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Jones DB, Harrison S, Anderson K, Shannon S, Betts RA. Rock glaciers represent hidden water stores in the Himalaya. Sci Total Environ 2021; 793:145368. [PMID: 33933287 DOI: 10.1016/j.scitotenv.2021.145368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
In the high mountains of Asia, ongoing glacier retreat threatens human and ecological systems through reduced water availability. Rock glaciers are climatically more resistant than glaciers and contain valuable water volume equivalents (WVEQ). Across High Mountain Asia (HMA) the WVEQ of rock glaciers is poorly quantified, and thus their hydrological significance versus glaciers is unknown. Here we present the first systematic assessment of Himalayan rock glaciers, totalling ~25,000 landforms with an areal coverage of ~3747 km2. We calculate the WVEQ of Himalayan rock glaciers to be 51.80 ± 10.36 km3. Their comparative importance versus glaciers (rock glacier: glacier WVEQ ratio) is 1:25, which means that they constitute hydrologically valuable long-term water stores. In the context of climate-driven glacier recession, their relative hydrological value will likely increase. These cryospheric stores should be included in future scenario modelling to understand their role in sustainable water management for HMA.
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Affiliation(s)
- D B Jones
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9EZ, UK.
| | - S Harrison
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9EZ, UK.
| | - K Anderson
- Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9EZ, UK.
| | - S Shannon
- Bristol Glaciology Centre, Department of Geographical Science, University Road, University of Bristol, BS8 1SS, UK.
| | - R A Betts
- Met Office Hadley Centre, FitzRoy Road, Exeter, EX1 3PB, UK; Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter, EX4 4QW, UK.
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2
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Jones DB, Ali E, Ning CG, Ferreira da Silva F, Ingólfsson O, Lopes MCA, Chakraborty HS, Madison DH, Brunger MJ. A dynamical (e,2e) investigation into the ionization of the outermost orbitals of R-carvone. J Chem Phys 2019; 151:124306. [PMID: 31575183 DOI: 10.1063/1.5123526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We report an experimental and theoretical investigation into the dynamics of electron-impact ionization of R-carvone. Experimental triple differential cross sections are obtained in asymmetric coplanar kinematic conditions for the ionization of the unresolved combination of the three outermost molecular orbitals (41a-39a) of R-carvone. These cross sections are compared with theoretical cross sections calculated within a molecular 3-body distorted wave (M3DW) framework employing either a proper orientation average or orbital average to account for the random orientation of the molecule probed in the experiment. Here, we observe that the overall scattering behavior observed in the experiment is fairly well reproduced within the M3DW framework when implementing the proper average over orientations. The character of the ionized orbitals also provides some qualitative explanation for the observed scattering behavior. This represents substantial progress when trying to describe the scattering dynamics observed for larger molecules under intermediate-impact energy and asymmetric energy sharing scattering conditions.
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Affiliation(s)
- D B Jones
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - E Ali
- Department of Natural Sciences, D. L. Hubbard Center for Innovation, Northwest Missouri State University, Maryville, Missouri 64468, USA
| | - C G Ning
- State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing 100084, China
| | - F Ferreira da Silva
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - O Ingólfsson
- Department of Chemistry and Science Institute, University of Iceland, 107 Reykjavík, Iceland
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-900, Brazil
| | - H S Chakraborty
- Department of Natural Sciences, D. L. Hubbard Center for Innovation, Northwest Missouri State University, Maryville, Missouri 64468, USA
| | - D H Madison
- Department of Physics, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - M J Brunger
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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3
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Gomes M, da Silva DGM, Fernandes ACP, Ghosh S, Pires WAD, Jones DB, Blanco F, García G, Brunger MJ, Lopes MCA. Electron scattering from 1-butanol at intermediate impact energies: Total cross sections. J Chem Phys 2019; 150:194307. [PMID: 31117791 DOI: 10.1063/1.5096211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We report experimental measurements of the absolute total cross sections (TCSs) for electron scattering from 1-butanol at impact energies in the range 80-400 eV. Those measurements were conducted by considering the attenuation of a collimated electron beam, at a given energy, through a gas cell containing 1-butanol, at a given pressure, and through application of the Beer-Lambert law to derive the required TCS. We also report theoretical results using the Independent-Atom Model with Screening Corrected Additivity Rule and Interference approach. Those results include the TCS, the elastic integral cross section (ICS), the ionization total ICS, and the sum over all excitation process ICSs with agreement at the TCS level between our measured and calculated results being encouraging.
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Affiliation(s)
- M Gomes
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-900, Brazil
| | - D G M da Silva
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-900, Brazil
| | - A C P Fernandes
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-900, Brazil
| | - S Ghosh
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-900, Brazil
| | - W A D Pires
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-900, Brazil
| | - D B Jones
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - F Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - G García
- Instituto de Física Fundamental, CSIC, Serano 113-bis, 28006 Madrid, Spain
| | - M J Brunger
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36036-900, Brazil
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Jones DB, Mendes M, Limão-Vieira P, Ferreira da Silva F, Jones NC, Hoffmann SV, Brunger MJ. Electronic structure and VUV photoabsorption measurements of thiophene. J Chem Phys 2019; 150:064303. [PMID: 30769978 DOI: 10.1063/1.5089505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The absolute photoabsorption cross sections for thiophene in the 5.0-10.7 eV range were measured using synchrotron radiation. New theoretical calculations performed at the time-dependent density functional theory level were used to qualitatively interpret the recorded photoabsorption spectrum. The calculations facilitated a re-analysis of the observed vibronic and Rydberg structures in the photoabsorption spectrum. Here a number of features have been re-assigned, while a number of other features have been assigned for the first time. This represents the most comprehensive and self-consistent assignment of the thiophene high-resolution photoabsorption spectrum to date.
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Affiliation(s)
- D B Jones
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - M Mendes
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - P Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - F Ferreira da Silva
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - N C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - S V Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - M J Brunger
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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Lozano AI, Oller JC, Jones DB, da Costa RF, Varella MTDN, Bettega MHF, Ferreira da Silva F, Limão-Vieira P, Lima MAP, White RD, Brunger MJ, Blanco F, Muñoz A, García G. Total electron scattering cross sections from para-benzoquinone in the energy range 1-200 eV. Phys Chem Chem Phys 2018; 20:22368-22378. [PMID: 30129642 DOI: 10.1039/c8cp03297a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Total electron scattering cross sections, from para-benzoquinone, for impact energies ranging between 1 to 200 eV, have been obtained by measuring the attenuation of a linear electron beam under magnetic confinement conditions. Random uncertainty limits on these values have been found to be within 5%. Systematic errors, due to the axial magnetic beam conditions in combination with the acceptance angle of the detector, have been evaluated by integrating our calculated independent atom model with the screening corrected additivity rule and interference term elastic differential cross sections over that detection acceptance angle. Our previous calculations and measurements on this molecule (Jones et al., J. Chem. Phys., 2018, 148, 124312 and J. Chem. Phys., 2018, 148, 204305), have been compiled and complemented with new elastic and inelastic scattering cross section calculations in order to obtain a comprehensive cross section data base, within the considered energy range, for modelling purposes. The self-consistency of the present data set has been evaluated by simulating the electron transport of 15 eV electrons in para-benzoquinone, and comparing those results with the observed transmitted intensity distribution.
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Affiliation(s)
- A I Lozano
- Instituto de Fisica Fundamental, CSIC, Serrano 113-bis, E-28006 Madrid, Spain.
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Thomas LL, Herd LK, Goodband BD, Dritz SS, Tokach MD, Woodworth JC, DeRouchey JM, Goncalves MAD, Jones DB. 315 Effects of Increasing Standardized Ileal Digestible Lysine during Gestation on Growth and Reproductive Performance of Gilts and Sows Under Commercial Conditions. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - L K Herd
- Kansas State University, Manhattan, KS
| | | | - S S Dritz
- Kansas State University, Manhattan, KS
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Abstract
Previous authors have considered that allergy to certain foodstuffs may play an important role in the aetiology of ulcerative colitis, but immunological evidence for dietary allergy in ulcerative colitis is inconclusive. A study is reported of 22 patients with ulcerative colitis, with matched controls, in whom total serum IgE and specific IgE to certain foodstuffs have been estimated by the Phadebas PRIST and RAST (Pharmacia) techniques. Allergens tested were egg-white, milk, wheat, rye, oat, fish (cod) and peanut. There was no significant difference in the total serum IgE levels and the food specific IgE activity between the two groups.
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8
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da Silva DGM, Gomes M, Ghosh S, Silva IFL, Pires WAD, Jones DB, Blanco F, Garcia G, Buckman SJ, Brunger MJ, Lopes MCA. Total cross sections for electron scattering by 1-propanol at impact energies in the range 40-500 eV. J Chem Phys 2017; 147:194307. [PMID: 29166110 DOI: 10.1063/1.5008621] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Absolute total cross section (TCS) measurements for electron scattering from 1-propanol molecules are reported for impact energies from 40 to 500 eV. These measurements were obtained using a new apparatus developed at Juiz de Fora Federal University-Brazil, which is based on the measurement of the attenuation of a collimated electron beam through a gas cell containing the molecules to be studied at a given pressure. Besides these experimental measurements, we have also calculated TCS using the Independent-Atom Model with Screening Corrected Additivity Rule and Interference (IAM-SCAR+I) approach with the level of agreement between them being typically found to be very good.
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Affiliation(s)
- D G M da Silva
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36936-900, Brazil
| | - M Gomes
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36936-900, Brazil
| | - S Ghosh
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36936-900, Brazil
| | - I F L Silva
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36936-900, Brazil
| | - W A D Pires
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36936-900, Brazil
| | - D B Jones
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - F Blanco
- Departamento de Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - G Garcia
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain
| | - S J Buckman
- Plasma Research Laboratories, Research School of Physics and Engineering, Australian National University, Canberra, ACT 0200, Australia
| | - M J Brunger
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG 36936-900, Brazil
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9
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Limão-Vieira P, Duflot D, Ferreira da Silva F, Lange E, Jones NC, Hoffmann SV, Śmiałek MA, Jones DB, Brunger MJ. Valence and lowest Rydberg electronic states of phenol investigated by synchrotron radiation and theoretical methods. J Chem Phys 2017; 145:034302. [PMID: 27448882 DOI: 10.1063/1.4955334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present the experimental high-resolution vacuum ultraviolet (VUV) photoabsorption spectra of phenol covering for the first time the full 4.3-10.8 eV energy-range, with absolute cross sections determined. Theoretical calculations on the vertical excitation energies and oscillator strengths were performed using time-dependent density functional theory and the equation-of-motion coupled cluster method restricted to single and double excitations level. These have been used in the assignment of valence and Rydberg transitions of the phenol molecule. The VUV spectrum reveals several new features not previously reported in the literature, with particular reference to the 6.401 eV transition, which is here assigned to the 3sσ/σ(∗)(OH)←3π(3a″) transition. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of phenol in the earth's atmosphere (0-50 km).
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Affiliation(s)
- P Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - D Duflot
- Univ. Lille, UMR 8523-Physique des Lasers Atomes et Molécules, F-59000 Lille, France
| | - F Ferreira da Silva
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - E Lange
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - N C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - S V Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C, Denmark
| | - M A Śmiałek
- Department of Control and Power Engineering, Faculty of Ocean Engineering and Ship Technology, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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10
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Jones DB, Neves RFC, Lopes MCA, da Costa RF, do N Varella MT, Bettega MHF, Lima MAP, García G, Limão-Vieira P, Brunger MJ. Theoretical and experimental differential cross sections for electron impact excitation of the electronic bands of furfural. J Chem Phys 2016; 144:124309. [PMID: 27036450 DOI: 10.1063/1.4944615] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report results from a joint experimental and theoretical investigation into electron scattering from the important industrial species furfural (C5H4O2). Specifically, differential cross sections (DCSs) have been measured and calculated for the electron-impact excitation of the electronic states of C5H4O2. The measurements were carried out at energies in the range 20-40 eV, and for scattered-electron angles between 10° and 90°. The energy resolution of those experiments was typically ∼80 meV. Corresponding Schwinger multichannel method with pseudo-potential calculations, for energies between 6-50 eV and with and without Born-closure, were also performed for a sub-set of the excited electronic-states that were accessed in the measurements. Those calculations were undertaken at the static exchange plus polarisation-level using a minimum orbital basis for single configuration interaction (MOB-SCI) approach. Agreement between the measured and calculated DCSs was qualitatively quite good, although to obtain quantitative accord, the theory would need to incorporate even more channels into the MOB-SCI. The role of multichannel coupling on the computed electronic-state DCSs is also explored in some detail.
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Affiliation(s)
- D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - R F C Neves
- Instituto Federal do Sul de Minas Gerais, Câmpus Poços de Caldas, Minas Gerais, Brazil
| | - M C A Lopes
- Departamento de Física, UFJF, Juiz de Fora, Minas Gerais 36036-900, Brazil
| | - R F da Costa
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo 09210-580, Brazil
| | - M T do N Varella
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, Brazil
| | - M H F Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, Curitiba, Paraná 81531-990, Brazil
| | - M A P Lima
- Instituto de Física "Gleb Wataghin," Universidade Estadual de Campinas, Campinas, São Paulo 13083-859, Brazil
| | - G García
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - P Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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11
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Jones DB, Neves RFC, Lopes MCA, da Costa RF, Varella MTDN, Bettega MHF, Lima MAP, García G, Blanco F, Brunger MJ. Excitation of vibrational quanta in furfural by intermediate-energy electrons. J Chem Phys 2015; 143:224304. [PMID: 26671372 DOI: 10.1063/1.4936631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report cross sections for electron-impact excitation of vibrational quanta in furfural, at intermediate incident electron energies (20, 30, and 40 eV). The present differential cross sections are measured over the scattered electron angular range 10°-90°, with corresponding integral cross sections subsequently being determined. Furfural is a viable plant-derived alternative to petrochemicals, being produced via low-temperature plasma treatment of biomass. Current yields, however, need to be significantly improved, possibly through modelling, with the present cross sections being an important component of such simulations. To the best of our knowledge, there are no other cross sections for vibrational excitation of furfural available in the literature, so the present data are valuable for this important molecule.
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Affiliation(s)
- D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - R F C Neves
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, MG, Brazil
| | - R F da Costa
- Instituto de Física "Gleb Wataghin," Universidade Estadual de Campinas, Campinas, 13083-859 São Paulo, Brazil
| | - M T do N Varella
- Instituto de Física, Universidade de São Paulo, CP 66318, 05315-970 São Paulo, São Paulo, Brazil
| | - M H F Bettega
- Departamento de Física, Universidade Federal do Paraná, CP 19044, 81531-990 Curitiba, Paraná, Brazil
| | - M A P Lima
- Instituto de Física "Gleb Wataghin," Universidade Estadual de Campinas, Campinas, 13083-859 São Paulo, Brazil
| | - G García
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - F Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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12
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Jones DB, Ellis-Gibbings L, García G, Nixon KL, Lopes MCA, Brunger MJ. Intermediate energy cross sections for electron-impact vibrational-excitation of pyrimidine. J Chem Phys 2015; 143:094304. [PMID: 26342367 DOI: 10.1063/1.4929907] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report differential cross sections (DCSs) and integral cross sections (ICSs) for electron-impact vibrational-excitation of pyrimidine, at incident electron energies in the range 15-50 eV. The scattered electron angular range for the DCS measurements was 15°-90°. The measurements at the DCS-level are the first to be reported for vibrational-excitation in pyrimidine via electron impact, while for the ICS we extend the results from the only previous condensed-phase study [P. L. Levesque, M. Michaud, and L. Sanche, J. Chem. Phys. 122, 094701 (2005)], for electron energies ⩽12 eV, to higher energies. Interestingly, the trend in the magnitude of the lower energy condensed-phase ICSs is much smaller when compared to the corresponding gas phase results. As there is no evidence for the existence of any shape-resonances, in the available pyrimidine total cross sections [Baek et al., Phys. Rev. A 88, 032702 (2013); Fuss et al., ibid. 88, 042702 (2013)], between 10 and 20 eV, this mismatch in absolute magnitude between the condensed-phase and gas-phase ICSs might be indicative for collective-behaviour effects in the condensed-phase results.
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Affiliation(s)
- D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - L Ellis-Gibbings
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - G García
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - K L Nixon
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais, Brazil
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais, Brazil
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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13
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da Silva GB, Neves RFC, Chiari L, Jones DB, Ali E, Madison DH, Ning CG, Nixon KL, Lopes MCA, Brunger MJ. Triply differential (e,2e) studies of phenol. J Chem Phys 2015; 141:124307. [PMID: 25273437 DOI: 10.1063/1.4896072] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We have measured (e,2e) triple differential cross sections (TDCS) for the electron-impact ionisation of phenol with coplanar asymmetrical kinematics for an incident electron energy of 250 eV. Experimental measurements of the angular distribution of the slow outgoing electrons at 20 eV are obtained when the incident electron scatters through angles of -5°, -10°, and -15°, respectively. The TDCS data are compared with calculations performed within the molecular 3-body distorted wave model. In this case, a mixed level of agreement, that was dependent on the kinematical condition being probed, was observed between the theoretical and experimental results in the binary peak region. The experimental intensity of the recoil features under all kinematical conditions was relatively small, but was still largely underestimated by the theoretical calculations.
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Affiliation(s)
- G B da Silva
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - R F C Neves
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - L Chiari
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - E Ali
- Department of Physics, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - D H Madison
- Department of Physics, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - C G Ning
- Department of Physics, State Key Laboratory of Low-Dimensional Quantum Physics, Tsinghua University, Beijing 100084, China
| | - K L Nixon
- Departamento de Física, UFJF, Juiz de Fora, 36036-330, MG, Brazil
| | - M C A Lopes
- Departamento de Física, UFJF, Juiz de Fora, 36036-330, MG, Brazil
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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14
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Neves RFC, Jones DB, Lopes MCA, Blanco F, García G, Ratnavelu K, Brunger MJ. Integral cross sections for electron impact excitation of vibrational and electronic states in phenol. J Chem Phys 2015; 142:194305. [PMID: 26001459 DOI: 10.1063/1.4921313] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on measurements of integral cross sections (ICSs) for electron impact excitation of a series of composite vibrational modes and electronic-states in phenol, where the energy range of those experiments was 15-250 eV. There are currently no other results against which we can directly compare those measured data. We also report results from our independent atom model with screened additivity rule correction computations, namely, for the inelastic ICS (all discrete electronic states and neutral dissociation) and the total ionisation ICS. In addition, for the relevant dipole-allowed excited electronic states, we also report f-scaled Born-level and energy-corrected and f-scaled Born-level (BEf-scaled) ICS. Where possible, our measured and calculated ICSs are compared against one another with the general level of accord between them being satisfactory to within the measurement uncertainties.
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Affiliation(s)
- R F C Neves
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais, Brazil
| | - F Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - G García
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - K Ratnavelu
- Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
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15
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Neves RFC, Jones DB, Lopes MCA, Nixon KL, de Oliveira EM, da Costa RF, Varella MTDN, Bettega MHF, Lima MAP, da Silva GB, Brunger MJ. Intermediate energy electron impact excitation of composite vibrational modes in phenol. J Chem Phys 2015; 142:194302. [PMID: 26001456 DOI: 10.1063/1.4921038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We report differential cross section results from an experimental investigation into the electron impact excitation of a number of the low-lying composite (unresolved) vibrational modes in phenol (C6H5OH). The measurements were carried out at incident electron energies in the range 15-40 eV and for scattered-electron angles in the range 10-90°. The energy resolution of those measurements was typically ∼80 meV. Calculations, using the GAMESS code, were also undertaken with a B3LYP/aug-cc-pVDZ level model chemistry, in order to enable us to assign vibrational modes to the features observed in our energy loss spectra. To the best of our knowledge, the present cross sections are the first to be reported for vibrational excitation of the C6H5OH molecule by electron impact.
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Affiliation(s)
- R F C Neves
- School of Chemical and Physical Sciences, Flinders University, G.P.O. Box 2100, Adelaide, SA 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, G.P.O. Box 2100, Adelaide, SA 5001, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil
| | - K L Nixon
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-900, Juiz de Fora, Minas Gerais, Brazil
| | - E M de Oliveira
- Instituto de Física 'Gleb Wataghin,' Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - R F da Costa
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580 Santo André, São Paulo, Brazil
| | - M T do N Varella
- Instituto de Física, Universidade de São Paulo, C.P. 66318, 05315-970 São Paulo, Brazil
| | - M H F Bettega
- Departamento de Física, Universidade Federal do Paraná, C.P. 19044, 81531-990 Curitiba, Paraná, Brazil
| | - M A P Lima
- Instituto de Física 'Gleb Wataghin,' Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
| | - G B da Silva
- Universidade Federal de Mato Grosso, Barra do Garças, Mato Grosso, Brazil
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, G.P.O. Box 2100, Adelaide, SA 5001, Australia
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16
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Builth-Williams JD, da Silva GB, Chiari L, Jones DB, Chaluvadi H, Madison DH, Brunger MJ. Dynamical (e,2e) studies of tetrahydropyran and 1,4-dioxane. J Chem Phys 2015; 140:214312. [PMID: 24908013 DOI: 10.1063/1.4880204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present experimental and theoretical results for the electron-impact ionization of the highest occupied molecular orbitals of tetrahydropyran and 1,4-dioxane. Using an (e,2e) technique in asymmetric coplanar kinematics, angular distributions of the slow ejected electron, with an energy of 20 eV, are measured when incident electrons at 250 eV ionize the target and scatter through an angle of either -10° or -15°. The data are compared with calculations performed at the molecular 3-body distorted wave level. Fair agreement between the theoretical model and the experimental measurements was observed. The similar structures for these targets provide key insights for assessing the limitations of the theoretical calculations. This study in turn facilitates an improved understanding of the dynamics in the ionization process.
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Affiliation(s)
- J D Builth-Williams
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - G B da Silva
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - L Chiari
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Hari Chaluvadi
- Department of Physics, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - D H Madison
- Department of Physics, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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17
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Do TPT, Duque HV, Lopes MCA, Konovalov DA, White RD, Brunger MJ, Jones DB. Differential cross sections for electron-impact vibrational-excitation of tetrahydrofuran at intermediate impact energies. J Chem Phys 2015; 142:124306. [PMID: 25833578 DOI: 10.1063/1.4915888] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We report differential cross sections (DCSs) for electron-impact vibrational-excitation of tetrahydrofuran, at intermediate incident electron energies (15-50 eV) and over the 10°-90° scattered electron angular range. These measurements extend the available DCS data for vibrational excitation for this species, which have previously been obtained at lower incident electron energies (≤20 eV). Where possible, our data are compared to the earlier measurements in the overlapping energy ranges. Here, quite good agreement was generally observed where the measurements overlapped.
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Affiliation(s)
- T P T Do
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - H V Duque
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais, Brazil
| | - D A Konovalov
- College of Science, Technology and Engineering, James Cook University, Townsville, Australia
| | - R D White
- College of Science, Technology and Engineering, James Cook University, Townsville, Australia
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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18
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Chellali A, Ahn W, Sankaranarayanan G, Flinn JT, Schwaitzberg SD, Jones DB, De S, Cao CGL. Preliminary evaluation of the pattern cutting and the ligating loop virtual laparoscopic trainers. Surg Endosc 2014; 29:815-21. [PMID: 25159626 DOI: 10.1007/s00464-014-3764-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/18/2014] [Indexed: 01/22/2023]
Abstract
INTRODUCTION The Fundamentals of Laparoscopic Surgery (FLS) trainer is currently the standard for training and evaluating basic laparoscopic skills. However, its manual scoring system is time-consuming and subjective. The Virtual Basic Laparoscopic Skill Trainer (VBLaST©) is the virtual version of the FLS trainer which allows automatic and real time assessment of skill performance, as well as force feedback. In this study, the VBLaST© pattern cutting (VBLaST-PC©) and ligating loop (VBLaST-LL©) tasks were evaluated as part of a validation study. We hypothesized that performance would be similar on the FLS and VBLaST© trainers, and that subjects with more experience would perform better than those with less experience on both trainers. METHODS Fifty-five subjects with varying surgical experience were recruited at the Learning Center during the 2013 SAGES annual meeting and were divided into two groups: experts (PGY 5, surgical fellows and surgical attendings) and novices (PGY 1-4). They were asked to perform the PC or the ligating loop task on the FLS and the VBLaST© trainers. Their performance scores for each trainer were calculated and compared. RESULTS There were no significant differences between the FLS and VBLaST© scores for either the PC or the ligating loop task. Experts' scores were significantly higher than the scores for novices on both trainers. CONCLUSION This study showed that the subjects' performance on the VBLaST© trainer was similar to the FLS performance for both tasks. Both the VBLaST-PC© and the VBLaST-LL© tasks permitted discrimination between the novice and expert groups. Although concurrent and discriminant validity has been established, further studies to establish convergent and predictive validity are needed. Once validated as a training system for laparoscopic skills, the system is expected to overcome the current limitations of the FLS trainer.
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Affiliation(s)
- A Chellali
- Department of Surgery, Cambridge Health Alliance, Harvard Medical School, Cambridge, MA, USA,
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19
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Limão-Vieira P, Duflot D, Hubin-Franskin MJ, Delwiche J, Hoffmann SV, Chiari L, Jones DB, Brunger MJ, Lopes MCA. Electronic states of tetrahydrofurfuryl alcohol (THFA) as studied by VUV spectroscopy and ab initio calculations. J Phys Chem A 2014; 118:6425-34. [PMID: 24742321 DOI: 10.1021/jp501634w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The electronic spectroscopy of isolated tetrahydrofurfuryl alcohol (THFA) in the gas phase has been investigated using high-resolution photoabsorption spectroscopy in the 5.0-10.8 eV energy-range, with absolute cross-section measurements derived. The He(I) photoelectron spectrum was also collected to quantify ionization energies in the 9-16 eV spectral region. These experiments are supported by the first high-level ab initio calculations performed on the excited states of the neutral molecule and on the ground and excited state of the positive ion. The good agreement between the theoretical results and the measurements allows us to quantify for the first time the electronic-state spectroscopy of THFA. The present work also considers the question of the lowest energy conformers of the molecule and its population distribution at room temperature.
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Affiliation(s)
- P Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
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20
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Chiari L, Duque HV, Jones DB, Thorn PA, Pettifer Z, da Silva GB, Limão-Vieira P, Duflot D, Hubin-Franskin MJ, Delwiche J, Blanco F, García G, Lopes MCA, Ratnavelu K, White RD, Brunger MJ. Differential cross sections for intermediate-energy electron scattering from α-tetrahydrofurfuryl alcohol: excitation of electronic-states. J Chem Phys 2014; 141:024301. [PMID: 25028013 DOI: 10.1063/1.4885856] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on measurements of differential cross sections (DCSs) for electron impact excitation of a series of Rydberg electronic-states in α-tetrahydrofurfuryl alcohol (THFA). The energy range of these experiments was 20-50 eV, while the scattered electron was detected in the 10°-90° angular range. There are currently no other experimental data or theoretical computations against which we can directly compare the present measured results. Nonetheless, we are able to compare our THFA DCSs with earlier cross section measurements for Rydberg-state electronic excitation for tetrahydrofuran, a similar cyclic ether, from Do et al. [J. Chem. Phys. 134, 144302 (2011)]. In addition, "rotationally averaged" elastic DCSs, calculated using our independent atom model with screened additivity rule correction approach are also reported. Those latter results give integral cross sections consistent with the optical theorem, and supercede those from the only previous study of Milosavljević et al. [Eur. Phys. J. D 40, 107 (2006)].
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Affiliation(s)
- L Chiari
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - H V Duque
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - P A Thorn
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Z Pettifer
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - G B da Silva
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - P Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - D Duflot
- Laboratoire de Physique des Lasers, Atomes et Molécules, UMR CNRS 8523, Université Lille, F-59655 Villeneuve d'Ascq Cedex, France
| | - M-J Hubin-Franskin
- Départment de Chimie, Université de Liège, Institut de Chimie-Bât. B6C, B-4000 Liège 1, Belgium
| | - J Delwiche
- Départment de Chimie, Université de Liège, Institut de Chimie-Bât. B6C, B-4000 Liège 1, Belgium
| | - F Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - G García
- Instituto de Física Fundamental, CSIC, Madrid E-28006, Spain
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
| | - K Ratnavelu
- Institute of Mathematical Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - R D White
- School of Engineering and Physical Sciences, James Cook University, Townsville, 4810 Queensland, Australia
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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21
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Duque HV, Chiari L, Jones DB, Pettifer Z, da Silva GB, Limão-Vieira P, Blanco F, García G, White RD, Lopes MCA, Brunger MJ. Intermediate-energy differential and integral cross sections for vibrational excitation in α-tetrahydrofurfuryl alcohol. J Chem Phys 2014; 140:214306. [PMID: 24908007 DOI: 10.1063/1.4879779] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Differential and integral cross section measurements, for incident electron energies in the 20-50 eV range, are reported for excitation of several composite vibrational modes in α-tetrahydrofurfuryl alcohol (THFA). Optimisation and frequency calculations, using GAUSSIAN 09 at the B3LYP/aug-cc-pVDZ level, were also undertaken for the two most abundant conformers of THFA, with results being reported for their respective mode classifications and excitation energies. Those calculations assisted us in the experimental assignments of the composite features observed in our measured energy loss spectra. There are, to the best of our knowledge, no other experimental or theoretical data currently available in the literature against which we can compare the present results.
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Affiliation(s)
- H V Duque
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - L Chiari
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Z Pettifer
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - G B da Silva
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - P Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - F Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Madrid E-28040, Spain
| | - G García
- Instituto de Física Fundamental, CSIC, Madrid E-28006, Spain
| | - R D White
- School of Engineering and Physical Sciences, James Cook University, Townsville, 4810 Queensland, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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22
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Jones DB, Bellm SM, Blanco F, Fuss M, García G, Limão-Vieira P, Brunger MJ. Differential cross sections for the electron impact excitation of pyrimidine. J Chem Phys 2013; 137:074304. [PMID: 22920117 DOI: 10.1063/1.4743961] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on differential cross section (DCS) measurements for the electron-impact excitation of the electronic states of pyrimidine. The energy range of the present measurements was 15-50 eV with the angular range of the measurements being 10°-90°. All measured DCSs displayed forward-peaked angular distributions, consistent with the relatively large magnitudes for the dipole moment and dipole polarizability of pyrimidine. Excitations to triplet states were found to be particularly important in some energy loss features at the lower incident electron energies. To the best of our knowledge there are no other experimental data or theoretical computations against which we can compare the present results.
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Affiliation(s)
- D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia.
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23
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Jones DB, Kakar S. In reply. J Hand Surg Am 2013; 38:209-10. [PMID: 23261203 DOI: 10.1016/j.jhsa.2012.10.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 10/27/2012] [Indexed: 02/02/2023]
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Selinger CP, Eaden J, Selby W, Jones DB, Katelaris P, Chapman G, McDonald C, McLaughlin J, Leong RWL, Lal S. Patients' knowledge of pregnancy-related issues in inflammatory bowel disease and validation of a novel assessment tool ('CCPKnow'). Aliment Pharmacol Ther 2012; 36:57-63. [PMID: 22568682 DOI: 10.1111/j.1365-2036.2012.05130.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/10/2012] [Accepted: 04/22/2012] [Indexed: 12/16/2022]
Abstract
BACKGROUND Inflammatory bowel diseases (IBD) require complex therapeutic decisions and life choices concerning pregnancy, but little is known about patient's knowledge of IBD and its treatment before and during pregnancy. AIM To develop a novel tool (Crohn's and Colitis Pregnancy Knowledge Score 'CCPKnow') to assess knowledge of pregnancy-related issues in IBD. The validated tool was then applied to determine knowledge in patients. METHOD Discriminate ability of 'CCPKnow' was validated in four groups with different levels of IBD knowledge. Reliability and readability were tested by Cronbach-α and Flesch-Kencaid. Construct validity was subsequently assessed against general IBD knowledge (CCKnow) in 145 women with IBD. Associations between patient factors and knowledge were studied. RESULTS Median CCPKnow scores differed significantly between the validation groups (P < 0.001). CCPKnow displayed excellent internal consistency, reliability (Cronbach-α 0.94), readability (reading age 9 years) and close correlation with CCKnow (Spearman's ρ 0.64; P < 0.001). Of 145 patients, 44.8% had poor, 27.6% adequate, 17.3% good and only 10.3% very good knowledge. Better knowledge was associated with Caucasian ethnicity, higher income, having a partner, having children, Crohn's and Colitis Association membership, longer disease duration and Crohn's disease. CONCLUSIONS Crohn's and Colitis Pregnancy Knowledge Score, a novel knowledge assessment tool of pregnancy and IBD, demonstrated excellent test characteristics. We found that nearly half of the women with IBD had poor knowledge, identifying a pressing need for better education.
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Affiliation(s)
- C P Selinger
- Gastroenterology and Liver Services, Concord Hospital, Sydney, NSW, Australia.
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25
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Builth-Williams JD, Bellm SM, Jones DB, Chaluvadi H, Madison DH, Ning CG, Lohmann B, Brunger MJ. Experimental and theoretical investigation of the triple differential cross section for electron impact ionization of pyrimidine molecules. J Chem Phys 2012; 136:024304. [PMID: 22260576 DOI: 10.1063/1.3675167] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cross-section data for electron impact induced ionization of bio-molecules are important for modelling the deposition of energy within a biological medium and for gaining knowledge of electron driven processes at the molecular level. Triply differential cross sections have been measured for the electron impact ionization of the outer valence 7b(2) and 10a(1) orbitals of pyrimidine, using the (e, 2e) technique. The measurements have been performed with coplanar asymmetric kinematics, at an incident electron energy of 250 eV and ejected electron energy of 20 eV, for scattered electron angles of -5°, -10°, and -15°. The ejected electron angular range encompasses both the binary and recoil peaks in the triple differential cross section. Corresponding theoretical calculations have been performed using the molecular 3-body distorted wave model and are in reasonably good agreement with the present experiment.
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Affiliation(s)
- J D Builth-Williams
- ARC Centre of Excellence for Antimatter-Matter Studies, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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Abstract
Scaphoid fractures that fail to unite are at risk of developing avascular necrosis and progressive structural collapse, thereby complicating attempts at revision surgical treatment. Vascularized bone grafts have demonstrated utility in promoting consolidation in the treatment of scaphoid nonunions complicated by avascular necrosis. Numerous pedicled and free vascularized grafts have been described with variable, but generally favorable, outcomes. Understanding the indications for different grafts is critical to the successful application of these techniques and grafts in the treatment of challenging scaphoid nonunions.
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Affiliation(s)
- D B Jones
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
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27
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Jones DB, Zenger KR, Jerry DR. In silico whole-genome EST analysis reveals 2322 novel microsatellites for the silver-lipped pearl oyster, Pinctada maxima. Mar Genomics 2011; 4:287-90. [PMID: 22118641 DOI: 10.1016/j.margen.2011.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 06/24/2011] [Accepted: 06/28/2011] [Indexed: 12/01/2022]
Abstract
Molecular stock improvement techniques such as marker assisted selection have great potential in accelerating selective breeding programmes for animal production industries. However, the discovery and application of trait/marker associations usually requires a large number of genome-wide polymorphic loci. Here, we present 2322 unique microsatellites for the silver-lipped pearl oyster, Pinctada maxima, a species of aquaculture importance throughout the Indo-Australian Archipelago for production of the highly valued South Sea pearl. More than 1.2 million Roche 454 expressed sequence tag (EST) reads were screened for microsatellite repeat motifs. A total of 12,604 sequences contained either a di, tri, tetra, penta or hexa microsatellite repeat motif (n ≥ 6), with 6435 of these sequences having sufficient flanking regions for primer development. All identified microsatellites with designed primers were condensed into 2322 unique clusters (i.e., unique loci) of which 360 were shown to be polymorphic based on multiple sequence reads with different repeat motifs. Genotyping of five microsatellite loci demonstrated that in silico evaluation of polymorphism levels was a very useful method for identification of polymorphic loci, with the variation uncovered being a lower bound. Gene Ontology annotations of sequences containing microsatellites suggest that most are derived from a diverse array of unique genes. This EST derived microsatellite database will be a valuable resource for future studies in genetic map construction, diversity analysis, quantitative trait loci analysis, association mapping and marker assisted selection, not only for P. maxima, but also closely related species within the genus Pinctada.
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Affiliation(s)
- D B Jones
- Aquaculture Genetics Research Program, School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia.
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Gould J, Ellsmere J, Fanelli R, Hutter M, Jones S, Pratt J, Schauer P, Schirmer B, Schwaitzberg S, Jones DB. Panel report: best practices for the surgical treatment of obesity. Surg Endosc 2010; 25:1730-40. [PMID: 21136099 DOI: 10.1007/s00464-010-1487-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 09/15/2010] [Indexed: 10/18/2022]
Abstract
BACKGROUND Bariatric surgery is a rapidly growing field. Advances in surgical technologies and techniques have raised concerns about patient safety. Bariatric surgeons and programs are under increased scrutiny from regulatory agencies, insurers, and public health officials to provide high quality and safe care for bariatric patients at all phases of care. METHODS During the 2009 annual meeting of the Society of American Gastrointestinal and Endoscopic Surgeons (SAGES), a panel of experts convened to provide updated information on patient safety and best practices in bariatric surgery. The following article is a summary of this panel presentation. RESULTS AND CONCLUSIONS Weight loss surgery is a field that is evolving and adapting to multiple external pressures. Safety concerns along with increasing public scrutiny have led to a systematic approach to defining best practices, creating standards of care, and identifying mechanisms to ensure that patients consistently receive the best and most effective care possible. In many ways, bariatric surgery and multidisciplinary bariatric surgery programs may serve as a model for other programs and surgical specialties in the near future.
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Affiliation(s)
- J Gould
- University of Wisconsin School of Medicine, 600 Highland Avenue, H4/726 Clinical Science Center, Madison, WI 53792, USA.
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Abstract
The success of vascularized bone grafts from the medial femoral condyle in various clinical applications has sparked renewed interest in the microvascular anatomy of this region. This study describes the arterial supply of the distal medial femoral condyle and its implications in harvesting vascularized bone grafts. The location, branching pattern, internal diameter, and distribution of perforators of the descending genicular artery and superior medial genicular artery in 19 fresh cadaveric lower limbs were recorded. The descending genicular artery was present in 89% and the superior medial genicular artery was present in 100% of specimens with average distances proximal to the articular surface of 13.7 cm and 5.2 cm, respectively. The average number of perforating vessels was greatest in the posterior distal quadrant of the condyle. The blood supply of the medial femoral condyle is plentiful and consistent making it a useful source for free vascularized bone grafts.
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Affiliation(s)
- H Yamamoto
- Mayo Clinic, Orthopedic Department, Rochester MN, USA
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Affiliation(s)
- W M Howell
- Molecular Immunology Group, Tenovus Laboratory, Southampton General Hospital, Tremona Road, Southampton SO16 6YD
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Wilkins BS, Jones DB. Sites of M-CSF messenger RNA production in bone marrow trephine biopsy specimens and long term cultures demonstrated by nonisotopic in situ hybridisation. Mol Pathol 2010; 48:M35-9. [PMID: 16695973 PMCID: PMC407917 DOI: 10.1136/mp.48.1.m35] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Aim-To develop methods of messenger RNA (mRNA) in situ hybridisation (ISH) for use with routinely processed bone marrow trephine biopsy specimens, decalcified using formic acid, and long term cultures in order to demonstrate sites of synthesis of mRNA encoding monocyte colony stimulating factor (M-CSF).Methods-Biotinylated oligonucleotide probes, directed against target sequences within M-CSF mRNA, were hybridised with sections from bone marrow trephine biopsy specimens and detected using Streptavidin-biotin alkaline phosphatase complex formation. Validation of results included demonstration of total mRNA and unrelated mRNA species in adjacent sections, with appropriate negative controls. Minor technical modifications were required to perform ISH with long term bone marrow cultures.Results-M-CSF mRNA was demonstrated successfully in trephine biopsy specimens and long term cultures. Biopsy specimens varied in their requirement for predigestion with proteinase K and in the strength of the final reaction product, presumably due to variation in fixation. M-CSF mRNA was present in myelocytes and promonocytes. No stromal production of M-CSF mRNA was detected in biopsy specimens. ISH using long term bone marrow cultures confirmed production of M-CSF mRNA by developing monocytes and macrophages. Weak M-CSF mRNA expression was also seen in stromal fibroblasts.Conclusions-ISH can be performed successfully with formic acid decalcified bone marrow trephine biopsy specimens and long term cultures. The presence of M-CSF mRNA in myelomonocytic cells suggests that an autocrine mechanism contributes to monocyte differentiation. The absence of detectable M-CSF mRNA in biopsy stroma and its presence in stromal fibroblasts within bone marrow cultures probably reflects reduced sensitivity of ISH following tissue fixation and processing.
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Affiliation(s)
- B S Wilkins
- University Department of Pathology, Level E, South Block, Southampton General Hospital, Tremona Road, Southampton SO 16 6YD
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Sharifian A, Humphris J, Leong RWL, Jones DB. Education and imaging. Gastrointestinal: Mycobacterium genavense enteritis in an immunosuppressed patient. J Gastroenterol Hepatol 2009; 24:1474. [PMID: 19702915 DOI: 10.1111/j.1440-1746.2009.05963.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- A Sharifian
- Department of Gastroenterology and Hepatology, Concord Repatriation General Hospital, Concord, New South Wales, Australia
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Endres S, Kratz M, Wunsch S, Jones DB. Zetos: a culture loading system for trabecular bone. Investigation of different loading signal intensities on bovine bone cylinders. J Musculoskelet Neuronal Interact 2009; 9:173-183. [PMID: 19724152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The objective of this investigation was to test the effects of different intensities (1000, 1500, 2000, 3000, and 4000 microstrain) of a physiological loading signal (jumping) on trabecular bone stiffness and osteoid thickness using the ZETOS culture and loading system. Fourty eight bovine bone samples were randomised equally across 6 groups: 5 loading groups and 1 control group. The bone samples were cultured for 26 days (DMEM high glucose medium) and subjected to mechanical stress on 23 days. The stiffness of the samples was determined each day before loading in the loading groups and every 3rd day in the control group. The stiffness measurements in the loaded groups were significantly higher than in the control group. The degree of stiffness increased continuously throughout the observation period in the 1500, 2000, and 3000 microstrain groups. Maximum stiffness was achieved in the 4000 microstrain after a very short time (8th loading day) and then remained constant to the end of the investigation. The osteoid thickness in this group was, however, not higher than in the 2000 and 3000 microstrain groups. The 2000 microstrain group showed the highest proportion of newly formed osteoid. The amounts of osteoid deposited in the 2000, 3000 and 4000 microstrain groups were significantly greater than in the control group. Moreover, a correlation between increasing intensity of the signal and increase in osteoid deposition was observed. Histological investigations were conducted on non-decalcified bone and showed a well-preserved trabecular architecture and cell morphology.
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Affiliation(s)
- S Endres
- Department of Orthopaedic Surgery Elisabeth-Klinik Bigge/Olsberg, Germany
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Qi H, Li DQ, Bian F, Chuang EY, Jones DB, Pflugfelder SC. Expression of glial cell-derived neurotrophic factor and its receptor in the stem-cell-containing human limbal epithelium. Br J Ophthalmol 2008; 92:1269-74. [PMID: 18723744 DOI: 10.1136/bjo.2007.132431] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AIM To evaluate the expression pattern of glial cell line-derived neurotrophic factor (GDNF) with its receptors GDNF family receptor alpha-1 (GFR alpha-1) and Ret in the human corneal and limbal tissues, as well as in the primary human limbal epithelial cultures (PHLEC). METHODS Expression of GDNF and its receptors, and the co-localisation with stem cell associated and differentiation markers were evaluated by immunofluorescent staining, western blot analysis and real-time PCR in the fresh human corneoscleral tissues, as well as in the PHLEC. Single cell colony-forming and wound-healing assays were also evaluated in PHLEC. RESULTS GDNF and GFR alpha-1 were found to be expressed by a subset of basal cells and co-localised with ATP-binding cassette, subfamily G (WHITE), member 2 (ABCG2) and p63, but not with cytokeratin 3 in the human limbal basal epithelium. In PHLEC, they were expressed by a small population of cells in the less differentiated stage. The GDNF and GFR alpha-1-positive subpopulations were enriched for the expression of ABCG2 and p63 (p<0.01). Recombinant human GDNF promoted the proliferation and wound healing of epithelial cells in the PHLEC. In contrast, Ret was abundantly located in the human corneal epithelium except for the basal cells of the limbal epithelium. CONCLUSION These findings indicate that GDNF and GFR alpha-1 may represent a property for the phenotype of human corneal epithelial precursor cells. GDNF may signal independently of Ret through GFR alpha-1 in the stem cell-containing limbal epithelium.
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Affiliation(s)
- H Qi
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
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von Loesecke HW, Gunderson FL, Hucker GJ, Jones DB, Kruse HD, Remington RE, Sherwood RC. Report of the Committee on Foods (Except Milk). (Public Health Aspects of Dehydrated Foods) : Food and Nutrition Section. Am J Public Health Nations Health 2008; 36:248-60. [PMID: 18016318 DOI: 10.2105/ajph.36.3.248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Goldfine AB, Mun EC, Devine E, Bernier R, Baz-Hecht M, Jones DB, Schneider BE, Holst JJ, Patti ME. Patients with neuroglycopenia after gastric bypass surgery have exaggerated incretin and insulin secretory responses to a mixed meal. J Clin Endocrinol Metab 2007; 92:4678-85. [PMID: 17895322 DOI: 10.1210/jc.2007-0918] [Citation(s) in RCA: 292] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CONTEXT AND OBJECTIVE Hyperinsulinemic hypoglycemia is newly recognized as a rare but important complication after Roux-en-Y gastric bypass (GB). The etiology of the syndrome and metabolic characteristics remain incompletely understood. Recent studies suggest that levels of incretin hormones are increased after GB and may promote excessive beta-cell function and/or growth. PATIENTS AND METHODS We performed a cross-sectional analysis of metabolic variables, in both the fasting state and after a liquid mixed-meal challenge, in four subject groups: 1) with clinically significant hypoglycemia [neuroglycopenia (NG)] after GB surgery, 2) with no symptoms of hypoglycemia at similar duration after GB surgery, 3) without GB similar to preoperative body mass index of the surgical cohorts, and 4) without GB similar to current body mass index of the surgical cohorts. RESULTS Insulin and C-peptide after the liquid mixed meal were both higher relative to the glucose level achieved in persons after GB with NG compared with asymptomatic individuals. Glucagon, glucagon-like peptide 1, and glucose-dependent insulinotropic peptide levels were higher in both post-GB surgical groups compared with both overweight and morbidly obese persons, and glucagon-like peptide 1 was markedly higher in the group with NG. Insulin resistance, assessed by homeostasis model assessment of insulin resistance, the composite insulin sensitivity index, or adiponectin, was similar in both post-GB groups. Dumping score was also higher in both GB groups but did not discriminate between asymptomatic and symptomatic patients. Notably, the frequency of asymptomatic hypoglycemia after a liquid mixed meal was high in post-GB patients. CONCLUSION A robust insulin secretory response was associated with postprandial hypoglycemia in patients after GB presenting with NG. Increased incretin levels may contribute to the increased insulin secretory response.
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Affiliation(s)
- A B Goldfine
- Joslin Diabetes Center, One Joslin Place, Boston, Massachusetts 02215, USA.
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Edwards MA, Grinbaum R, Schneider BE, Walsh A, Ellsmere J, Jones DB. Benchmarking hospital outcomes for laparoscopic adjustable gastric banding. Surg Endosc 2007; 21:1950-6. [PMID: 17484002 DOI: 10.1007/s00464-007-9302-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2007] [Revised: 01/14/2007] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
BACKGROUND Since the Food and Drug Administration (FDA) approval of laparoscopic adjustable gastric bands (LAGB) in June 2001, the number LAGB procedures performed in the United States has increased exponentially. This study aimed to benchmark the authors' initial hospital experience to FDA research trials and evidence-based literature. METHODS Over a 2-year period, 87 consecutive patients with a mean age of 43 years (range, 21-64 years) and a body mass index of 45.6 kg/m2 (range, 35-69 kg/m2) underwent an LAGB procedure at the authors' institution. The authors conducted a retrospective review of the outcomes including conversion, reoperation, mortality, perforation, erosion, prolapse, port dysfunction, excess weight loss, and changes in comorbidities, then compared the data with published benchmarks. RESULTS Gender, age, and body mass index were comparable with those of other series. Perioperative adverse events included acute stoma obstruction (n = 1) and respiratory complications (n = 2). Delayed complications included gastric prolapse (n = 4) and port reservoir malposition (n = 4). Five bands were explanted. The mean follow-up period was 14 months (n = 79). The mean percentage of excess weight loss was 30% (range, 4.7-69%) at 6 months, 41% (range, 9.6-82%) at 12 months, and 47% (range, 14-92%) at 24 months. Comorbidities resolved included diabetes (74%), hypertension (57%), gastroesophageal reflux disease (55%) and dyslipidemia (38%). CONCLUSIONS The short-term outcomes for LAGB were comparable with published benchmarks. With adequate weight loss, most patients achieve significant improvement in obesity-related illnesses. With new bariatric accreditation standards and mandates required for financial reimbursement, hospitals will need to demonstrate that their clinical outcomes are consistent with best practices. The authors' early experience shows that LAGB achieves significant weight loss with low mortality and morbidity rates. Despite a more gradual weight loss, most patients achieve excellent weight loss with corresponding improvement of comorbidities within the first 2 years postoperatively.
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Affiliation(s)
- M A Edwards
- Department of Surgery, Medical College of Georgia, 1120 15th Street, BI 4072, Augusta, GA 30912, USA.
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van der Poorten D, Kwok A, Lam T, Ridley L, Jones DB, Ngu MC, Lee AU. Twenty-year audit of percutaneous liver biopsy in a major Australian teaching hospital. Intern Med J 2006; 36:692-9. [PMID: 17040353 DOI: 10.1111/j.1445-5994.2006.01216.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND To examine the changes in indications, patient characteristics, safety and outcomes in consecutive patients undergoing percutaneous core liver biopsies in a major Australian teaching hospital over a period of two decades. METHODS A retrospective audit was carried out on all percutaneous core liver biopsies from a single institution between 1996 and 2005. This was combined with 10 years of data already reported on for the years 1986-1995 to detect trends in indications and outcomes. RESULTS Medical records from 1398 patients were included for analysis. Over a 20-year period, the most common indications for liver biopsy were hepatitis C (37.8%), hepatitis B (26.4%) and abnormal liver function tests (22.2%). Twelve major complications (1.0%) were seen; 10 episodes of haemorrhage, 1 bile leak and 1 visceral perforation. Seven of these patients had an abnormal baseline coagulation profile; a significant risk for major haemorrhage (P < 0.001), resulting in three deaths. All deaths occurred in inpatients with major comorbidities. Minor complications occurred in 13.6% of patients, with multiple passes a significant risk factor. Whereas the overall major and minor complication rates were independent of operator experience inadequate specimens were more frequently obtained by the registrar. CONCLUSION This large series extending over two decades shows that despite advances in biopsy techniques, the rates of both minor and major complications remain significant. Of particular concern are the procedure-related deaths. Identifying factors that may increase risk requires further scrutiny and careful patient selection needs to be undertaken.
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Affiliation(s)
- D van der Poorten
- Department of Gastroenterology and Hepatology, Concord Repatriation General Hospital, Sydney, Australia.
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Schwaitzberg SD, Jones DB, Grunwaldt L, Rattner DW. Laparoscopic hernia in the light of the Veterans Affairs Cooperative Study 456: more rigorous studies are needed. Surg Endosc 2006; 19:1288-9. [PMID: 16025196 DOI: 10.1007/s00464-004-8271-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Affiliation(s)
- C O Johns
- Protein Investigation Laboratory, Bureau of Chemistry, Department of Agriculture, Washington
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Jones DB, Wang F, Winkler DA, Brunger MJ. Orbital based electronic structural signatures of the guanine keto G-7H/G-9H tautomer pair as studied using dual space analysis. Biophys Chem 2006; 121:105-20. [PMID: 16464529 DOI: 10.1016/j.bpc.2005.12.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 12/12/2005] [Accepted: 12/12/2005] [Indexed: 11/27/2022]
Abstract
Electronic structural signatures of the guanine-7H and guanine-9H tautomers have been investigated on an orbital by orbital basis using dual space analysis. A combination of density functional theory (B3LYP/TZVP), the statistical average of model orbital potentials (SAOP/TZ2P) method and outer valence Green's function theory (OVGF/TZVP) has been used to generate optimal tautomer geometries and accurate ionization energy spectra for the guanine tautomer pair. The present work found that the non-planar form for both of the guanine keto pair possesses lower energies than their corresponding planar counterparts, and that the canonical form of the guanine-7H tautomer has slightly lower total energy than guanine-9H. This latter result is in agreement with previous experimental and theoretical findings. In the planar guanine pair the geometric parameters and anisotropic molecular properties are compared, focusing on changes caused by the mobile proton transfer. It is demonstrated that the mobile proton only causes limited disturbance to isotropic properties, such as geometry and the energetics, of the guanine keto tautomer pair. The exception to this general statement is for related local changes such as the N((7))-C((8)) and C((8))-N((9)) bond length resonance between the single and double bonds, reflecting the nitrogen atom being bonded with the mobile proton in the tautomers. The mobile proton distorts the electron distribution of the tautomers, which leads to significant changes in the molecular anisotropic properties. The dipole moment of guanine-7H is altered by about a factor of three, from 2.23 to 7.05 D (guanine-9H), and the molecular electrostatic potentials also reflect significant electron charge distortion. The outer valence orbital momentum distributions, which were obtained using the plane wave impulse approximation (PWIA), have demonstrated quantitatively that the outer valence orbitals of the tautomer pair can be divided into three groups. That is orbitals 1a''-7a'' and 18a', which do not have visible alternations in the tautomeric process (which consist of either pi orbitals or are close to the inner valence shell); a second group comprising orbitals 19a'-22a', 25a', 26a', 28a', 29a' and 31a', which show small perturbations as a result of the mobile hydrogen locations; and group three, orbitals 23a', 24a', 27a', 30a' and 32a', which demonstrate significant changes due to the mobile proton transfer and are therefore considered as signature orbitals of the G-7H/G-9H keto tautomeric process.
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Affiliation(s)
- D B Jones
- School of Chemistry, Physics and Earth Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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Davies CM, Jones DB, Stoddart MJ, Koller K, Smith E, Archer CW, Richards RG. Mechanically loaded ex vivo bone culture system 'Zetos': systems and culture preparation. Eur Cell Mater 2006; 11:57-75; discussion 75. [PMID: 16612792 DOI: 10.22203/ecm.v011a07] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
This paper introduces the culture preparation of ovine, bovine and human cancellous bone cores to be used in an explants model Zetos. The three dimensional (3D) bone cores were prepared and evaluated for all three animals. Bone cells in vivo constantly interact with each other, migratory cells, surrounding extracellular matrix (ECM) and interstitial fluid in a microenvironment, which continuously responds to various endogenous and exogenous stimuli. The Zetos system was designed to culture and mechanically load viable cancellous bone explants in their near natural microenvironment. This 3D ex vivo system bridges the current gap between in vitro and in vivo methods. One aim of this work was to compare the macro and micro-architecture of ovine, bovine and human cancellous bone tissue in preparation for culture within the Zetos system in order to determine the optimal source of experimental material. A second aim was to optimise the preparations of the bone cores as well as develop techniques involved during tissue maintenance. Bone core response was visualised using histological and immunohistochemical methods. The results demonstrate that cancellous bone explants vary greatly in trabecular density and bone volume depending on species, age and location. Sheep and human samples displayed the greatest variation between bones cores when compared to bovine. Even cores taken from the same animal possessed very different characteristics. The histology demonstrated normal bone and cell structure after the core preparation. Immunohistochemistry results demonstrated antigen retention after preparation methods.
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Affiliation(s)
- C M Davies
- AO Research Institute, AO Foundation, Davos, Switzerland
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Jones DB, Lourie GM, Peljovich AE. Intrauterine vascular deficiency secondary to methylenetetrahydrofolate reductase deficiency: 2 case reports. Am J Orthop (Belle Mead NJ) 2006; 35:183-5. [PMID: 16689517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Affiliation(s)
- D Bradley Jones
- Department of Orthopaedic Surgery, Atlanta Medical Center, The Hand Treatment Center, Children's Healthcare of Atlanta at Scottish Rite Hospital, Atlanta, Georgia, USA
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Abstract
AIMS To estimate the propensity of keratomycosis for parallel or secondary bacterial infection and to explore affinities among fungal and bacterial co-isolates. METHODS A retrospective review of laboratory records over 24 years yielded 152 episodes of culture positive fungal keratitis. After collating 65 corneal specimens having bacterial co-isolates, polymicrobial co-infection was defined as detection of concordant bacteria on smear and culture or on two or more different media. RESULTS 30 (20%) keratomycoses met laboratory criteria for polymicrobial infection. The risk of bacterial co-infection was 3.2 (95% confidence interval, 1.7 to 5.8) times greater with yeast keratitis than with filamentous fungal keratitis. CONCLUSIONS Bacterial co-infection occasionally complicates fungal keratitis, particularly candidiasis.
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Affiliation(s)
- J C Pate
- Department of Opthalmology and Visual Science, University of Kentucky College of Medicine, Lexington, KY, USA
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Park GJH, Katelaris PH, Jones DB, Seow F, Lin BPC, Le Couteur DG, Ngu MC. The C-caffeine breath test distinguishes significant fibrosis in chronic hepatitis B and reflects response to lamivudine therapy. Aliment Pharmacol Ther 2005; 22:395-403. [PMID: 16128677 DOI: 10.1111/j.1365-2036.2005.02623.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND The 13C-caffeine breath test is a non-invasive, quantitative test of liver function. AIM To determine the utility of the 13C-caffeine breath test in chronic hepatitis B virus and its ability to monitor response to lamivudine. METHODS Forty-eight chronic hepatitis B virus patients and 24 controls underwent the 13C-caffeine breath test. In 28 patients commenced on lamivudine, 13C-caffeine breath tests were performed at 1 week (n = 12) and after 1 year of therapy. RESULTS Patients with Metavir F0-1 fibrosis (2.30 +/- 1.02 Delta per thousand per 100 mg caffeine) had a 13C-caffeine breath test similar to controls (2.31 +/- 0.85, P = 0.96). However, patients with F2-3 fibrosis (1.59 +/- 0.78, P = 0.047) and cirrhotic patients (0.99 +/- 0.33, P = 0.001) had a decreased 13C-caffeine breath test. Fibrosis correlated best with the 13C-caffeine breath test (r(s) = -0.62, P < 0.001). The 13C-caffeine breath test independently predicted significant (F > or = 2) and advanced (F > or = 3) fibrosis and yielded the greatest area under the receiver operating characteristic curve (0.91 +/- 0.04) for predicting advanced fibrosis. The 13C-caffeine breath test was unaltered by 1 week of lamivudine but improved by 61% (P < 0.001) in responders to long-term lamivudine, whereas in those with viraemia and elevated alanine aminotransferase, values remained stable or deteriorated. CONCLUSION The 13C-caffeine breath test distinguishes chronic hepatitis B virus-related fibrosis and detects improvement in liver function in response to long-term lamivudine.
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Affiliation(s)
- G J-H Park
- Department of Gastroenterology and Hepatology, The University of Sydney, Concord Hospital, Concord, NSW, Australia.
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Hoberg M, Gratz HH, Noll M, Jones DB. Mechanosensitivity of human osteosarcoma cells and phospholipase C β2 expression. Biochem Biophys Res Commun 2005; 333:142-9. [PMID: 15939402 DOI: 10.1016/j.bbrc.2005.05.088] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Accepted: 05/18/2005] [Indexed: 11/22/2022]
Abstract
Bone adapts to mechanical load by osteosynthesis, suggesting that osteoblasts might respond to mechanical stimuli. We therefore investigated cell proliferation and phospholipase C (PLC) expression in osteoblasts. One Hertz uniaxial stretching at 4000 microstrains significantly increased the proliferation rates of human osteoblast-like osteosarcoma cell line MG-63 and primary human osteoblasts. However, U-2/OS, SaOS-2, OST, and MNNG/HOS cells showed no significant changes in proliferation rate. We investigated the expression pattern of different isoforms of PLC in these cell lines. We were able to detect PLC beta1, beta3, gamma1, gamma2, and delta1 in all cells, but PLC beta2 was only detectable in the mechanosensitive cells. We therefore investigated the possible role of PLC beta2 in mechanotransduction. Inducible antisense expression for 24h inhibited the translation of PLC beta1 in U-2/OS cells by 35% and PLC beta2 in MG-63 by 29%. Fluid shear flow experiments with MG-63 lacking PLC beta2 revealed a significantly higher level of cells losing attachment to coverslips and a significantly lower number of cells increasing intracellular free calcium.
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Affiliation(s)
- M Hoberg
- Department of Orthopaedics, University of Tuebingen, Germany.
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Abstract
In order to assess how bone substitute materials determine bone formation in vivo it is useful to understand the mechanisms of the material surface/tissue interaction on a cellular level. Artificial materials are used in two applications, as biomaterials alone or as a scaffold for osteoblasts in a tissue engineering approach. Recently, many efforts have been undertaken to improve bone regeneration by the use of structured material surfaces. In vitro studies of bone cell responses to artificial materials are the basic tool to determine these interactions. Surface properties of materials surfaces as well as biophysical constraints at the biomaterial surface are of major importance since these features will direct the cell responses. Studies on osteoblastlike cell reactivity towards materials will have to focus on the different steps of protein and cell reactions towards defined surface properties. The introduction of new techniques allows nowadays the fabrication of materials with ordered surface structures. This paper gives a review of present knowledge on the various stages of osteoblast reactions on material surfaces, focused on basic cell events under in vitro conditions. Special emphasis is given to cellular reactions towards ordered nano-sized topographies.
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Affiliation(s)
- U Meyer
- Department of Cranio-Maxillofacial Surgery, University of Münster, Waldeyerstr. 30, D-48149 Münster. Germany.
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Maithel SK, Villegas L, Stylopoulos N, Dawson S, Jones DB. Simulated laparoscopy using a head-mounted display vs traditional video monitor: an assessment of performance and muscle fatigue. Surg Endosc 2004; 19:406-11. [PMID: 15624063 DOI: 10.1007/s00464-004-8177-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Accepted: 10/12/2004] [Indexed: 11/30/2022]
Abstract
BACKGROUND The direction of visual gaze may be an important ergonomic factor that affects operative performance. We designed a study to determine whether a head-mounted display (HMD) worn by the surgeon would improve task performance and/or reduce muscle fatigue during a laparoscopic task when compared to the use of a traditional video monitor display (VMD). METHODS Surgical residents (n = 30) were enrolled in the study. A junior group, consisting of 15 postgraduate year (PGY) = 1 subjects with no previous laparoscopic experience, and a senior group, consisting of 15 PGY 4 and PGY 5 subjects with experience, completed a laparoscopic task that was repeated four times using the Computer Enhanced Laparoscopic Training System (CELTS). Groups alternated between using the HMD with the task placed in a downward frontal position and the VMD with the task at a 30 degrees lateral angle. The CELTS module assessed task completion time, depth perception, path length of instruments, response orientation, motion smoothness; the system then generated an overall score. Electromyography (EMG) was used to record sternocleidomastoid muscle activity. Display preference was surveyed. RESULTS The senior residents performed better than the junior residents overall on all parameters (p < 0.05) except for motion smoothness, where there was no difference. In both groups, the HMD significantly improved motion smoothness when compared to the VMD (p < 0.05). All other parameters were equal. There was less muscle fatigue when using the VMD (p < 0.05). We found that 66% of the junior residents but only 20% of the senior residents preferred the HMD. CONCLUSIONS The CELTS module demonstrated evidence of construct validity by differentiating the performances of junior and senior residents. By aligning the surgeon's visual gaze with the instruments, HMD improved smoothness of motion. Experienced residents preferred the traditional monitor display. Although the VMD produced less muscle fatigue, inexperienced residents preferred the HMD, possibly because of improved smoothness of motion.
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Affiliation(s)
- S K Maithel
- Department of Minimally Invasive Surgery, Beth Israel Deaconess Medical Center, 330 Brookline Ave, Boston, MA 02215, USA
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Jones DB, Provost DA, DeMaria EJ, Smith CD, Morgenstern L, Schirmer B. Optimal management of the morbidly obese patient SAGES appropriateness conference statement. Surg Endosc 2004; 18:1029-37. [PMID: 15162240 DOI: 10.1007/s00464-004-8132-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Accepted: 03/12/2004] [Indexed: 10/26/2022]
Abstract
BACKGROUND Obesity is a growing health problem that contributes to numerous life-threatening or disabling disorders, including coronary artery disease, hypertension, type 2 diabetes mellitus, hyperlipidemia, degenerative joint disease, and obstructive sleep apnea. Significant weight reduction in the morbidly obese improves or reverses associated illness and benefits well-being. The purpose of the SAGES Appropriateness Conference was to summarize the state of the art for open and laparoscopic operations for the morbidly obese. METHODS The English literature comparing bariatric procedures was reviewed and grouped by level of evidence by three surgeons (BS, LV, and CC). From more than 1,500 articles, all conference participants were provided with reprints and table summaries of no less than 50 selected manuscripts. Ten experts were requested to present reviews and make evidence-based arguments for and against the open and laparoscopic approaches in written format. An expert panel of six surgeons, including an ethicist and patient, commented on implications of data presented. The finalized statement was e-mailed to all participants for approval and comment. RESULTS Consensus statements were achieved on various aspects of morbid obesity, including indications for surgery, resolution of comorbid illnesses with significant weight loss, and the importance of committed bariatric program. Our panel of experts agreed, in general, to the advantages of laparoscopic approaches compared to open operations in skilled hands. CONCLUSIONS Laparoscopic Roux-en-Y gastric bypass (RYGB) affords improved short-term recovery compared to open gastric bypass. Laparoscopic adjustable banding can be performed with lower average mortality than either RYGB or any of the malabsorptive operations, and it produces variable degrees of short-term weight loss. Prospective randomized trials are needed to compare gastric bypass, malabsorptive, and restrictive procedures.
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Affiliation(s)
- D B Jones
- Harvard Medical School, Section of Minimally Invasive Surgery, Bariatric Program, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.
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