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Search Results: 1 - 10 of 46398 matches for " Michael Dean "
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Surface Characterization of As-Spun and Supercontracted Nephila clavipes Dragline Silk  [PDF]
Benoit Faugas, Michael S. Ellison, Delphine Dean, Marian S. Kennedy
Journal of Surface Engineered Materials and Advanced Technology (JSEMAT) , 2013, DOI: 10.4236/jsemat.2013.33A004
Abstract:

Dragline spider silks have relatively high mass-based mechanical properties (tensile strength, elongation to break and rupture energy) and are environmentally responsive (supercontraction). In order to produce new synthetic fibers with these properties, many research groups have focused on identifying the chemical composition of these fibers and the structure of the fiber core. Since each fiber also has an outer skin, our study will provide a detailed understanding of the silk surface morphology, the response of the surface morphology to environmental conditions and processing variables, and also determine if the silk surface has a definitive patterning of charged amino acids. Specifically, by using force microscopy and functionalized nanoparticles, the present study examines 1) how the silk surface (topography, average roughness) is altered due to prior mechanical loading (viz. reeling speed), 2) alterations in morphology due to environmental conditions (supercontraction, storage time), and 3) the negatively and positively charged regions along with the surface using both force and nanoparticle mapping. Roughness data taken on dragline silk collected from Nephila clavipes spiders revealed that the surface comprised both smooth (5 nm RMS) and rough (65 nm RMS) regions. Supercontracted silk (from immersion in0.01 MPBS during AFM testing) showed higher surface roughness values compared to spider silk tested in the air, indicating that the surface might be reorganized during supercontraction. No correlation was found between surface roughness and neither collection speed nor aging time for the as-spun or supercontracted fiber, demonstrating the surface stability of the dragline silk over time in terms of roughness. Both the force microscopy and the nanoparticle methods suggested that the density of negatively charged amino acids (glutamic acid, aspartic acid) was higher than that of the positively charged amino acids (lysine, asparagine, and histidine).

Haplotype structure and linkage disequilibrium in chemokine and chemokine receptor genes
Vanessa J Clark, Michael Dean
Human Genomics , 2004, DOI: 10.1186/1479-7364-1-4-255
Abstract: SNP haplotypes, estimated from unphased genotypes using the Expectation-Maximization-algorithm, are described in a cluster of four CC-chemokine receptor genes (CCR3, CCR2, CCR5 and CCRL2) on chromosome 3p21, and a cluster of three CC-chemokine genes [MPIF-1 (CCL23) PARC (CCL18) and MIP- 1α (CCL3)] on chromosome 17q11-12. The 32 base pair (bp) deletion in exon 4 of CCR5 was also included in the haplotype analysis of 3p21. A total of 87.5 per cent of the variation of 14 biallelic loci scattered over 150 kilobases of 3p21 is explained by 11 haplotypes which have a frequency of at least 1 per cent in the total sample. An analysis of haplotype blocks in this region indicates recombination between CCR2 and CCR5, although long-range pairwise linkage disequilibrium across the region appears to remain intact on two common haplotypes. A reduced-median network demonstrates a clear relationship between 3p21 haplotypes, rooted by the putative ancestral haplotype determined by direct sequencing of four primate species. Analysis of six SNPs on 17q11-12 indicates that 97.5 per cent of the variation is explained by 15 haplotypes, representing at least 1 per cent of the total sample. Additionally, a possible signature of selection at a non-synonymous coding SNP (M106V) in the MPIF-1 (CCL23) gene warrants further study. We anticipate that the results of this study of chemokine and chemokine receptor variation will be applicable to more extensive surveys of long-range haplotype structure in these gene regions and to association studies of HIV-1 disease and cancer.
Characterisation of SNP haplotype structure in chemokine and chemokine receptor genes using CEPH pedigrees and statistical estimation
Vanessa J Clark, Michael Dean
Human Genomics , 2004, DOI: 10.1186/1479-7364-1-3-195
Abstract: For the 3p21 single nucleotide polymorphism (SNP) data, haplotypes determined by pedigree analysis and haplotypes generated by the EM algorithm were nearly identical. Linkage disequilibrium, measured by the D' statistic, was nearly maximal across the 150 kb region, with complete disequilibrium maintained at the extremes between CCR3-Y17Y and CCRL2-1243V. D'-values calculated from estimated haplotypes on 3p21 had high concordance with pairwise comparisons between pedigree-phased chromosomes. Conversely, there was less agreement between analyses of haplotype frequencies and linkage disequilibrium using estimated haplotypes when compared with pedigree-phased haplotypes of SNPs on chromosome 17q11-12. These results suggest that, while estimations of haplotype frequency and linkage disequilibrium may be relatively simple in the 3p21 chemokine receptor cluster in population samples, the more complex environment on chromosome 17q11-12 will require a higher resolution haplotype analysis.
Molecular Cloning and Characterization of the Human ErbB4 Gene: Identification of Novel Splice Isoforms in the Developing and Adult Brain
Wei Tan,Michael Dean,Amanda J. Law
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0012924
Abstract: ErbB4 is a growth factor receptor tyrosine kinase essential for neurodevelopment. Genetic variation in ErbB4 is associated with schizophrenia and risk-associated polymorphisms predict overexpression of ErbB4 CYT-1 isoforms in the brain in the disorder. The molecular mechanism of association is unclear because the polymorphisms flank exon 3 of the gene and reside 700 kb distal to the CYT-1 defining exon. We hypothesized that the polymorphisms are indirectly associated with ErbB4 CYT-1 via splicing of exon 3 on the CYT-1 background. We report via cloning and sequencing of adult and fetal human brain cDNA libraries the identification of novel splice isoforms of ErbB4, whereby exon 3 is skipped (del.3). ErbB4 del.3 transcripts exist as CYT-2 isoforms and are predicted to produce truncated proteins. Furthermore, our data refine the structure of the human ErbB4 gene, clarify that juxtamembrane (JM) splice variants of ErbB4, JM-a and JM-b respectively, are characterized by the replacement of a 75 nucleotide (nt) sequence with a 45-nt insertion, and demonstrate that there are four alternative exons in the gene. Our analyses reveal that novel splice variants of ErbB4 exist in the developing and adult human brain and, given the failure to identify ErbB4 del.3 CYT-1 transcripts, suggest that the association of risk polymorphisms in the ErbB4 gene with CYT-1 transcript levels is not mediated via an exon 3 splicing event.
The ABC transporter gene family of Daphnia pulex
Armin Sturm, Phil Cunningham, Michael Dean
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-170
Abstract: We identified 64 ABC proteins in the Daphnia genome, which possesses members of all current ABC subfamilies A to H. To unravel phylogenetic relationships, ABC proteins of Daphnia were compared to those from yeast, worm, fruit fly and human. A high conservation of Daphnia of ABC transporters was observed for proteins involved in fundamental cellular processes, including the mitochondrial half transporters of the ABCB subfamily, which function in iron metabolism and transport of Fe/S protein precursors, and the members of subfamilies ABCD, ABCE and ABCF, which have roles in very long chain fatty acid transport, initiation of gene transcription and protein translation, respectively. A number of Daphnia proteins showed one-to-one orthologous relationships to Drosophila ABC proteins including the sulfonyl urea receptor (SUR), the ecdysone transporter ET23, and the eye pigment precursor transporter scarlet. As the fruit fly, Daphnia lacked homologues to the TAP protein, which plays a role in antigene processing, and the cystic fibrosis transmembrane conductance regulator (CFTR), which functions as a chloride channel. Daphnia showed two proteins homologous to MDR (multidrug resistance) P-glycoproteins (ABCB subfamily) and six proteins homologous to MRPs (multidrug resistance-associated proteins) (ABCC subfamily). However, lineage specific gene duplications in the ABCB and ABCC subfamilies complicated the inference of function. A particularly high number of gene duplications were observed in the ABCG and ABCH subfamilies, which have 23 and 15 members, respectively.The in silico characterisation of ABC transporters in the Daphnia pulex genome revealed that the complement of ABC transporters is as complex in crustaceans as that other metazoans. Not surprisingly, among currently available genomes, Daphnia ABC transporters most closely resemble those of the fruit fly, another arthropod.ATP-binding cassette (ABC) proteins constitute one of the largest protein superfamilies and a
Translating clinical training into practice in complex mental health systems: Toward opening the 'Black Box' of implementation
Greer Sullivan, Dean Blevins, Michael R Kauth
Implementation Science , 2008, DOI: 10.1186/1748-5908-3-33
Abstract: Our experiences appear to be consonant with the implementation model proposed by Fixsen. In this paper we offer a modified version of the Fixsen model with separate components related to training and implementation.This report further reinforces what others have noted, namely that educational interventions intended to change clinical practice should employ a multilevel approach if patients are to truly benefit from new skills gained by clinicians. We utilize an implementation research model to illustrate how the aims of the second intervention were realized and sustained over the 12-month follow-up period, and to suggest directions for future implementation research. The present report attests to the validity of, and contributes to, the emerging literature on implementation research.There is an ongoing need within healthcare systems to train clinicians to deliver evidence-based care, particularly when clinicians are well past their initial training. Educational programs may be especially challenging in mental health because adequate training in many therapeutic techniques, such as cognitive behavioral therapy or psychosocial rehabilitation skills, is typically time consuming and labor intensive for both the trainer and trainee. Once clinicians are trained, implementing new practices in treatment settings in complex health systems poses additional challenges [1-3].In this debate paper, we describe a series of training interventions for mental health providers undertaken by the Department of Veterans Affairs (VA) South Central Mental Illness Research, Education, and Clinical Center (SC MIRECC) in a large, geographically dispersed network of care, Veterans Integrated Service Network 16 (VISN 16). The experience we gained from these interventions has informed our thinking about training and implementation basics. Now we are preparing to test some of the implementation components that we have delineated through our direct experiences.The first intervention consisted of a
Birkhoff's Theorem for Panstochastic Matrices
Dean L. Alvis,Michael K. Kinyon
Mathematics , 1999,
Abstract: The panstochastic analogue of Birkhoff's Theorem on doubly-stochastic matrices is proved in the case $n=5$. It is shown that this analogue fails when $n>1$, $n \ne 5$.
Designing and Deploying Online Field Experiments
Eytan Bakshy,Dean Eckles,Michael S. Bernstein
Computer Science , 2014,
Abstract: Online experiments are widely used to compare specific design alternatives, but they can also be used to produce generalizable knowledge and inform strategic decision making. Doing so often requires sophisticated experimental designs, iterative refinement, and careful logging and analysis. Few tools exist that support these needs. We thus introduce a language for online field experiments called PlanOut. PlanOut separates experimental design from application code, allowing the experimenter to concisely describe experimental designs, whether common "A/B tests" and factorial designs, or more complex designs involving conditional logic or multiple experimental units. These latter designs are often useful for understanding causal mechanisms involved in user behaviors. We demonstrate how experiments from the literature can be implemented in PlanOut, and describe two large field experiments conducted on Facebook with PlanOut. For common scenarios in which experiments are run iteratively and in parallel, we introduce a namespaced management system that encourages sound experimental practice.
Goodman’s New Riddle of Induction  [PDF]
Dean Lubin
Open Journal of Philosophy (OJPP) , 2012, DOI: 10.4236/ojpp.2012.21009
Abstract: In this paper, I consider Goodman’s new riddle of induction and how we should best respond to it. Noticing that all the emeralds so far observed are green, we infer (project) that all emeralds are green. However, all emeralds so far observed are also grue, so we could also infer that they are grue. Only one of these inductive inferences or projections could, however, be valid. For the hypothesis that all emeralds are green predicts that the next observed emerald will be green; whereas the hypothesis that they are grue predicts that it will blue. Goodman’s new riddle is the problem of saying why the inductive inference involving “green” is the valid one. Goodman’s own solution appeals to the idea of entrenchment. His idea is that “green” is a more entrenched predicate than “grue” in the sense that it has figured many more times in our past projections than has “grue”. In his view, this explains why “green” is projectible (can be used in valid inductive inferences) whereas “grue” isn’t. I argue that this response doesn’t go far enough and that we additionally need an explanation of why “green” is more entrenched than “grue”—that we are otherwise left with the unsatisfactory view that its superior entrenchment is a mere linguistic accident. I try to supplement Goodman’s solution with an explanation of this kind. I argue that “grue” is not entrenched be- cause past successful inductions involving “green” show that past projections that could have been made using what I call “grue-like” predicates—predicates which are like “grue” except that the times featuring in their definitions are past—would have been unsuccessful.
Modeling Population Growth: Exponential and Hyperbolic Modeling  [PDF]
Dean Hathout
Applied Mathematics (AM) , 2013, DOI: 10.4236/am.2013.42045
Abstract:

A standard part of the calculus curriculum is learning exponential growth models. This paper, designed to serve as a teaching aid, extends the standard modeling by showing that simple exponential models, relying on two points to fit parameters do not do a good job in modeling population data of the distant past. Moreover, they provide a constant doubling time. Therefore, the student is introduced to hyperbolic modeling, and it is demonstrated that with only two population data points, an amazing amount of information can be obtained, such as reasonably accurate doubling times that are a function of t, as well as accurate estimates of such entertaining topics as the total number of people that have ever lived on earth.

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