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Search Results: 1 - 10 of 254868 matches for " David L. Stenoien "
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Enhanced top-down characterization of histone post-translational modifications
Zhixin Tian, Nikola Toli?, Rui Zhao, Ronald J Moore, Shawna M Hengel, Errol W Robinson, David L Stenoien, Si Wu, Richard D Smith, Ljiljana Pa?a-Toli?
Genome Biology , 2012, DOI: 10.1186/gb-2012-13-10-r86
Abstract: Histones are important chromatin proteins that act as spools to package and order DNA into structural and manageable chromosomes. Core histones are modified by multiple post-translational modifications (PTMs) such as lysine acetylation, lysine or arginine methylation, and serine or threonine phosphorylation, among others. These PTMs generate a 'histone code' [1] that is implicated in chromatin-related cellular processes [2] including transcription [3], replication [4], repair [5], and alternative splicing [6].Although core histones comprise only four families (H4, H2B, H2A, and H3), each family has thousands of potential isoforms generated by different combinations of PTMs and protein sequence variation. Traditional antibody-based methods target specific isoforms, typically analyzing one PTM at a time, which makes it virtually impossible to measure combinatorial modifications occurring within the same histone molecule. Recently, high-throughput bottom-up [7] and middle-down [8] proteomic methods demonstrated potential for global characterization of PTMs on histone tails. However, these methods are ill-suited for characterizing multiple PTMs dispersed along the entire protein sequence that have been previously discovered to have significant participation in chromatin regulation [2,9-11].Top-down proteomic and high-throughput approaches are clearly required to identify and quantify the modulation of multiple intra-molecular histone modifications that synergistically regulate histone functions. Recently, a global top-down study demonstrated the feasibility of intact protein analysis for this purpose by identifying more than 300 histone isoforms using extensive fractionation and customized bioinformatics for global proteome characterization [12]. In histone-focused studies, top-down approaches using an offline two-dimensional liquid chromatography (2D LC) separation and Fourier transform mass spectrometry (FTMS) characterized 34 H4 isoforms from approximately 150 μg of
Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation
Feng Yang,Katrina M. Waters,John H. Miller,Marina A. Gritsenko,Rui Zhao,Xiuxia Du,Eric A. Livesay,Samuel O. Purvine,Matthew E. Monroe,Yingchun Wang,David G. Camp II,Richard D. Smith,David L. Stenoien
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0014152
Abstract: High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation.
Availability of Information on Reptile Health and Welfare from Stores Selling Reptiles  [PDF]
David L. Williams, Rebecca Jackson
Open Journal of Veterinary Medicine (OJVM) , 2016, DOI: 10.4236/ojvm.2016.63007
Abstract: The popularity of keeping reptiles such as snakes and lizards is ever increasing. The health and welfare of these animals depends on the knowledge and understanding of their environmental and nutritional needs. But where does a new owner of these species obtain such information? This study aims to investigate what information is available in pet shops and stores for the reptile owning public and how well this information is imparted. Our findings show that there is a lot of excellent advice on the husbandry of reptiles in some shops while others offer less advice. It is hoped that through this study areas of downfall on primary knowledge can be recognized so that all shops can aspire to the highest levels of information.
Long-term phenotypic characterization of human bone marrow and adipose tissue derived mesenchymal stromal cells  [PDF]
Dean L. Glettig, David L. Kaplan
Stem Cell Discovery (SCD) , 2013, DOI: 10.4236/scd.2013.32015
Abstract:

We present methods to characterize mesenchymal stromal cells (MSC) over long time periods in vitro. The methods entail passaging cells multiple times and performing differentiation studies with the cells at each passage. Using an array of surface markers and flow cytometric quantification, the data can be correlated to traditional measures of differentiation such as PCR and staining. Using these methods to quantify the amount of differentiation, we concluded that many common MSC markers do not specifically define MSCs with true stem cell properties. Additionally, adipose-derived as opposed to bone marrow-derived MSCs show long-term CD34+ labeling. The methods described can be used to help identify stem cell markers and to characterize the state of stem cells in vitro. Compiling these data from multiple laboratories would be helpful to determine source, extraction and culture methods needed to obtain high yields of useful stem cells.

Efficacy of a Topical Aromatic Rub (Vicks VapoRub®)-Speed of Action of Subjective Nasal Cooling and Relief from Nasal Congestion  [PDF]
Ron Eccles, Martez Jawad, David L. Ramsey, J. David Hull
Open Journal of Respiratory Diseases (OJRD) , 2015, DOI: 10.4236/ojrd.2015.51002
Abstract: Vicks VapoRub® (VVR) is a pharmaceutical preparation containing a combination of levomenthol, eucalyptus oil, turpentine oil and camphor as active ingredients, and thymol, cedarwood oil, and white soft paraffin as excipients. VVR is a petrolatum-based ointment to be either applied topically to the chest, throat, and back or added to hot water and the aromatic vapours inhaled. When used topically, the actives are evaporated by body temperature and inspired. The main therapeutic effects are the feeling of relief from nasal congestion and relief from cough. These were primarily experienced by patients as the trigeminal and olfactory impact of the aromatics and were hypothesized to be experienced within minutes. This was a randomized, single-(Investigator) blind, controlled, 2-arm (VVR vs. petrolatum), parallel design pilot study in 50 otherwise healthy adult patients suffering from common cold and experiencing nasal congestion. Speed to detection of a sensation of nasal cooling and nasal decongestion was assessed following application of the recommended amount of product. The time to first experience of a sensation of nasal cooling was significantly (p < 0.001) faster for patients who received VVR compared to control (median times of 23 and 99 seconds respectively). VVR delivered a statistically significant sensation of nasal cooling at all times from 12 seconds to 15 minutes after product application. The time to first experience of a sensation of nasal decongestion was significantly (p = 0.0102) faster for patients who received VVR compared to control (median times of 62 and 126 seconds respectively). VVR delivered a statistically significant sensation of nasal decongestion at all times from 62 seconds to 15 minutes after product application. No adverse events were reported during the study. Conclusion: Patients using Vicks VapoRub® as directed experienced significant differences from control for sensation of nasal cooling in 12 seconds and the sensation of nasal decongestion in 62 seconds.
A Patient Bill of Rights for Psychotropic Prescription: A Call for a Higher Standard of Care  [PDF]
Barry L. Duncan, David O. Antonuccio
International Journal of Clinical Medicine (IJCM) , 2011, DOI: 10.4236/ijcm.2011.24061
Abstract: The pharmaceutical industry has made it very difficult to know what the clinical trial evidence actually is regarding psychotropics. Consequently, primary care physicians and other front-line practitioners are at a disadvantage when attempting to adhere to the ethical and scientific mandates of evidence based prescriptive practice. This article calls for a higher standard of prescriptive care derived from a risk/benefit analysis of clinical trial evidence. The authors assert that current prescribing practices are often empirically unsound and unduly influenced by pharmaceutical company interests, resulting in unnecessary risks to patients. In the spirit of evidenced based medicine’s inclusion of patient values as well as the movement toward health home and integrated care, we present a patient bill of rights for psychotropic prescription. We then offer guidelines to raise the bar of care equal to the available science for all prescribers of psychiatric medications.
Knight’s Tours on 3 x n Chessboards with a Single Square Removed  [PDF]
Amanda M. Miller, David L. Farnsworth
Open Journal of Discrete Mathematics (OJDM) , 2013, DOI: 10.4236/ojdm.2013.31012
Abstract: The following theorem is proved: A knights tour exists on all 3 x n chessboards with one square removed unless: n is even, the removed square is (i, j) with i + j odd, n = 3 when any square other than the center square is removed, n = 5, n = 7 when any square other than square (2, 2) or (2, 6) is removed, n = 9 when square (1, 3), (3, 3), (1, 7), (3, 7), (2, 4), (2, 6), (2, 2), or (2, 8) is removed, or when square (1, 3), (2, 4), (3, 3), (1, n – 2), (2, n – 3), or (3, n – 2) is removed.
Counting the Number of Squares Reachable in k Knight’s Moves  [PDF]
Amanda M. Miller, David L. Farnsworth
Open Journal of Discrete Mathematics (OJDM) , 2013, DOI: 10.4236/ojdm.2013.33027
Abstract:

Using geometric techniques, formulas for the number of squares that require k moves in order to be reached by a sole knight from its initial position on an infinite chessboard are derived. The number of squares reachable in exactly k moves are 1, 8, 32, 68, and 96 for k = 0, 1, 2, 3, and 4, respectively, and 28k – 20 for k ≥ 5. The cumulative number of squares reachable in k or fever moves are 1, 9, 41, and 109 for k = 0, 1, 2, and 3, respectively, and 14k2 6k + 5 for k ≥ 4. Although these formulas are known, the proofs that are presented are new and more mathematically accessible then preceding proofs.

Testing for a Zero Proportion  [PDF]
Jonathan R. Bradley, David L. Farnsworth
Open Journal of Statistics (OJS) , 2013, DOI: 10.4236/ojs.2013.34029
Abstract: Tests for a proportion that may be zero are described. The setting is an environment in which there can be misclassifications or misdiagnoses, giving the possibility of nonzero counts from false positives even though no real examples may exist. Both frequentist and Bayesian tests and analyses are presented, and examples are given.
Fitting Full X-Ray Diffraction Patterns for Quantitative Analysis: A Method for Readily Quantifying Crystalline and Disordered Phases  [PDF]
Steve J. Chipera, David L. Bish
Advances in Materials Physics and Chemistry (AMPC) , 2013, DOI: 10.4236/ampc.2013.31A007
Abstract:

Fitting of full X-ray diffraction patterns is an effective method for quantifying abundances during X-ray diffraction (XRD) analyses. The method is based on the principal that the observed diffraction pattern is the sum of the individual phases that compose the sample. By adding an internal standard (usually corundum) to both the observed patterns and to those for individual pure phases (standards), all patterns can all be normalized to an equivalent intensity based on the internal standard intensity. Using least-squares refinement, the individual phase proportions are varied until an optimal match is reached. As the fitting of full patterns uses the entire pattern, including background, disordered and amorphous phases are explicitly considered as individual phases, with their individual intensity profiles or “amorphous humps” included in the refinement. The method can be applied not only to samples that contain well-ordered materials, but it is particularly well suited for samples containing amorphous and/or disordered materials. In cases with extremely disordered materials where no crystal structure is available for Rietveld refinement or there is no unique intensity area that can be measured for a traditional RIR analysis, full-pattern fitting may be the best or only way to readily obtain quantitative results. This approach is also applicable in cases where there are several coexisting highly disordered phases. As all phases are considered as discrete individual components, abundances are not constrained to sum to 100%.

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