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Joyce KE, Smith KE, Henderson G, Greig G, Bambra C. Patient perspectives of Condition Management Programmes as a route to better health, well-being and employability. Fam Pract 2010; 27:101-9. [PMID: 19948563 DOI: 10.1093/fampra/cmp083] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Condition Management Programmes (CMPs), delivered through primary care settings, have been identified as possible vehicles to facilitate return to work for individuals with chronic health problems. There is little research, however, which examines how such programmes are received by patients. OBJECTIVE To explore patients' experiences of CMPs in terms of health, well-being and employability. METHODS Four focus groups and nine semi-structured interviews were conducted in order to capture patients' (n = 25) perceptions and experiences regarding participation in one of five different CMPs: Cardiac Rehabilitation, Counselling, Lower Back Pain Services, Smoking Cessation and a GP Exercise Referral Programme. RESULTS Experiences of the CMPs were generally positive. Respondents reported improved health behaviours (specifically better diets and increased exercise), positive psychosocial outcomes (including increased self-esteem, confidence and social support) and in some cases, return to work. However, concerns were expressed about the shortness of interventions and their accessibility. CONCLUSIONS Although condition management appears to have been well received by participants, the findings also illustrate that there is no 'one size fits all' template for CMPs. Rather, interventions should be adapted to take account of the dynamics of specific conditions, the context in which the intervention is based and the characteristics of the individuals involved.
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Learmonth T, Glans PA, Guo JH, Greenblatt M, Smith KE. Electronic excitations in the correlated metal BaV(0.98)Ti(0.02)S(3) studied using resonant inelastic soft x-ray scattering. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:025504. [PMID: 21386258 DOI: 10.1088/0953-8984/22/2/025504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Electronic excitations in the correlated metal BaTi(0.02)V(0.98)S(3) have been studied using resonant inelastic soft x-ray scattering at the V L edge. The intensities of the intra-atomic d-d(*) excitations and the elastic x-ray scattering feature are found to be temperature dependent, with the intensity increasing with decreasing temperature until saturation is reached near 100 K. The behavior of the spectral features is interpreted as evidence of a shift in the 3d electrons from more band-like states at higher temperature to more localized states at low temperature.
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Jeong HK, Noh HJ, Kim JY, Colakerol L, Glans PA, Jin MH, Smith KE, Lee YH. Comment on "Near-edge X-ray absorption fine-structure investigation of graphene". PHYSICAL REVIEW LETTERS 2009; 102:099701-099702. [PMID: 19392571 DOI: 10.1103/physrevlett.102.099701] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Indexed: 05/27/2023]
Abstract
A Comment on the Letter by D. Pacilé et al., Phys. Rev. Lett. 101, 066806 (2008)10.1103/PhysRevLett.101.066806. The authors of the Letter offer a Reply.
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DeMasi A, Piper LFJ, Zhang Y, Reid I, Wang S, Smith KE, Downes JE, Peltekis N, McGuinness C, Matsuura A. Electronic structure of the organic semiconductor Alq3 (aluminum tris-8-hydroxyquinoline) from soft x-ray spectroscopies and density functional theory calculations. J Chem Phys 2009; 129:224705. [PMID: 19071937 DOI: 10.1063/1.3030975] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The element-specific electronic structure of the organic semiconductor aluminum tris-8-hydroxyquinoline (Alq(3)) has been studied using a combination of resonant x-ray emission spectroscopy, x-ray photoelectron spectroscopy, x-ray absorption spectroscopy, and density functional theory (DFT) calculations. Resonant and nonresonant x-ray emission spectroscopy were used to measure directly the carbon, nitrogen and oxygen 2p partial densities of states in Alq(3), and good agreement was found with the results of DFT calculations. Furthermore, resonant x-ray emission at the carbon K-edge is shown to be able to measure the partial density of states associated with individual C sites. Finally, comparison of previous x-ray emission studies and the present data reveal the presence of clear photon-induced damage in the former.
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Harrington BE, Smith KE, Hunter DJ, Marks L, Blackman TJ, McKee L, Greene A, Elliott E, Williams GH. Health inequalities in England, Scotland and Wales: stakeholders' accounts and policy compared. Public Health 2008; 123:e24-8. [PMID: 19084881 DOI: 10.1016/j.puhe.2008.10.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVES The election of a Labour government in 1997 brought the issue of health inequalities firmly back on to the policy agenda across the UK. Since then, in the wake of devolution, the need to tackle health inequalities has been highlighted as a policy priority in all three mainland UK countries, albeit with varying degrees of emphasis. This paper reports on a major cross-national study, funded by the Economic and Social Research Council, investigating how National Health Service bodies, local councils and partnerships make sense of their work on health inequalities, and examining the difference made by the contrasting approaches that have been taken to performance assessment in England, Wales and Scotland. STUDY DESIGN Case studies, semi-structured interviews and analysis of key policy statements. METHODS In order to explore how health inequalities have been approached by the three governments (noting that there was a change in governments in Wales and Scotland during this time), key policy statements published between May 1997 and May 2007 were analysed. Concurrently, data from stakeholder interviews carried out in 2006 in case study areas in each country were analysed to determine the extent of alignment between policy and practice at local level. RESULTS This paper suggests that claims about the extent of health policy divergence in post-devolution Britain may have been exaggerated. It finds that, whilst the three countries have taken differing approaches to performance assessment and the setting of targets, policy approaches to health inequalities up until 2007 appear to have been remarkably similar. Furthermore, the first round of interview data suggest that variations in local understandings of, and responses to, health inequalities cannot always be clearly distinguished along national lines. CONCLUSIONS Based on the policy analysis, devolution in the UK does not appear to have resulted in substantively different national policy approaches to health inequalities. Indeed, the overall analysis suggests that (prior to the 2007 elections in Scotland and Wales) the differences between local areas within countries may be of as much interest as those between countries.
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Fuller CC, Jawahir SL, Leano FT, Bidol SA, Signs K, Davis C, Holmes Y, Morgan J, Teltow G, Jones B, Sexton RB, Davis GL, Braden CR, Patel NJ, Deasy MP, Smith KE. A multi-state Salmonella Typhimurium outbreak associated with frozen vacuum-packed rodents used to feed snakes. Zoonoses Public Health 2008; 55:481-7. [PMID: 18833597 DOI: 10.1111/j.1863-2378.2008.01118.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
From December 2005 through January 2006, the Minnesota Department of Health (MDH) identified four human clinical isolates of Salmonella Typhimurium that were indistinguishable by pulsed-field gel electrophoresis (PFGE). During routine interviews, three of the cases reported attending the same junior high school and two handled snakes in the science classroom. MDH collected environmental samples from the school's science classroom for Salmonella culturing; these included environmental samples and frozen vacuum-packed mice purchased over the internet to feed the classroom snakes. Through PulseNet, a national molecular subtyping surveillance network for enteric bacteria, 21 human S. Typhimurium isolates with indistinguishable PFGE patterns were identified in the United States since December 2005. Each state determined whether these human cases had recent exposure to snakes fed vacuum-packed rodents. Texas state officials conducted tracebacks of the vacuum-packed mice and collected samples at the breeding facility. Nineteen of 21 cases were interviewed, and seven reported contact with frozen vacuum-packed rodents from the same internet-based supplier in Texas. In Minnesota, the outbreak PFGE subtype of S. Typhimurium was isolated from the snakes, frozen feed rodents, and the classroom environment. Three human cases were identified in Michigan, Pennsylvania, and Wyoming. The outbreak PFGE subtype of S. Typhimurium was isolated from the Pennsylvania case's frozen rodents and the Michigan case's pet snake. The outbreak PFGE subtype of S. Typhimurium was also isolated from the supplier's rodent facility. This was a S. Typhimurium outbreak associated with frozen rodents. Human transmission likely occurred through direct contact with snakes and contaminated environmental surfaces. This report represents the second recent multi-state salmonellosis outbreak associated with commercially distributed rodents. Stronger oversight of the commercial rodent industry is warranted.
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Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 2008; 37:D755-61. [PMID: 18996895 PMCID: PMC2686463 DOI: 10.1093/nar/gkn875] [Citation(s) in RCA: 303] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.
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Smith KE, Schwab AP, Banks MK. Dissipation of PAHs in saturated, dredged sediments: a field trial. CHEMOSPHERE 2008; 72:1614-1619. [PMID: 18547603 DOI: 10.1016/j.chemosphere.2008.03.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Revised: 03/04/2008] [Accepted: 03/07/2008] [Indexed: 05/11/2023]
Abstract
Sediments dredged from navigable rivers often contain elevated concentrations of recalcitrant, potentially toxic organic compounds such as polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). The presence of these compounds often requires that the sediments be stored in fully contained disposal facilities. A 3-year field study was conducted at the Jones Island disposal facility in Milwaukee, Wisconsin, to compare bioremediation of PAHs in contaminated dredged sediments in the absence of plants to phytoremediation with Salix nigra (black willow) (SX61), Spartina pectinata (prairie cord grass), Carex aquatalis (lake sedge), Lolium multiflorum (annual rye), and Scirpus fluviatilis (bulrush). Nine PAHs were detected initially in the sediments. Over the 3-year experiment, acenaphthene dissipation ranged from 94% to 100%, whereas anthracene, benzo[a]pyrene and indo[1,2,3-cd]pyrene generally had modest decreases in concentration (0-30% decrease). The remaining five PAHs ranged in degree of disappearance from 23% to 82%. Planted treatments did not enhance PAH dissipation relative to those without plants, but treatments with high biomass yield and high transpiration plant species had significantly less removal of PAHs than unplanted controls. Significant, negative correlations between nitrogen removal and decreases in PAH concentration suggest that competition for nutrients between plants and microorganisms may have impeded the microbial degradation of PAHs in the rhizosphere of the more rapidly growing plant species.
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Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 2007; 36:D773-9. [PMID: 18086701 PMCID: PMC2238835 DOI: 10.1093/nar/gkm966] [Citation(s) in RCA: 403] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.
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Badn W, Hegardt P, Fellert MA, Darabi A, Esbjörnsson M, Smith KE, Janelidze S, Salford LG, Visse E, Siesjö P. Inhibition of inducible nitric oxide synthase enhances anti-tumour immune responses in rats immunized with IFN-gamma-secreting glioma cells. Scand J Immunol 2007; 65:289-97. [PMID: 17309784 DOI: 10.1111/j.1365-3083.2007.01901.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Interferon gamma (IFN-gamma) has successfully been used in immunotherapy of different experimental tumours. Mechanistically, IFN-gamma has extensive effects on the immune system including release of nitric oxide (NO) by upregulation of the inducible nitric oxide synthase (iNOS). NO has putative immunosuppressive effects but could also play a role in killing of tumour cells. Therefore, the aim of the present study was to clarify whether inhibition of iNOS in rats immunized with glioma cells (N32) producing IFN-gamma (N32-IFN-gamma), could enhance the anti-tumour immune response. Initially, both a selective iNOS, l-N(6)-(1-Iminoethyl)-l-lysine (l-NIL), and non-selective, N-nitro-l-arginine methyl ester (l-NAME), inhibitor of NOS were tested in vitro. After polyclonal stimulation with LPS and SEA, both l-NIL and l-NAME enhanced proliferation and production of IFN-gamma from activated rat splenocytes and this effect was inversely correlated to the production of NO. However, l-NIL had a broader window of efficacy and a lower minimal effective dose. When rats were immunized with N32-IFN-gamma, and administered NOS inhibitors by intraperitoneal (i.p.) mini-osmotic pumps, only splenocytes of rats treated with l-NIL, but not l-NAME, displayed an enhanced proliferation and production of IFN-gamma when re-stimulated with N32 tumour cells. Based on these findings, l-NIL was administered concurrently with N32-IFN-gamma cells to rats with intracerebral (i.c.) tumours resulting in a prolonged survival. These results show that inhibition of iNOS can enhance an IFN-gamma-based immunotherapy of experimental i.c. tumours implying that NO released after immunization has mainly immunosuppressive net effects.
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Guo JH, Gupta A, Sharma P, Rao KV, Marcus MA, Dong CL, Guillen JMO, Butorin SM, Mattesini M, Glans PA, Smith KE, Chang CL, Ahuja R. X-ray spectroscopic study of the charge state and local ordering of room-temperature ferromagnetic Mn-doped ZnO. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2007; 19:172202. [PMID: 21690936 DOI: 10.1088/0953-8984/19/17/172202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The charge state and local ordering of Mn doped into a pulsed laser deposited single-phase thin film of ZnO are investigated by using x-ray absorption spectroscopy at the O K-edge, Mn K-edge and L-edge, and x-ray emission spectroscopy at the O K-edge and Mn L-edge. This film is ferromagnetic at room temperature. EXAFS measurement shows that Mn(2+) replaces the Zn site in tetrahedral symmetry, and there is no evidence for either metallic Mn or MnO in the film. Upon Mn doping, the top of O 2p valence band extends into the bandgap, indicating additional charge carriers being created.
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Smith KE, Schwab AP, Banks MK. Phytoremediation of polychlorinated biphenyl (PCB)-contaminated sediment: a greenhouse feasibility study. JOURNAL OF ENVIRONMENTAL QUALITY 2007; 36:239-44. [PMID: 17215232 DOI: 10.2134/jeq2006.0089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Contaminated sediments dredged from navigable waterways often are placed in confined disposal facilities to prevent further spread of the pollutants. Reducing contaminants to acceptable levels would allow for disposal of the sediments and further dredging activity. A greenhouse study was conducted to evaluate plant treatments and the addition of an organic amendment to decrease the concentration of PCB congeners found in Arochlor 1260. Sediment treated with the amendment and either low transpiring plants or no plants had the greatest removal of the PCB congeners. High-transpiring plants apparently prevented the highly reducing conditions required for reductive dechlorination of highly chlorinated PCBs. Most likely, the amendment provided labile carbon that initiated the reducing conditions needed for dechlorination. The sediment moisture content and moisture-related plant parameters were significant predictors of the PCB loss. Carex aquatalis and Spartina pectinata are predicted to be the most effective plant treatments for phytoremediation of PCBs.
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88
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Wolinsky TD, Swanson CJ, Smith KE, Zhong H, Borowsky B, Seeman P, Branchek T, Gerald CP. The Trace Amine 1 receptor knockout mouse: an animal model with relevance to schizophrenia. GENES BRAIN AND BEHAVIOR 2006; 6:628-39. [PMID: 17212650 DOI: 10.1111/j.1601-183x.2006.00292.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trace amines have been implicated in a number of neuropsychiatric disorders including depression and schizophrenia. Although long known to modulate neurotransmission indirectly through the release of catecholamines, the identification of the Trace Amine 1 receptor (TA1) offers a mechanism by which trace amines can influence synaptic activity directly. TA1 binds and is activated by trace amines such as beta-phenylethylamine and tyramine. Our pharmacological characterization of mouse TA1 showed that, as in rat and primate, amphetamine is an agonist at this receptor but with surprisingly high potency. Without selective ligands for TA1 that do not also possess catecholamine-releasing properties, however, it has not been possible to study its physiological role in the central nervous system. To that end, a line of mice lacking the TA1 receptor was generated to characterize its contribution to the regulation of behavior. Compared with wild-type littermates, TA1 knockout (KO) mice displayed a deficit in prepulse inhibition. Knockout animals, in which the TA1-agonist influence of amphetamine was absent, showed enhanced sensitivity to the psychomotor-stimulating effect of this drug, which was temporally correlated with significantly larger increases in the release of both dopamine and norepinephrine in the dorsal striatum and associated with a 262% increase in the proportion of striatal high-affinity D2 receptors. TA1 therefore appears to play a modulatory role in catecholaminergic function and represents a potentially novel mechanism for the treatment of neuropsychiatric disorders. Furthermore, the TA1 KO mouse may provide a useful model for the development of treatments for some positive symptoms of schizophrenia.
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MESH Headings
- Amphetamine/pharmacology
- Animals
- Anxiety/genetics
- Anxiety/psychology
- Behavior, Animal/physiology
- Catecholamines/metabolism
- Central Nervous System Stimulants/pharmacology
- Cloning, Molecular
- Disease Models, Animal
- Dopamine Uptake Inhibitors/pharmacology
- Dose-Response Relationship, Drug
- Fever/genetics
- Fever/physiopathology
- Fever/psychology
- Gene Targeting
- Male
- Mice
- Mice, Knockout
- Microdialysis
- Motor Activity/physiology
- Phenotype
- Receptors, Dopamine D2/drug effects
- Receptors, Dopamine D2/genetics
- Receptors, Dopamine D2/physiology
- Receptors, G-Protein-Coupled/drug effects
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/physiology
- Recognition, Psychology/physiology
- Reflex, Startle/genetics
- Reflex, Startle/physiology
- Schizophrenia/genetics
- Schizophrenic Psychology
- Stress, Psychological/genetics
- Stress, Psychological/physiopathology
- Stress, Psychological/psychology
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89
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Voetsch AC, Kennedy MH, Keene WE, Smith KE, Rabatsky-Ehr T, Zansky S, Thomas SM, Mohle-Boetani J, Sparling PH, McGavern MB, Mead PS. Risk factors for sporadic Shiga toxin-producing Escherichia coli O157 infections in FoodNet sites, 1999-2000. Epidemiol Infect 2006; 135:993-1000. [PMID: 17147834 PMCID: PMC2870643 DOI: 10.1017/s0950268806007564] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
To monitor risk factors for illness, we conducted a case-control study of sporadic Shiga toxin-producing Escherichia coli O157 (STEC O157) infections in 1999-2000. Laboratory-confirmed cases of STEC O157 infection were identified through active laboratory surveillance in all or part of seven states. Patients and age-matched controls were interviewed by telephone using a standard questionnaire. Information was collected on demographics, clinical illness, and exposures to food, water, and animals in the 7 days before the patient's illness onset. During the 12-month study, 283 patients and 534 controls were enrolled. STEC O157 infection was associated with eating pink hamburgers, drinking untreated surface water, and contact with cattle. Eating produce was inversely associated with infection. Direct or indirect contact with cattle waste continues to be a leading identified source of sporadic STEC O157 infections.
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90
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Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent WJ. The UCSC genome browser database: update 2007. Nucleic Acids Res 2006; 35:D668-73. [PMID: 17142222 PMCID: PMC1669757 DOI: 10.1093/nar/gkl928] [Citation(s) in RCA: 226] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at .
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91
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Payne DJ, Egdell RG, Walsh A, Watson GW, Guo J, Glans PA, Learmonth T, Smith KE. Electronic origins of structural distortions in post-transition metal oxides: experimental and theoretical evidence for a revision of the lone pair model. PHYSICAL REVIEW LETTERS 2006; 96:157403. [PMID: 16712195 DOI: 10.1103/physrevlett.96.157403] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Indexed: 05/03/2023]
Abstract
Structural distortions in post-transition metal oxides are often explained in terms of the influence of sp hybrid "lone pairs." Evidence is presented here showing that this model must be revised. The electronic structures of prototypically distorted alpha-PbO and alpha-Bi2O3 have been measured by high-resolution x-ray photoemission and soft x-ray emission spectroscopies. In contrast with the expectations of the lone pair model, a high density of metal 6s states is observed at the bottom of the valence band. The measurements are consistent with the results of density functional theory calculations.
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Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 2006; 34:D590-8. [PMID: 16381938 PMCID: PMC1347506 DOI: 10.1093/nar/gkj144] [Citation(s) in RCA: 902] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at .
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93
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Valla T, Fedorov AV, Johnson PD, Glans PA, McGuinness C, Smith KE, Andrei EY, Berger H. Quasiparticle spectra, charge-density waves, superconductivity, and electron-phonon coupling in 2H-NbSe2. PHYSICAL REVIEW LETTERS 2004; 92:086401. [PMID: 14995798 DOI: 10.1103/physrevlett.92.086401] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Indexed: 05/24/2023]
Abstract
High-resolution photoemission has been used to study the electronic structure of the charge-density wave (CDW) and superconducting dichalcogenide, 2H-NbSe2. From the extracted self-energies, important components of the quasiparticle interactions have been identified. In contrast to previously studied TaSe2, the CDW transition does not affect the electronic properties significantly. The electron-phonon coupling is identified as a dominant contribution to the quasiparticle self-energy and is shown to be very anisotropic (k dependent) and much stronger than in TaSe2.
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Rassin DK, Smith KE. Nutritional approaches to improve cognitive development during infancy: antioxidant compounds. ACTA PAEDIATRICA (OSLO, NORWAY : 1992). SUPPLEMENT 2003; 92:34-41. [PMID: 12948003 DOI: 10.1111/j.1651-2227.2003.tb00661.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wall R, Cruickshank I, Smith KE, French NP, Holme AS. Development and validation of a simulation model for blowfly strike of sheep. MEDICAL AND VETERINARY ENTOMOLOGY 2002; 16:335-346. [PMID: 12510885 DOI: 10.1046/j.1365-2915.2002.00394.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A comprehensive simulation model for sheep blowfly strike due to Lucilia sericata (Meigen) (Diptera: Calliphoridae), which builds on previously published versions but also incorporates important new empirical data, is used to explain patterns of lamb and ewe strike recorded on 370 farms in south-west, south-east and central England and Wales. The model is able to explain a significant percentage of the variance in lamb strike incidence in all four regions, and ewe strike in three of the four regions. The model is able to predict the start of seasonal blowfly strike within one week in three of the four regions for both ewes and lambs, and within 3 weeks in the fourth region. It is concluded that the accuracy of the model will allow it to be used to assess the likely efficacy of new control techniques and the effects of changes in existing husbandry practices on strike incidence. The model could also be used to give sheep farmers advance warning of approaching strike problems. However, the ability to forecast future strike patterns is dependent on the accuracy of the weather projections; the more long-term the forecast, the more approximate the prediction is likely to be. When applied on a regional basis, model forecasts indicate expected average patterns of strike incidence and may not therefore be appropriate for individual farmers whose husbandry practices differ substantially from the average.
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96
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Assel MA, Landry SH, Swank PR, Steelman L, Miller-Loncar C, Smith KE. How do mothers' childrearing histories, stress and parenting affect children's behavioural outcomes? Child Care Health Dev 2002; 28:359-68. [PMID: 12296871 DOI: 10.1046/j.1365-2214.2002.00285.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Information is needed to understand the role of low to moderate levels of mothers' emotional stress and child characteristics (i.e. prematurity) on parenting behaviours and their impact on children's behaviour that might be deemed 'challenging' but not 'disordered'. METHODS The direct and indirect relations of maternal childrearing history and emotional stress, and observed parenting practices when children were 3 years of age on 4-year child behavioural outcomes was examined in a sample of low-income families with a term (n=112) or preterm (n=180) child. Parenting practices included displays of warmth and restrictiveness when interacting with their children. Child outcomes at 4 years included observation of social initiations with their mothers and maternal report of social and attentional problems. RESULTS A Structural Equation Model building approach guided by specific hypotheses indicated that preterm as compared to full-term children had more maternal reported social and attentional problems but did not differ in observed social initiating skills. Greater negative maternal childrearing history indirectly influenced social initiating skills through its direct influence on maternal emotional stress. Greater maternal emotional stress directly influenced mothers' parenting that, in turn, directly influenced social initiating. Prematurity and a more negative childrearing history had a direct negative influence on the maternal report of social and attentional behavioural outcomes. CONCLUSIONS These findings delineate the effects of prematurity and maternal parenting on the behaviour of 4-year-old-children and extend current knowledge of the influence of parental emotional stress on parenting. Even milder levels can negatively influence parenting, and in turn, contribute to children's less well developed social skills. The issues raised in this study could help with the identification and prioritization of medical and psychological services.
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97
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Landry SH, Smith KE, Swank PR, Assel MA, Vellet S. Does early responsive parenting have a special importance for children's development or is consistency across early childhood necessary? Dev Psychol 2001. [PMID: 11370914 DOI: 10.1037//0012-1649.37.3.387] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The role of early versus ongoing maternal responsiveness in predicting cognitive and social development was examined in home visits for mothers, full-term children (n = 103), and medically low-risk (n = 102) and high-risk (n = 77) preterm children at 5 ages. There were 4 maternal clusters based on warm and contingent responsiveness behaviors observed early (at 6, 12, and 24 months) and late (at 3 and 4 years): high early, high late; high early, low late; low early, moderate late; and low early, low late. Children, especially preterm children, showed faster cognitive growth when mothers were consistently responsive. Social growth was similar in the consistently responsive (high-high) and the early-responsive inconsistent (high-low) clusters, but greater deceleration at 4 years among children with mothers in the inconsistent cluster refuted the notion of a unique role for early responsiveness. The importance of consistent responsiveness, defined by an affective-emotional construct, was evident even when a broader constellation of parenting behaviors was considered.
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98
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Naimi TS, LeDell KH, Boxrud DJ, Groom AV, Steward CD, Johnson SK, Besser JM, O'Boyle C, Danila RN, Cheek JE, Osterholm MT, Moore KA, Smith KE. Epidemiology and clonality of community-acquired methicillin-resistant Staphylococcus aureus in Minnesota, 1996-1998. Clin Infect Dis 2001; 33:990-6. [PMID: 11528570 DOI: 10.1086/322693] [Citation(s) in RCA: 294] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2001] [Revised: 03/13/2001] [Indexed: 11/03/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has emerged among patients in the general population who do not have established risk factors for MRSA. Records from 10 Minnesota health facilities were reviewed to identify cases of MRSA infection that occurred during 1996-1998 and to identify which cases were community acquired. Susceptibility testing and pulsed-field gel electrophoresis (PFGE) subtyping were performed on available isolates. A total of 354 patients (median age, 16 years) with community-acquired MRSA (CAMRSA) infection were identified. Most case patients (299 [84%]) had skin infections, and 103 (29%) were hospitalized. More than 90% of isolates were susceptible to all antimicrobial agents tested, with the exception of beta-lactams and erythromycin. Of 334 patients treated with antimicrobial agents, 282 (84%) initially were treated with agents to which their isolates were nonsusceptible. Of 174 Minnesota isolates tested, 150 (86%) belonged to 1 PFGE clonal group. CAMRSA infections were identified throughout Minnesota; although most isolates were genetically related and susceptible to multiple antimicrobials, they were generally nonsusceptible to initial empirical therapy.
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99
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Wall R, Pitts KM, Smith KE. Pre-adult mortality in the blowfly Lucilia sericata. MEDICAL AND VETERINARY ENTOMOLOGY 2001; 15:328-334. [PMID: 11583452 DOI: 10.1046/j.0269-283x.2001.00316.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Populations of the blowfly, Lucilia sericata (Meigen) (Diptera: Calliphoridae), have a considerable potential for rapid increase; the lifetime reproductive output of each adult female has been estimated to be between 130 and 172 eggs. Nevertheless, in the field, absolute population densities of this species are relatively low. To account for this difference, the levels of mortality affecting the eggs, feeding and wandering larvae and pupae of L. sericata were assessed in the field and laboratory. Percentage egg hatch was dependent on relative humidity with no egg eclosion at humidities below 50%; there was no significant effect of temperature on egg hatch. On infested sheep, the mean mortality of feeding larvae was 53%, but this ranged widely from 0% to 96%. There was no effect of atmospheric temperature or humidity on the mortality of feeding larvae in vivo. In the laboratory, only 10% of wandering larvae pupariated at 10 degrees C. At above 20 degrees C pupariation was consistently almost 100%. Percentage emergence increased from 0% at 10 degrees C to about 80% between 20 and 30 degrees C. The upper lethal temperature for pupae was approached at 35 degrees C. Analysis of the predation of pupae in the field revealed a weak, but significant curvilinear relationship between temperature and proportionate mortality and a median mortality of 0.49% per 24 h exposure (interquartile range = 5.2%). There was no evidence of density dependence in pupal predation. Overall, it is estimated that pre-adult mortality accounts for losses of approximately 97% of each generation, but this figure is subject to considerable variation depending on factors such as climate, time of year and host susceptibility.
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100
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Hedberg CW, Smith KE, Besser JM, Boxrud DJ, Hennessy TW, Bender JB, Anderson FA, Osterholm MT. Limitations of pulsed-field gel electrophoresis for the routine surveillance of Campylobacter infections. J Infect Dis 2001; 184:242-4. [PMID: 11424025 DOI: 10.1086/322005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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