Life Sciences Commons^™

Improved Peak Detection And Quantification Of Mass Spectrometry Data Acquired From Surface-Enhanced Laser Desorption And Ionization By Denoising Spectra With The Undecimated Discrete Wavelet Transform, Kevin R. Coombes, Spiros Tsavachidis, Jeffrey S. Morris, Keith A. Baggerly, Henry M. Kuerer

Jeffrey S. Morris

Background: Mass spectrometry, especially surface enhanced laser desorption and ionization (SELDI) is increasingly being used to find disease-related proteomic patterns in complex mixtures of proteins derived from tissue samples or from easily obtained biological fluids such as serum, urine, or nipple aspirate fluid. Questions have been raised about the reproducibility and reliability of peak quantifications using this technology. For example, Yasui and colleagues opted to replace continuous measures of the size of a peak by a simple binary indicator of its presence or absence in their analysis of a set of spectra from prostate cancer patients.

Methods: We collected nipple …

Pooling Information Across Different Studies And Oligonucleotide Microarray Chip Types To Identify Prognostic Genes For Lung Cancer., Jeffrey S. Morris, Guosheng Yin, Keith A. Baggerly, Chunlei Wu, Li Zhang

Jeffrey S. Morris

Our goal in this work is to pool information across microarray studies conducted at different institutions using two different versions of Affymetrix chips to identify genes whose expression levels offer information on lung cancer patients’ survival above and beyond the information provided by readily available clinical covariates. We combine information across chip types by identifying “matching probes” present on both chips, and then assembling them into new probesets based on Unigene clusters. This method yields comparable expression level quantifications across chips without sacrificing much precision or significantly altering the relative ordering of the samples. We fit a series of multivariable …

Heat And Mass Transfer During Baking : Product Quality Aspects, H Hadiyanto Et Al

Hadiyanto

Most food product qualities are developed during heating processes. Therefore the internal heating and mass transfer of water are important aspects in food processing. Heating of food products is mostly induced by convection heating. However, the number applications of convective heating in combination with microwave heating are growing. Convection heating only promotes heating on the surface while microwave induce internal heating. This paper focuses on effect of convection heating sources to changes of quality properties in bakery products such as brownness and texture. Heat convection and conduction, and moisture migration due to diffusion and convection are the key to changes …

Community Hospital Risk Management, Vikas Singh

Vikas Singh

EXECUTIVE SUMMARY:

The Panacea community hospital in the Hot springs County, Arkansas is a big community hospital 52-inpatient beds providing medical. Surgical, mental health, pediatrics, Ob-gyn services and emergency care.

Of late there has been serious concern about the patient safety and quality of patient care delivered by the hospital. Close examination for the causes of the unsatisfactory quality of care and patient safety reveals that the hospital lacks proper and adequately supported risk management department. One employee only who is a part of the Quality Improvement cell sees the risk management program of the hospital and there is lack …

Expression Of G-Protein Inwardly Rectifying Potassium Channels (Girks) In Lung Cancer Cell Lines, Howard Plummer 3rd, Madhu Dhar, Maria Cekanova Ms, Rndr, Phd, Hildegard Schuller

Maria Cekanova MS, RNDr, PhD

BACKGROUND: Previous data from our laboratory has indicated that there is a functional link between the beta-adrenergic receptor signaling pathway and the G-protein inwardly rectifying potassium channel (GIRK1) in human breast cancer cell lines. We wanted to determine if GIRK channels were expressed in lung cancers and if a similar link exists in lung cancer. METHODS: GIRK1-4 expression and levels were determined by reverse transcription polymerase chain reaction (RT-PCR) and real-time PCR. GIRK protein levels were determined by western blots and cell proliferation was determined by a 5-bromo-2'-deoxyuridine (BrdU) assay. RESULTS: GIRK1 mRNA was expressed in three of six small …

Post-Germination Changes In Hevea Brasiliensis Seeds Proteome, Wong Pooi Fong

Wong Pooi Fong

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry methods were established and utilized to examine the changes in protein expressions associated with post-germination of Hevea brasiliensis seed. No significant differences in the total number of proteins were observed but characteristic protein spots were present in both proteomes. The mature dry seed proteome contained clusters of proteins of about 36.5 and 23 kDa at pH 4-7 and a group of basic proteins at similar to pH 10. The presence of the 23 kDa proteins was markedly reduced in the post-germinated seed proteome. Approximately 60% of the proteins noted in the germinated …

Serum Proteomics Profiling: A Young Technology Begins To Mature, Kevin R. Coombes, Jeffrey S. Morris, Jianhua Hu, Sarah R. Edmondson, Keith A. Baggerly

Jeffrey S. Morris

No abstract provided.

Methanogen Diversity Evidenced By Molecular Characterization Of Methyl Coenzyme M Reductase A (Mcra) Genes In Hydrothermal Sediments Of The Guaymas Basin, Ashita Dhillon, Mark Lever, Karen Lloyd, Daniel B. Albert, Mitchell L. Sogin, Andreas Teske

Karen Lloyd

The methanogenic community in hydrothermally active sediments of Guaymas Basin (Gulf of California, Mexico) was analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Members of the Methanomicrobiales and Methanosarcinales dominated the mcrA and 16S rRNA clone libraries from the upper 15 cm of the sediments. Within the H2/CO2- and formate-utilizing family Methanomicrobiales, two mcrA and 16S rRNA lineages were closely affiliated with cultured species of the genera Methanoculleus and Methanocorpusculum. The most frequently recovered mcrA PCR amplicons within the Methanomicrobiales did not branch with any cultured genera. Within the nutritionally versatile …

Signal In Noise: Evaluating Reported Reproducibility Of Serum Proteomic Tests For Ovarian Cancer, Keith A. Baggerly, Jeffrey S. Morris, Sarah R. Edmonson, Kevin R. Coombes

Jeffrey S. Morris

Proteomic profi ling of serum initially appeared to be dramatically effective for diagnosis of early-stage ovarian cancer, but these results have proven diffi cult to reproduce. A recent publication reported good classifi cation in one dataset using results from training on a much earlier dataset, but the authors have since reported that they did not perform the analysis as described. We examined the reproducibility of the proteomic patterns across datasets in more detail. Our analysis reveals that the pattern that enabled successful classifi cation is biologically implausible and that the method, properly applied, does not classify the data accurately. We …

Temporal Patterns In Fall Migrant Communities In Yucatan, Mexico, Jill L. Deppe, John T. Rotenberry

Jill L Deppe

We quantified temporal turnover in the composition of fall migrant landbird communities along the northern coast of the Yucatan Peninsula using Detrended Correspondence Analysis. The presence of winter residents of many migrant species at the site prevented turnover from being complete. However, early and late season transient communities shared few, if any, species in common. Point-count surveys showed greater compositional change than net surveys that included winter residents. The rate of species turnover was generally slow until the middle of the season, when it reached a maximum, and decreased again toward the end of the season as species composition began …

Influence Of Stem Cutting And Glyphosate Treatment Of Lonicera Maackii, An Exotic And Invasive Species, On Stem Regrowth And Native Species Richness, Henry R. Owen, A. L. Mcdonnell, A. M. Mounteer, B. L. Todd

Henry R. Owen

Lonicera maackii (Rupr.) Herder (Caprifoliaceae), Amur honeysuckle, is an exotic and invasive species in the United States that has quickly overtaken disturbed habitats in the eastern and midwestern United States, as well as in Ontario, Canada. A reduction of light due to its dense canopy, extended growing season compared to native species, and production of numerous basal sprouts allow L. maackii to outcompete its native counterparts. Eradication of this species can be difficult and time-consuming. This research was undertaken to identify how L. maackii influences species diversity and species re-establishment and to determine an efficient and effective eradication method. A …

Morphological Divergence Of Native And Recently Established Populations Of White Sands Pupfish (Cyprinodon Tularosa), Michael L. Collyer, James M. Novak, Craig A. Stockwell

James M. Novak

We used landmark-based geometric morphometric methods to describe patterns of body shape variation and shape covariation with size among populations of the threatened White Sands Pupfish (Cyprinodon tularosa), a species that occurs in dissimilar aquatic habitats. White Sands Pupfish populations include two genetically distinct, native populations that have been historically isolated in Salt Creek, a saline river, and Malpais Spring, a brackish spring. In addition, two populations were established approximately 30 years before this study by translocation of fish from Salt Creek to Lost River (a saline river) and Mound Spring (a brackish spring). We found significant body shape variation …

Evidence For A General Species-Time-Area Relationship, Peter B. Adler, Ethan P. White, William K. Lauenroth, Dawn M. Kaufman, Andrew Rassweiler, James A. Rusak

Ethan P White

The species–area relationship (SAR) plays a central role in biodiversity research, and recent work has increased awareness of its temporal analogue, the species– time relationship (STR). Here we provide evidence for a general species–time–area relationship (STAR), in which species number is a function of the area and time span of sampling, as well as their interaction. For eight assemblages, ranging from lake zooplankton to desert rodents, this model outperformed a sampling-based model and two simpler models in which area and time had independent effects. In every case, the interaction term was negative, meaning that rates of species accumulation in space …

Brain Mappings Of The Arithmetic Processing In Children And Adults., Fábio T. Rocha, Armando F. Rocha, Eduardo Massad, Renee Menezes

Armando F Rocha

Despite the increasing number of experimental mapping showing that human arithmetic cognition is supported by widely spread neural circuits; the theoretical reasoning about these data remains mostly metaphorical and guided by a connectionist approach. Although neurons at distinct areas in the brain are assumed to take charge of different duties in the solution of the experimental task, the results are always discussed by hypothesizing some association between the different areas without questioning any difference of behavior at the level of the neurons at each of these areas. Here, the brain is assumed as Distributed Intelligent Processing System (DIPS) formed by …

Houses Of Straw, David A. Bainbridge

David A Bainbridge

Straw bale building offers high performance at a low cost. Bale building, developed on the grasslands of Nebraska at turn of the last century, has been rediscovered. High insulation values and high interior thermal mass make straw bales a good choice for passive solar design.

Effects Of Seedling Source Variation On Nitrogen Metabolism And Biomass Production In Albizia Lebbek, Ajeet Kaur, Azamal Husen Dr., T.C. Pokhriyal

Dr. Azamal Husen

No abstract provided.

Mathematical Modeling Of The Hypothalamic-Pituitary-Adrenal System Activity, Zeljko D. Cupic

Zeljko D Cupic

No abstract provided.

Use Of Critical Incident Reports In Medical Education: A Perspective, William T. Branch Jr. Md, Macp

William T.Branch Jr.MD

Critical incident reports are now being widely used in medical education. They are short narrative accounts focusing on the most important professional experiences of medical students, residents, and other learners. As such, critical incident reports are ideally suited for addressing values and attitudes, and teaching professional development. This manuscript describes critical incident reports and gives examples of their use, provides a theoretical underpinning that explains their effectiveness, and describes the educational impacts of critical incident reports and similar methods that use reflective learning. The author recommends critical incident reports as an especially effective means to address learners' most deeply held …

Viable Blastocystis Cysts In Scottish And Malaysian Sewage Samples, Tan Tian Chye

Tan Tian Chye

Blastocystis cysts were detected in 38% (47/123) (37 Scottish, 17 Malaysian) of sewage treatment works. Fifty percent of influents (29% Scottish, 76% Malaysian) and 28% of effluents (9% Scottish, 60% Malaysian) contained viable cysts. Viable cysts, discharged in effluent, provide further evidence for the potential for waterborne transmission of Blastocystis.

More Than Meets The Eye: Investigating Imagery Type, Direction, And Outcome, Sanna Nordin, Jennifer Cumming

Jennifer Cumming

The effects of imagery direction on self-efficacy and performance in a dart throwing task were examined. Two imagery types were investigated: skill-based cognitive specific (CS) and confidence-based motivational general-mastery (MG-M). Seventy-five novice dart throwers were randomly allocated to one of three conditions: (a) facilitative imagery, (b) debilitative imagery, or (c) control. After 2 imagery interventions, the debilitative imagery group rated their self-efficacy significantly lower than the facilitative group and performed significantly worse than either the facilitative group or the control group. Efficacy ratings remained constant across trials for the facilitative group, but decreased significantly for both the control group and …

Professional Dancers Describe Their Imagery: Where, When, What, Why, And How, Sanna M. Nordin, Jennifer Cumming

Jennifer Cumming

In-depth semistructured interviews were conducted with 14 male and female professional dancers from several dance forms. Interviews were primarily based in the 4 Ws framework (Munroe, Giacobbi, Jr., Hall, & Weinberg, 2000), which meant exploring Where, When, Why, and What dancers image. A dimension describing How the dancers employed imagery also emerged. What refers to imagery content, and emerged from two categories: Imagery Types and Imagery Characteristics. Why represents the reason an image is employed and emerged from five categories: Cognitive Reasons, Motivational Reasons, Artistic Reasons, Healing Reasons, and No reason – Triggered Imagery. There were also large individual differences …

Detection Of Oncogenic Mutations In The Egfr Gene In Lung Adenocarcinoma With Differential Sensitivity To Egfr Tyrosine Kinase Inhibitors, Torstein Tengs

Dr. Torstein Tengs

The complete sequencing of the human genome and the development of molecularly targeted cancer therapy have promoted efforts to identify systematically the genetic alterations in human cancer. By high-throughput sequencing of tyrosine kinase genes in human non-small-cell lung cancer, we identified somatic mutations in the kinase domain of the epidermal growth factor receptor tyrosine kinase gene (EGFR) that are correlated with clinical response to EGFR tyrosine kinase inhibitors (TKIs). We have shown that these mutant forms of EGFR induce oncogenic transformation in different cellular systems. Cells whose growth depends on EGFR with mutations in exons 19 and 21 are sensitive …

Effects Of Dissolved Sulfide, Ph, And Temperature On Growth And Survival Of Marine Hyperthermophilic Archaea, Karen Lloyd, Virginia P. Edgcomb, Stephen J. Molyneaux, Simone Böer, Carl O. Wirsen, Michael S. Atkins, Andreas Teske

Karen Lloyd

The ability of metabolically diverse hyperthermophilic archaea to withstand high temperatures, low pHs, high sulfide concentrations, and the absence of carbon and energy sources was investigated. Close relatives of our study organisms, Methanocaldococcus jannaschii, Archaeoglobus profundus, Thermococcus fumicolans, and Pyrococcus sp. strain GB-D, are commonly found in hydrothermal vent chimney walls and hot sediments and possibly deeper in the subsurface, where highly dynamic hydrothermal flow patterns and steep chemical and temperature gradients provide an ever-changing mosaic of microhabitats. These organisms (with the possible exception of Pyrococcus strain GB-D) tolerated greater extremes of low pH, high sulfide concentration, and high temperature …

Lack Of Antigen-Specific Tissue Remodeling In Mice Deficient In The Macrophage Galactose-Type Calcium-Type Lectin 1/Cd301a., Thandi M. Onami, K. Sato, Y. Imai, N. Higashi, Y. Kumamoto, S. M. Hedrick, T. Irimura

Thandi M. Onami

Macrophage galactose-type C-type lectins (MGLs), which were recently named CD301, have 2 homologues in mice: MGL1 and MGL2. MGLs are expressed on macrophages and immature dendritic cells. The persistent presence of granulation tissue induced by a protein antigen was observed in wild-type mice but not in mice lacking an endogenous, macrophage-specific, galactose-type calcium-type lectin 1 (MGL1) in an air pouch model. The anti-MGL1 antibody suppressed the granulation tissue formation in wild-type mice. A large number of cells, present only in the pouch of MGL1-deficient mice, were not myeloid or lymphoid lineage cells and the number significantly declined after administration of …

Molecular Characterization Of A Isoenzyme Of The Targeting Peptide Degrading Protease, Prep2- Catalysis, Subcellular Localization, Expression And Evolution, S. Bhushan, A. Stahl, S. Nilsson, B. Lefebvre, D. Mcwilliams, S.J. Wright, M. Seki, D.A. Liberles, K. Shinozaki, Barry D. Bruce, M. Boutry, E. Glaser

Barry D. Bruce

We have previously identified a zinc metalloprotease involved in the degradation of mitochondrial and chloroplast targeting peptides, the presequence protease (PreP). In the Arabidopsis thaliana genomic database, there are two genes that correspond to the protease, the zinc metalloprotease (AAL90904) and the putative zinc metalloprotease (AAG13049). We have named the corresponding proteins AtPreP1 and AtPreP2, respectively. AtPreP1 and AtPreP2 show significant differences in their targeting peptides and the proteins are predicted to be localized in different compartments. AtPreP1 was shown to degrade both mitochondrial and chloroplast targeting peptides and to be dual targeted to both organelles using an ambiguous targeting …

Girls On The Run: Preparing Girls For A Lifetime Of Self-Respect And Healthy Living, Mary Schutten

Mary C. Schutten

No abstract provided.

Reduced Macrophage Apoptosis Is Associated With Accelerated Atherosclerosis In Low-Denstiy Lipoprotein Receptor-Null Mice, Michael Sinensky, J. Liu, D. P. Thweke, Y. R. Su, M. F. Linton, S. Fazio

Michael Sinensky

Objective— The majority of apoptotic cells in atherosclerotic lesions are macrophages. However, the pathogenic role of macrophage apoptosis in the development of atherosclerosis remains unclear. Elevated expression of Bax, one of the pivotal proapoptotic proteins of the Bcl-2 family, has been found in human atherosclerotic plaques. Activation of Bax also occurs in free cholesterol-loaded and oxysterol-treated mouse macrophages. In this study, we examined the effect of Bax deficiency in bone marrow-derived leukocytes on the development of atherosclerosis in low-density lipoprotein receptor-null (LDLR−/−) mice. Methods and Results— Fourteen 8-week-old male LDLR−/− mice were lethally irradiated and reconstituted with either wild-type (WT) …

Assessing Cultural And Ecological Variation In Ethnobiological Research: The Importance Of Gender, Jeanine M. Pfeiffer

Jeanine M. Pfeiffer

Contending that a significant portion of current ethnobiological research continues to overlook cultural variation in traditional ecological knowledge (TEK) and practice, this paper explores the potential impacts of gender-imbalanced research on data collection, hypothesis testing, and the formulation and application of ethnobiological inventories and theories. A multidisciplinary review of over 220 studies addresses commonly held stereotypes underlying gender-imbalanced field research and demonstrates the need for more inclusive, finely-tuned studies which disaggregate indigenous knowledge and practice by gender. The paper outlines factors underlying gender-based spatial and temporal variation in ecosystem exposure and traditional ecological knowledge in rural societies worldwide, and discusses …