non-AMD controls and OR 2.79, p = 2.78 x 10(-19), blood donor controls and OR 1.83, p = 0.008; non-AMD controls and OR 1.39, p = 0.039; blood donor controls), respectively. Previously, …

Involvement Of Inflammation In Tau Pathology And Mechanisms That Drive Neurodegeneration In Alzheimer's Disease, Lisette T. Arnaud

Dissertations, Theses, and Capstone Projects

Two of the hallmarks of neurodegenerative disorders, such as Alzheimer's disease (AD), are (1) the appearance of proteinaceous deposits in inclusion bodies containing aggregates of ubiquitinated proteins and (2) activated microglia and astrocytes surrounding the diseased neurons. In Alzheimer's disease, the intracellular inclusion bodies are known as neurofibrilary tangles (NFT). The mechanisms leading to inclusion body formation and their role in the progression of neurodegeneration are still largely unknown.

Many of the proteins that accumulate in inclusion bodies depend on the ubiquitin/proteasome pathway (UPP) for their degradation. This pathway is responsible for the bulk (∼80%) of intracellular protein degradation. Because …

Rapid Dissemination Of Francisella Tularensis And The Effect Of Route Of Infection, S. S. Ojeda, Z. J. Wang, Chris A. Mares, T. A. Chang, Q. Li, E. G. Morris, P. A. Jerabek, J. M. Teale

Biology Faculty Publications (Archived)

Background. Francisella tularensis subsp. tularensis is classified as a Category A bioweapon that is capable of establishing a lethal infection in humans upon inhalation of very few organisms. However, the virulence mechanisms of this organism are not well characterized. Francisella tularensis subsp. novicida, which is an equally virulent subspecies in mice, was used in concert with a microPET scanner to better understand its temporal dissemination in vivo upon intranasal infection and how such dissemination compares with other routes of infection. Adult mice were inoculated intranasally with F. tularensis subsp. novicida radiolabeled with 64Cu and imaged by microPET at 0.25, 2 …

Ecosystem Properties Of Urban Land Covers At The Aboveground-Belowground Interface, Loren B. Byrne, Mary Ann Bruns, Ke Chung Kim

Arts & Sciences Faculty Publications

Understanding of ecological differences among urban land covers can guide the sustainable management of urbanized landscapes for conservation of ecosystem services. The objective of our study was to compare ecosystem properties at the aboveground–belowground interface of three land cover types commonly found in residential landscapes: lawns, bark mulch, and gravel mulch. Using unmowed vegetation as a reference land cover, we measured surface soil variables (to 5 cm depth), CO2 fluxes, and ground temperatures in experimental field plots within 3 years after their creation. Each land cover had a distinctive set of ecosystem properties. Mulched plots had significantly warmer soil and …

Introduction To Ecological Landscaping: A Holistic Description And Framework To Guide The Study And Management Of Urban Landscape Parcels, Loren B. Byrne, Parwinder Grewal

Arts & Sciences Faculty Publications

Urbanized ecosystems and urban human populations are expanding around the world causing many negative environmental effects. A challenge for achieving sustainable urban social ecological systems is understanding how urbanized landscapes can be designed and managed to minimize negative outcomes. To this end, an interdisciplinary Ecological Landscaping conference was organized to examine the interacting sociocultural and ecological causes and consequences of landscaping practices and products. This special issue of Cities and the Environment contains a diverse set of articles arising from that conference. In this introductory paper, we describe the meaning of ecological landscaping and a new conceptual framework that helps …

Evolutionary Physiology: The Extent Of C4 And Cam Photosynthesis In The Genera Anacampseros And Grahamia Of The Portulacaceae, Lonnie J. Guralnick, Amanda Cline, Monica Smith, Rowan F. Sage

Arts & Sciences Faculty Publications

The Portulacaceae is one of the few terrestrial plant families known to have both C(4) and Crassulacean acid metabolism (CAM) species. There may be multiple origins of the evolution of CAM within the Portulacaceae but the only clear evidence of C(4) photosynthesis is found in members of the genus Portulaca. In the Portulaca, CAM succulent tissue is overlaid with the C(4) tissue in a unique fashion where both pathways are operating simultaneously. Earlier reports have shown that the clade containing the genera Anacampseros and Grahamia may also contain C(4) photosynthetic species similar to the Portulaca, which would indicate multiple origins …

Laboratory Diagnosis Of Clostridium Difficile In The Republic Of Ireland: A Survey Of Irish Microbiology Laboratories., Denise Drudy, F. Fitzpatrick, A. Oza, A. Gilleece, A. M. O’Byrne

Articles

The Health Protection Surveillance Centre (HPSC) established a group to produce national guidelines for Clostridium difficile in Ireland in 2006. A laboratory questionnaire was distributed to determine current C. difficile diagnostic practices. Twenty-nine out of 44 laboratories providing C. difficile diagnostic services to 34 hospitals responded. Twenty-five out of 29 (86%) laboratories processed specimens for C. difficile and four (13.8%) forwarded specimens to another laboratory. Sixteen laboratories (64%) processed specimens for other healthcare facilities. None routinely examined stool for C. difficile, seven (28%) examined specimens only when requested to do so and 18 (72%) used specific selection criteria, including testing …

Update Of Clostridium Difficile Infection Due To Pcr Ribotype 027 In Europe, 2008, Denise Drudy, E. J. Kuijper, F. Barbut, J. S. Brazier

Articles

Since the emergence of a new virulent strain of Clostridium difficile characterised as toxinotype III, North American pulsedfield type 1 (NAP1), restriction-endonuclease analysis group type BI and PCR-ribotype 027 (Type 027), multiple outbreaks have been reported in North America and Europe [1-9]. The increased virulence of C. difficile Type 027 is thought to be associated with a 1 base pair deletion at position 117 of the tcdC gene which leads to an increased or prolonged production of toxins A and B, and possibly the production of a binary toxin [1-3]. However, these virulence factors are not unique for Type 027 …

Single Walled Carbon Nanotubes Induce Indirect Cytotoxicity By Medium Depletion In A549 Lung Cells, Gordon Chambers, Alan Casey, Fiona Lyng, Maria Davoren, Eva Herzog (Thesis), Hugh Byrne

Articles

The ability of two types of single walled carbon nanotubes (SWCNT), namely Arc Discharge (AD) and HiPco® single walled carbon nanotubes, to induce an indirect cytotoxicity in A549 lung cells by means of medium depletion was investigated. The nanotubes were dispersed in a commercial cell culture medium and subsequently removed by centrifugation and filtration. Spectroscopic analysis confirmed the removal of the nanotubes and showed differing degrees of alteration of the composition of the medium upon the removal of the nanotubes. The ability to induce an indirect cytotoxic effect by altering the medium was evaluated using two endpoints, namely the Alamar …

Polyomaviruses In Pediatric Renal Disease, Julie Moran

Masters

BK virus (BKV) and JC virus (JCV) are ubiquitous in the human population and frequently reactivate during periods of immune suppression. The emergence of polyomavirus-associated diseases among renal and hematopoietic stem cell transplant recipients has highlighted the lack of knowledge of the natural history of BKV and JCV in humans. In the pediatric population, in particular, immune suppressive therapy is commonly used as a treatment for primary renal diseases. To date, there has been limited investigation of polyomavirus reactivation in pediatric patients with renal transplants or with primary renal disease. Given the association of polyomavirus reactivation with the use of …

Ecotoxicological Investigations Of Pharmaceutical Compounds On A Battery Of Freshwater Test Species., Elaine Minagh

Masters

Currently interest in pharmaceuticals as potential environmental contaminants has increases significantly. This is due to the awareness of the possible adverse effects to human health and the environment caused by such contaminants. Within the past few years, the highly prescribed antidepressants, selective serotonin reuptake inhibitors (SSRI), have received attention as their occurrence in the environment has been recently documented. Prior to this, there was very little known about the ecotoxicity of SSRIs, and in particular sertraline hydrochloride. Similarly the cholesterol-lowering drugs, known as statins are among the most frequently prescribed agents in Ireland and worldwide for the treatment of coronary …

Use Of Trees By The Texas Ratsnake (Elaphe Obsoleta) In Eastern Texas, Josh B. Pierce, Robert R. Fleet, Lance D. Mcbrayer, D. Craig Rudolph

Biology: Faculty Publications

We present information on the use of trees by Elaphe obsoleta (Texas Ratsnake) in a mesic pine-hardwood forest in eastern Texas. Using radiotelemetry, seven snakes (3 females, 4 males) were relocated a total of 363 times from April 2004 to May 2005, resulting in 201 unique locations. Snakes selected trees containing cavities and used hardwoods and snags for a combined 95% of arboreal locations. Texas Ratsnake arboreal activity peaked during July and August, well after the peak of avian breeding activity, suggesting arboreal activity involves factors other than avian predation.

Biological Networks: Modeling And Structural Analysis, Emad Y. Ramadan

Computer Science Theses & Dissertations

Biological networks are receiving increased attention due to their importance in understanding life at the cellular level. There exist many different kinds of biological networks, and different models have been proposed for them. In this dissertation we focus on suitable network models for representing experimental data on protein interaction networks and protein complex networks (protein complexes are groups of proteins that associate to accomplish some function in the cell), and to design algorithms for exploring such networks. Our goal is to enable biologists to identify the general principles that govern the organization of protein-protein interaction networks and protein complex networks. …

Potential Of Sequential Cropping In The Management Of Root-Knot Nematodes In Okra, A. N. Mweke, J. W. Kimenju, A. A. Seif, E. W. Mutitu, G. K. Mutua

All Peer-Reviewed Publications

The response of different crops to a mixed population of root-knot nematodes, Meloidogyne javanica and M. incognita and their potential as suppressants in sequential cropping systems was evaluated in greenhouse and field experiments. Crops rated as resistant were five maize cultivars, four sorghum cultivars, two millet varieties, guwar and two pigeonpea cultivars which had galling indices ranging between 1.4-3.6. cowpea cv. K80 was rated as moderately resistant with a galling index of 4 while greengram and cowpea cv. KKI were rated as susceptible with galling indices ranging from 5.6 to 7.4. Four crops namely sweetcorn, babycorn, maize cv. Pioneer (Ph3253) …

An Investigation Into The I-Stat Chem8+ System For The Measurement Of Sodium, Potassium, Urea & Creatinine., Gene Ferris

Theses

In the hospital environment Point of Care Testing (POCT) can be an invaluable tool in Emergency departments, Theatres, Intensive Care Units and Paediatric wards by providing rapid test results without the need for transport and laboratory processing. The study design included the collection and duplicate analysis of patient samples firstly using the i-STAT and then on the Architect c8000, a routine laboratory analyser. Statistical analysis was performed in order to determine if there is a statistically significant difference in results between the i-STAT POCT system and current laboratory instrumentation. The parameters analysed were the vital biochemical parameters Sodium (Na), Potassium …

Analysis Of Adenovirus And Bovine Coronavirus., Kevin Lane

Theses

This investigation involved the analysis of selected gastroenteritis viruses, adenovirus and bovine coronavirus, obtained from faecal samples, collected from hospital and diagnostic laboratories respectively in Cork city, Ireland. The viruses isolated from these samples were subjected to analysis using cell culture and nucleic acid extraction. In addition adenovirus was analysed using PCR and PCR followed by restriction endonuclease digest. Many samples contained more than one gastroenteritis virus, the virus of interest and a natural co-infection with rotavirus species. Rotavirus infections in Ireland have been extensively studied and we were interested in studying singly and doubly infect samples.

Bovine enteric coronavirus …

Epidemiology And Drug Resistant Profiles Of Candida Species, In Cork Hospitals., Emma Mccurtin

Theses

Candida causes superficial infections in healthy individuals; however in the immunocompromised host Candida can cause invasive, systemic infections and is a significant cause of morbidity and mortality. This is not due to a more virulent phenotype but to a weakened immune system unable to fight this opportunistic pathogen. The immunocompromised population is ever increasing, due to medical advancements and more aggressive treatments, and hence is the need for epidemiological data of these potentially life threatening infections. The aim of this study was to provide an epidemiological snapshot, of Candida infections from the immunocompromised population in Cork hospitals. Surveillance programmes from …

Design Of A Multiplex Pcr Assay For The Detection Of Neisseria Gonorrhoeae., Elizabeth J. O'Callaghan

Theses

The incidence of N. gonorrhoeae infections in Ireland has been steadily increasing since 2003. Culture is currently the preferred method of diagnosis, however the sensitivity of culture can be low. In recent years there has been increased interest in non-culture techniques such as polymerase chain reaction (PCR). Many of the PCR assays available have been shown to cross-react with commensal organisms, producing false positive results. This study aimed to improve the detection of N. gonorrhoeae by designing a multiplex PCR assay that used two N. gonorrhoeae genes as targets, thereby providing dual detection and confirmation of a positive result. PCR …

Gender Bias Of Cardiovascular Risk In Caucasian Type Ii Diabetics: A Haemostatic Explanation?, William Quirke

Theses

People with type II diabetes are disproportionately affected by cardiovascular disease compared to those without diabetes. The relative risk of cardiovascular disease caused by type II diabetes is higher in females than in males. This risk has not been fully explained by traditional risk factors and attention has turned to the possible role of haemostatic abnormalities in explaining the excess cardiovascular morbidity and mortality among diabetic females. We examined specific parameters of the coagulation (factor VII, factor VIII, von Willebrand factor, fibrinogen) and fibrinolytic (plasminogen activator inhibitor- 1, thrombin-activatable fibrinolysis inhibitor) system in 113 Irish Caucasian type II diabetics to …

Regulation Of Exercise Intensity In Well-Trained Cyclists, Chris Abbiss

Theses: Doctorates and Masters

It is known that exercise performance may be improved if athletes select the optimal regulation of pace during exercise. Despite this knowledge, the best possible strategies that may delay the development of fatigue and ensure optimal performance during a variety of exercise tasks are not yet known. Thus, the primary purpose of the six research studies contained within this doctoral thesis was to describe pacing strategies and improve our understanding of factors that influence the regulation of intensity during self-paced exercise.

The Evaluation Of Midazolam On Head Injured Patients In The Prehospital Setting, Dragana Klinac

Theses: Doctorates and Masters

Midazolam (Hypnovel ®) is the only sedating agent used by paramedics at St John Ambulance Service W.A. in the management of many conditions including seizure activities, antisocial or uncontrollable behaviours, back pain incidents and head injuries. Midazolam, with a rapid absorption, fast onset of action and short duration on neurological activity, has been accepted as a safe and effective agent in prehospital treatment since the late-1990s. Often, if a patient is not complying with treatment or is uncontrollable or aggressive, paramedics are required to sedate the individual. This study primarily examines the use of midazolam for the sedation of unmanageable …

Organochlorine Pesticide Contamination And Its Potential Effects On Eggshell Characteristics Of Dickcissels (Spiza Americana), Bridget Wall '08

Honors Projects

Dickcissels (Spiza americana) are small, sparrow-like songbirds that nest in grasslands in the U.S. and winter in Venezuela. Fanners in Venezuela intentionally spray dickcissel flocks with organochlorine (DC) and other illegal pesticides in an attempt to kill them when they feed in both rice and sorghum fields. Previous studies have shown that organochlorine (DC) pesticide' contaminants (e.g., DDT) have significantly reduced eggshell thickness in eagles and falcons.. Although DDT was banned in the United States more than twenty years ago, DC compounds and their metabolites still persist in wildlife, possibly resulting in reduced reproductive success and in disrupted endocrine systems …