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Search Results: 1 - 10 of 237205 matches for " Alan R. Smith "
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Normalization and missing value imputation for label-free LC-MS analysis
Karpievitch Yuliya V,Dabney Alan R,Smith Richard D
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-s16-s5
Abstract: Shotgun proteomic data are affected by a variety of known and unknown systematic biases as well as high proportions of missing values. Typically, normalization is performed in an attempt to remove systematic biases from the data before statistical inference, sometimes followed by missing value imputation to obtain a complete matrix of intensities. Here we discuss several approaches to normalization and dealing with missing values, some initially developed for microarray data and some developed specifically for mass spectrometry-based data.
Cosmological surveys with the Australian Square Kilometre Array Pathfinder
Alan R. Duffy,Adam Moss,Lister Staveley-Smith
Physics , 2011, DOI: 10.1071/AS11013
Abstract: This is a design study into the capabilities of the Australian Square Kilometre Array Pathfinder in performing a full-sky low redshift neutral hydrogen survey, termed WALLABY, and the potential cosmological constraints one can attain from measurement of the galaxy power spectrum. We find that the full sky survey will likely attain 0.6 million redshifts which, when combined with expected Planck CMB data, will constrain the Dark Energy equation of state to 20%, representing a coming of age for radio observations in creating cosmological constraints.
Report on Gamma-Ray Analysis of Seaweed Samples from Naturespirit Herbs LLC
Eric B. Norman,Keenan Thomas,Pedro Guillaumon,Alan R. Smith
Physics , 2014,
Abstract: Five seaweed samples from Naturespirit Herbs LLC were counted using low-background high-resolution gamma-ray detectors to search for evidence of contamination from the Fukushima reactor accident. No evidence of Cs-134 was observed in any of the samples. Very low levels of Cs-137 were observed and are attributed to fallout from atmospheric nuclear weapons testing. However, these levels of Cs-137 are small compared to the levels of the naturally occurring K-40 observed from these seaweed samples.
Normalizers of Irreducible Subfactors
Roger R. Smith,Stuart A. White,Alan D. Wiggins
Mathematics , 2007,
Abstract: We consider normalizers of an irreducible inclusion $N\subseteq M$ of $\mathrm{II}_1$ factors. In the infinite index setting an inclusion $uNu^*\subseteq N$ can be strict, forcing us to also investigate the semigroup of one-sided normalizers. We relate these normalizers of $N$ in $M$ to projections in the basic construction and show that every trace one projection in the relative commutant $N'\cap < M,e_N>$ is of the form $u^*e_Nu$ for some unitary $u\in M$ with $uNu^*\subseteq N$. This enables us to identify the normalizers and the algebras they generate in several situations. In particular each normalizer of a tensor product of irreducible subfactors is a tensor product of normalizers modulo a unitary. We also examine normalizers of irreducible subfactors arising from subgroup--group inclusions $H\subseteq G$. Here the normalizers are the normalizing group elements modulo a unitary from $L(H)$. We are also able to identify the finite trace $L(H)$-bimodules in $\ell^2(G)$ as double cosets which are also finite unions of left cosets.
Adenocarcinomas after Prophylactic Surgery for Familial Adenomatous Polyposis  [PDF]
Joan C. Smith, Michael W. Sch?ffer, Billy R. Ballard, Duane T. Smoot, Alan J. Herline, Samuel E. Adunyah, Amosy E. M’Koma
Journal of Cancer Therapy (JCT) , 2013, DOI: 10.4236/jct.2013.41033

The incidence of familial adenomatous polyposis (FAP) is one in 7,000 to 12,000 live births. Virtually, all surgically untreated patients with FAP inevitably develop colorectal-cancer in their lifetime because they carry the adenomatous polyposis coli gene. Thus prophylactic proctocolectomy is indicated. Surgical treatment of FAP is still controversial. There are however, four surgical options: ileorectal anastomosis, restorative proctocolectomy with ileal pouch-anal anastomosis, proctocolectomy with ileostomy, and proctocolectomy with continent-ileostomy. Conventional proctocolectomy options largely lie between colectomy with ileorectal anastomosis or ileal pouch-anal anastomosis. Detractors of ileal pouch-anal anastomosis prefer ileorectal anastomosis because of better functional results and quality of life. The functional outcome of total colectomy with ileorectal anastomosis is undoubtedly far superior to that of the ileoanal pouch; however, the risk for rectal cancer is increased by 30%. Even after mucosectomy, inadvertent small mucosal residual islands remain. These residual islands carry the potential for the development of subsequent malignancy. We reviewed the literature (1975-2012) on the incidence, nature, and possible etiology of subsequent ileal-pouch and anal transit zone adenocarcinoma after prophylactic surgery procedure for FAP. To date there are 24 studies reporting 92 pouch-related cancers; 15 case reports, 4 prospective and 5 retrospective studies. Twenty three of 92 cancers (25%) developed in the pouch mucosa and 69 (75%) in anal transit zone (ATZ). Current recommendation for pouch surveillance and treatment are presented. Data suggest lifetime surveillance of these patients.

Using Integrated Enterprise Systems to Achieve Strategic Goals: A case study of a dual mode university
Alan Smith
International Review of Research in Open and Distance Learning , 2005,
Abstract: Since 1999, the University of Southern Queensland has embarked on a range of initiatives designed to improve the infrastructure and systems used to support its widely ranging activities in teaching and learning and research and its expansion into new international markets. This has involved the careful selection and implementation of various enterprise systems, together with the use of horizontal process teams. The results of this approach are now being realized, with demonstrable improvements to many university services, together with significant cost efficiencies. This paper discusses the reasons for the changes, the processes used to drive the changes through the various university committee structures, and the outcomes of the implementation of the enterprise systems.
Western Australian Marsupials Are Multiply Infected with Genetically Diverse Strains of Toxoplasma gondii
Shuting Pan, R. C. Andrew Thompson, Michael E. Grigg, Natarajan Sundar, Andrew Smith, Alan J. Lymbery
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045147
Abstract: Five different organs from 16 asymptomatic free-ranging marsupial macropods (Macropus rufus, M. fuliginosus, and M. robustus) from inland Western Australia were tested for infection with Toxoplasma gondii by multi-locus PCR-DNA sequencing. All macropods were infected with T. gondii, and 13 had parasite DNA in at least 2 organs. In total, 45 distinct T. gondii genotypes were detected. Fourteen of the 16 macropods were multiply infected with genetically distinct T. gondii genotypes that often partitioned between different organs. The presence of multiple T. gondii infections in macropods suggests that native mammals have the potential to promote regular cycles of sexual reproduction in the definitive felid host in this environment.
Genetic Analysis of Lice Supports Direct Contact between Modern and Archaic Humans
David L. Reed,Vincent S. Smith,Shaless L. Hammond,Alan R. Rogers,Dale H. Clayton
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0020340
Abstract: Parasites can be used as unique markers to investigate host evolutionary history, independent of host data. Here we show that modern human head lice, Pediculus humanus, are composed of two ancient lineages, whose origin predates modern Homo sapiens by an order of magnitude (ca. 1.18 million years). One of the two louse lineages has a worldwide distribution and appears to have undergone a population bottleneck ca. 100,000 years ago along with its modern H. sapiens host. Phylogenetic and population genetic data suggest that the other lineage, found only in the New World, has remained isolated from the worldwide lineage for the last 1.18 million years. The ancient divergence between these two lice is contemporaneous with splits among early species of Homo, and cospeciation analyses suggest that the two louse lineages codiverged with a now extinct species of Homo and the lineage leading to modern H. sapiens. If these lice indeed codiverged with their hosts ca. 1.18 million years ago, then a recent host switch from an archaic species of Homo to modern H. sapiens is required to explain the occurrence of both lineages on modern H. sapiens. Such a host switch would require direct physical contact between modern and archaic forms of Homo.
Orientation Cues for High-Flying Nocturnal Insect Migrants: Do Turbulence-Induced Temperature and Velocity Fluctuations Indicate the Mean Wind Flow?
Andy M. Reynolds,Don R. Reynolds,Alan D. Smith,Jason W. Chapman
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015758
Abstract: Migratory insects flying at high altitude at night often show a degree of common alignment, sometimes with quite small angular dispersions around the mean. The observed orientation directions are often close to the downwind direction and this would seemingly be adaptive in that large insects could add their self-propelled speed to the wind speed, thus maximising their displacement in a given time. There are increasing indications that high-altitude orientation may be maintained by some intrinsic property of the wind rather than by visual perception of relative ground movement. Therefore, we first examined whether migrating insects could deduce the mean wind direction from the turbulent fluctuations in temperature. Within the atmospheric boundary-layer, temperature records show characteristic ramp-cliff structures, and insects flying downwind would move through these ramps whilst those flying crosswind would not. However, analysis of vertical-looking radar data on the common orientations of nocturnally migrating insects in the UK produced no evidence that the migrants actually use temperature ramps as orientation cues. This suggests that insects rely on turbulent velocity and acceleration cues, and refocuses attention on how these can be detected, especially as small-scale turbulence is usually held to be directionally invariant (isotropic). In the second part of the paper we present a theoretical analysis and simulations showing that velocity fluctuations and accelerations felt by an insect are predicted to be anisotropic even when the small-scale turbulence (measured at a fixed point or along the trajectory of a fluid-particle) is isotropic. Our results thus provide further evidence that insects do indeed use turbulent velocity and acceleration cues as indicators of the mean wind direction.
The angiotensin-converting enzyme (ACE) gene family of Anopheles gambiae
Susan Burnham, Judith A Smith, Alison J Lee, R Elwyn Isaac, Alan D Shirras
BMC Genomics , 2005, DOI: 10.1186/1471-2164-6-172
Abstract: TBLASTN and sequence analysis of cDNAs revealed that the A. gambiae genome contains nine genes (AnoACE genes) which code for proteins with similarity to mammalian ACE. Eight of these genes code for putative single domain enzymes similar to other insect ACEs described so far. AnoACE9, however, has several features in common with mammalian somatic ACE such as a two domain structure and a hydrophobic C terminus. Four of the AnoACE genes (2, 3, 7 and 9) were shown to be expressed at a variety of developmental stages. Expression of AnoACE3, AnoACE7 and AnoACE9 is induced by a blood meal, with AnoACE7 showing the largest (approximately 10-fold) induction.Genes coding for two-domain ACEs have arisen several times during the course of evolution suggesting a common selective advantage to having an ACE with two active-sites in tandem in a single protein. AnoACE7 belongs to a sub-group of insect ACEs which are likely to be membrane-bound and which have an unusual, conserved gene structure.In mammals, angiotensin-converting enzyme (EC, ACE, peptidyl-dipeptidase A), an important member of the M2 peptidase family, is found on the surface of endothelial cells and is best known for its role in the biosynthesis of angiotensin II, as well as the degradation of circulating bradykinin and the haemoregulatory peptide, N-acetyl SDKP [1-3]. Mammalian ACE exists as two isoforms, a somatic form (sACE, 150–180 kDa) and a smaller protein (germinal ACE, 90–110 kDa) found exclusively in adult testes. The ACE gene comprises twenty-six exons and two promoters, and has clearly arisen by gene duplication [4]. The somatic promoter drives expression of the larger protein (exons 1–12 and exons 14–26), which consists of two very similar domains connected in tandem by a short inter-domain peptide. Each domain possesses a functional peptidase active site and they are commonly called the N- and C-domains after their relative position to the amino and carboxy termini. The bulk of the protein inclu
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