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Sanders TJ, Allen JL, Horvat J, Lewis RA. Theoretical modeling of the terahertz spectrum of l-tyrosine leads to experimental verification of previously unobserved vibrational mode. J Chem Phys 2023; 159:105103. [PMID: 37702359 DOI: 10.1063/5.0165307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
We have calculated the theoretical terahertz spectrum of the amino acid l-tyrosine using density functional theory (DFT). We tried two electron density functionals, Perdew-Burke-Ernzerhof (PBE) and PBE-d3. PBE-d3 includes dispersion corrections to build in van der Waals interactions, which play a role in intermolecular bonding. Both DFT models predicted a low-frequency mode that has not been previously reported. We designed an experiment to search for this mode. Using a deliberately thick sample, intense synchrotron radiation, low temperatures, and temperature variation has enabled us to observe a new resonance at 1.79 ±0.01 THz. While the PBE and PBE-d3 spectra are similar and both match the low-energy experimental data, overall the PBE-d3 appears to be slightly superior. Further refinement still of the functional may lead to even better agreement with experiment above 2.4 THz.
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Affiliation(s)
- T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong NSW 2522, Australia
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd., Clayton, VIC 3168, Australia
| | - J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong NSW 2522, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong NSW 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong NSW 2522, Australia
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Lewis RA, Kashongwe OB, Bebe BO. Quantifying production losses associated with foot and mouth disease outbreaks on large-scale dairy farms in Rift valley, Kenya. Trop Anim Health Prod 2023; 55:293. [PMID: 37608201 DOI: 10.1007/s11250-023-03707-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 07/28/2023] [Indexed: 08/24/2023]
Abstract
Foot and Mouth Disease (FMD) is a contagious viral disease to which dairy cattle are highly susceptible. An outbreak of FMD in a dairy herds can cause a drop in milk yield, increase mastitis infections, and force culling. These production losses can be substantial, but farmers undervalue the magnitude of the loss that they incur. The study quantified the association of FMD outbreaks with milk yield, mastitis incidences, and culling rates. The data was from three large-scale dairy farms with a recent history (2008 to 2018) of FMD outbreaks in a region endemic for the prevalence of serotype C of the FMD virus since the mid-1980s in the Rift valley of Kenya. A total of 507 cows were monitored for three consecutive periods of six weeks before, during, and after FMD outbreaks. Relative to the period before and after the disease outbreak, production losses were marked during the outbreak. A disease outbreak was associated with up to 4.7% of the cows drying off (n = 24) and milk production dropped by 16.1%. The incidence of mastitis increased from 5.4% to 21.5% (OR = 3.31, CI = 2.27, 4.83) and culling rates increased from 0.59% to 3.8% (OR = 6.71, CI = 1.99, 22.58).
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Affiliation(s)
- R A Lewis
- Department of Animal Sciences, Faculty of Agriculture, University of Egerton, Njoro, Kenya.
- Department of Animal Production, Faculty of Natural Resources and Environmental Studies, University of Juba, Juba, South Sudan.
| | - O B Kashongwe
- Department of Animal Sciences, Faculty of Agriculture, University of Egerton, Njoro, Kenya
| | - B O Bebe
- Department of Animal Sciences, Faculty of Agriculture, University of Egerton, Njoro, Kenya
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Allen JL, Sanders TJ, Horvat J, Lewis RA, Rule KC. Determination of Vibrational Modes of l-Alanine Single Crystals by a Combination of Terahertz Spectroscopy Measurements and Density Functional Calculations. Phys Rev Lett 2023; 130:226901. [PMID: 37327443 DOI: 10.1103/physrevlett.130.226901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Density-functional theory may be used to predict both the frequency and the dipole moment of the fundamental oscillations of molecular crystals. Suitably polarized photons at those frequencies excite such oscillations. Thus, in principle, terahertz spectroscopy may confirm the calculated fundamental modes of amino acids. However, reports to date have multiple shortcomings: (a) material of uncertain purity and morphology and diluted in a binder material is employed; (b) consequently, vibrations along all crystal axes are excited simultaneously; (c) data are restricted to room temperature, where resonances are broad and the background dominant; and (d) comparison with theory has been unsatisfactory (in part because the theory assumes zero temperature). Here, we overcome all four obstacles, in reporting detailed low-temperature polarized THz spectra of single-crystal l-alanine, assigning vibrational modes using density-functional theory, and comparing the calculated dipole moment vector direction to the electric field polarization of the measured spectra. Our direct and detailed comparison of theory with experiment corrects previous mode assignments for l-alanine, and reveals unreported modes, previously obscured by closely spaced spectral absorptions. The fundamental modes are thereby determined.
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Affiliation(s)
- J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - K C Rule
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales 2234, Australia
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Sanders TJ, Allen JL, Plathe R, Appadoo D, Horvat J, Lewis RA. Terahertz tyrosine modes. Spectrochim Acta A Mol Biomol Spectrosc 2023; 286:121970. [PMID: 36302282 DOI: 10.1016/j.saa.2022.121970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/08/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
We have measured the terahertz spectrum of pure l-tyrosine at nineteen temperatures in the range 6K to 300K using a synchrotron as the source of radiation. By fitting the temperature dependence of the observed modes with a Bose-Einstein model, we determine unequivocal low-frequency modes of l-tyrosine at absolute zero temperature occur at 1.02 ± 0.01, 1.61 ± 0.01, 1.97 ± 0.01, and 2.19 ± 0.01THz. This determination is consistent with the more reliable of the earlier measurements. We conclude that many of the recently reported features in the terahertz spectrum of l-tyrosine are experimental artefacts.
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Affiliation(s)
- T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia.
| | - J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R Plathe
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - D Appadoo
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
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Allen JL, Sanders TJ, Plathe R, Appadoo D, Horvat J, Lewis RA. Temperature-dependent terahertz spectroscopy of l-phenylalanine. Spectrochim Acta A Mol Biomol Spectrosc 2021; 260:119922. [PMID: 34058666 DOI: 10.1016/j.saa.2021.119922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/27/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Undiluted l-phenylalanine has been cooled to 6K and its transmission spectrum obtained under terahertz radiation from a synchrotron source. Three distinct absorption bands are evident: at 1.37, 2.14, and 2.32THz. Each of these tracks to lower frequency ("redshifts") as the temperature is increased from 6 to 250K. The observed shifts are in the range of 0.1-0.2THz. The form of the temperature dependence is well accounted for by a Bose-Einstein model, from which the zero-temperature frequency of each mode and the characteristic temperature of the associated phonon bath may be estimated. At 6K a fourth band is evident, at 2.65THz. However, the depth of this, touching the noise floor, coupled with the increasing opacity of the sample with temperature for frequencies beyond 2.5THz, makes it difficult to track. The frequencies of all four modes are in good accord with and thus confirm a previous calculation.
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Affiliation(s)
- J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia.
| | - T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R Plathe
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - D Appadoo
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
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Sanders TJ, Allen JL, Horvat J, Lewis RA. High-quality, temperature-dependent terahertz spectroscopy of single crystalline L-alanine: Experiment and density-functional theory. J Chem Phys 2021; 154:244311. [PMID: 34241345 DOI: 10.1063/5.0054063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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
For the first time, the terahertz transmittance spectra of l-alanine have been measured using a single crystal. Measurements were obtained over a large temperature range (12-300 K) and revealed 18 absorptions between 20 and 250 cm-1. These modes were sharp and symmetric, a feature of single crystals and low temperatures. The spectra were directly compared to those of a powdered pellet sample. Raman spectroscopy and x-ray diffraction were used to confirm the sample's structure and purity. With increasing temperature, all modes exhibit spectral redshift, well described by a Bose-Einstein model, indicating the phonon origin of the absorptions. The exceptions are the 91 and 128 cm-1 modes. The former blueshifts. The latter initially blueshifts but transitions to redshifting. Both behaviors are anomalous. Density-functional theory modeling helped assign all the observed modes.
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Affiliation(s)
- T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia
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Sanders TJ, Allen JL, Plathe R, Horvat J, Lewis RA. The 3, 5, 6, and 7 THz resonances of α-glycine. Spectrochim Acta A Mol Biomol Spectrosc 2021; 253:119544. [PMID: 33631628 DOI: 10.1016/j.saa.2021.119544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Using an optically thin single crystal sample, mounted in a cryostat permitting cooling to 6 K, and a synchrotron as a bright light source, exceptionally well defined absorption spectra of well-characterised α-glycine have been obtained in the spectral range 2.5-7.5 THz (approximately 80-240 cm-1). Four separate resonances have been observed, respectively at 93, 152, 188, and 223 cm-1 at the lowest temperature. Each reduces in frequency (redshifts) as temperature increases. The origin of this observed behaviour is attributed to a phonon-mediated anharmonicity in the crystal potential.
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Affiliation(s)
- T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia.
| | - J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R Plathe
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
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Abstract
The terahertz (THz) spectrum of dl-alanine has been measured for the first time at cryogenic temperatures and with a pure sample. Several sharp absorptions are observed, over a wide frequency range (0.8-4.8 THz), at 8 K. The sample structure and purity were confirmed with both Raman spectroscopy and X-ray diffraction. Temperature dependent spectra revealed redshifting, with increasing temperature, for all modes except one at 2.70 THz. This mode exhibits blueshifting until ≈120 K, where it starts to redshift. A Bose-Einstein distribution has been used to model the frequency shift with temperature for the four lowest energy modes. Strong correlations between the fits and data indicate that these modes are caused by phonon excitation in an anharmonic potential. Density functional theory has also been used to identify the origin of these low frequency modes. They are attributed to large scale molecular vibrations.
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Affiliation(s)
- T J Sanders
- Institute of Superconducting and Electronic Materials, School of Physics, University of Wollongong, Wollongong, NSW 2522, Australia.
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Allen JL, Sanders TJ, Horvat J, Lewis RA. Anharmonicity-driven redshift and broadening of sharp terahertz features of α-glycine single crystal from 20 K to 300 K: Theory and experiment. Spectrochim Acta A Mol Biomol Spectrosc 2021; 244:118635. [PMID: 32858447 DOI: 10.1016/j.saa.2020.118635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
For the first time, large single crystals of the simplest amino acid, glycine, have been used to determine the temperature dependence of its terahertz spectrum. High-quality spectra with very sharp absorption features are observed at cryogenic temperatures. The α-glycine structure and the purity of the crystals were verified via Raman spectroscopy and X-ray diffraction. Spectral redshift with increasing temperature was observed for all absorption bands in the terahertz region (10-250 cm-1, or 1-8 THz) over the temperature range of 20-300 K. X-ray diffraction revealed expansion in all planes of the crystal lattice over the same temperature range. A Bose-Einstein distribution was used to model the frequency position shift of the two lowest-energy fundamental modes at 50 cm-1 and 69 cm-1. On this basis, we attribute the observed redshift and broadening with increasing temperature to the anharmonic potential associated with the phonon bath.
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Affiliation(s)
- J L Allen
- Institute for Superconducting and Electronic Materials, School of Physics, University of Wollongong, Wollongong, NSW 2522, Australia.
| | - T J Sanders
- Institute for Superconducting and Electronic Materials, School of Physics, University of Wollongong, Wollongong, NSW 2522, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials, School of Physics, University of Wollongong, Wollongong, NSW 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials, School of Physics, University of Wollongong, Wollongong, NSW 2522, Australia
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Abstract
OBJECTIVE To estimate the daily dietary energy intake for me to maintain a constant body weight. How hard can it be? DESIGN Very introspective study. SETTING At home. In lockdown. (Except every Tuesday afternoon and Saturday morning, when I went for a run.) PARTICIPANTS: Me. n=1. MAIN OUTCOME MEASURES My weight, measured each day. RESULTS Sleeping, I shed about a kilogram each night (1.07 (SD 0.25) kg). Running 5 km, I shed about half a kilogram (0.57 (SD 0.15) kg). My daily equilibrium energy intake is about 10 000 kJ (10 286 (SD 201) kJ). Every kJ above (or below) 10 000 kJ adds (or subtracts) about 40 mg (35.4 (SD 3.2) mg). CONCLUSIONS Body weight data show persistent variability, even when the screws of control are tightened and tightened.
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Affiliation(s)
- R A Lewis
- School of Physics, Faculty of Engineering and Information Sciences, University of Wollongong, Wollongong NSW 2522, Australia
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Squires AD, Zaczek AJ, Lewis RA, Korter TM. Identifying and explaining vibrational modes of quinacridones via temperature-resolved terahertz spectroscopy: absorption experiments and solid-state density functional theory simulations. Phys Chem Chem Phys 2020; 22:19672-19679. [PMID: 32830208 DOI: 10.1039/d0cp03150j] [Citation(s) in RCA: 4] [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: 01/22/2023]
Abstract
Quinacridone and its substituted analogs are pigments widely used in art and industry. The temperature dependence of the crystal structures of two quinacridone polymorphs (β and γ), along with the common variant 2,9-dimethylquinacridone, were investigated using powder X-ray diffraction and terahertz spectroscopy. These were then compared with solid-state density functional theory simulations of both structures and vibrations. X-ray patterns were collected at eight temperatures in the range 13-298 K and terahertz spectra at fifteen temperatures in the range 20-300 K. Simulations were at absolute zero and at appropriate expansions to model room temperature. It was found that some of the powder X-ray diffraction features in only β-quinacridone (15.7°, 19.7° and 31.2° at 13 K) underwent anomalous shifting with temperature change. We attribute this to the unique coplanar hydrogen bonding pattern of β-quinacridone compared to the other solids, with the unusual diffraction peaks originating from crystallographic planes perpendicular to the a axis intermolecular hydrogen bonds. This observation coincides with a contraction of the a axis with heating and results from its relatively weak N-HO hydrogen bonds and significant C-HH-C repulsions. Associated with this anomalous contraction, for β-quinacridone only spectral peaks are seen to increase in energy with temperature.
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Affiliation(s)
- A D Squires
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia.
| | - Adam J Zaczek
- Department of Chemistry, Syracuse University, 1-1014 Center for Science and Technology, Syracuse, New York 13244-4100, USA.
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia.
| | - Timothy M Korter
- Department of Chemistry, Syracuse University, 1-1014 Center for Science and Technology, Syracuse, New York 13244-4100, USA.
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Lord J, McMullan DJ, Eberhardt RY, Rinck G, Hamilton SJ, Quinlan-Jones E, Prigmore E, Keelagher R, Best SK, Carey GK, Mellis R, Robart S, Berry IR, Chandler KE, Cilliers D, Cresswell L, Edwards SL, Gardiner C, Henderson A, Holden ST, Homfray T, Lester T, Lewis RA, Newbury-Ecob R, Prescott K, Quarrell OW, Ramsden SC, Roberts E, Tapon D, Tooley MJ, Vasudevan PC, Weber AP, Wellesley DG, Westwood P, White H, Parker M, Williams D, Jenkins L, Scott RH, Kilby MD, Chitty LS, Hurles ME, Maher ER. Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study. Lancet 2019; 393:747-757. [PMID: 30712880 PMCID: PMC6386638 DOI: 10.1016/s0140-6736(18)31940-8] [Citation(s) in RCA: 352] [Impact Index Per Article: 70.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Fetal structural anomalies, which are detected by ultrasonography, have a range of genetic causes, including chromosomal aneuploidy, copy number variations (CNVs; which are detectable by chromosomal microarrays), and pathogenic sequence variants in developmental genes. Testing for aneuploidy and CNVs is routine during the investigation of fetal structural anomalies, but there is little information on the clinical usefulness of genome-wide next-generation sequencing in the prenatal setting. We therefore aimed to evaluate the proportion of fetuses with structural abnormalities that had identifiable variants in genes associated with developmental disorders when assessed with whole-exome sequencing (WES). METHODS In this prospective cohort study, two groups in Birmingham and London recruited patients from 34 fetal medicine units in England and Scotland. We used whole-exome sequencing (WES) to evaluate the presence of genetic variants in developmental disorder genes (diagnostic genetic variants) in a cohort of fetuses with structural anomalies and samples from their parents, after exclusion of aneuploidy and large CNVs. Women were eligible for inclusion if they were undergoing invasive testing for identified nuchal translucency or structural anomalies in their fetus, as detected by ultrasound after 11 weeks of gestation. The partners of these women also had to consent to participate. Sequencing results were interpreted with a targeted virtual gene panel for developmental disorders that comprised 1628 genes. Genetic results related to fetal structural anomaly phenotypes were then validated and reported postnatally. The primary endpoint, which was assessed in all fetuses, was the detection of diagnostic genetic variants considered to have caused the fetal developmental anomaly. FINDINGS The cohort was recruited between Oct 22, 2014, and June 29, 2017, and clinical data were collected until March 31, 2018. After exclusion of fetuses with aneuploidy and CNVs, 610 fetuses with structural anomalies and 1202 matched parental samples (analysed as 596 fetus-parental trios, including two sets of twins, and 14 fetus-parent dyads) were analysed by WES. After bioinformatic filtering and prioritisation according to allele frequency and effect on protein and inheritance pattern, 321 genetic variants (representing 255 potential diagnoses) were selected as potentially pathogenic genetic variants (diagnostic genetic variants), and these variants were reviewed by a multidisciplinary clinical review panel. A diagnostic genetic variant was identified in 52 (8·5%; 95% CI 6·4-11·0) of 610 fetuses assessed and an additional 24 (3·9%) fetuses had a variant of uncertain significance that had potential clinical usefulness. Detection of diagnostic genetic variants enabled us to distinguish between syndromic and non-syndromic fetal anomalies (eg, congenital heart disease only vs a syndrome with congenital heart disease and learning disability). Diagnostic genetic variants were present in 22 (15·4%) of 143 fetuses with multisystem anomalies (ie, more than one fetal structural anomaly), nine (11·1%) of 81 fetuses with cardiac anomalies, and ten (15·4%) of 65 fetuses with skeletal anomalies; these phenotypes were most commonly associated with diagnostic variants. However, diagnostic genetic variants were least common in fetuses with isolated increased nuchal translucency (≥4·0 mm) in the first trimester (in three [3·2%] of 93 fetuses). INTERPRETATION WES facilitates genetic diagnosis of fetal structural anomalies, which enables more accurate predictions of fetal prognosis and risk of recurrence in future pregnancies. However, the overall detection of diagnostic genetic variants in a prospectively ascertained cohort with a broad range of fetal structural anomalies is lower than that suggested by previous smaller-scale studies of fewer phenotypes. WES improved the identification of genetic disorders in fetuses with structural abnormalities; however, before clinical implementation, careful consideration should be given to case selection to maximise clinical usefulness. FUNDING UK Department of Health and Social Care and The Wellcome Trust.
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Affiliation(s)
| | - Dominic J McMullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | | | | | - Susan J Hamilton
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Elizabeth Quinlan-Jones
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK; Centre for Women's and Newborn Health, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | | | - Rebecca Keelagher
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Sunayna K Best
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Georgina K Carey
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Rhiannon Mellis
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Sarah Robart
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Ian R Berry
- The Leeds Genetics Laboratory, St James's University Hospital, Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Deirdre Cilliers
- Oxford Genomic Medicine Centre, Nuffield Orthopaedic Centre, Oxford, UK
| | - Lara Cresswell
- Department of Cytogenetics, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Sandra L Edwards
- Cytogenetics Service, Norfolk and Norwich University Hospital Foundation Trust, Norwich, UK
| | - Carol Gardiner
- West of Scotland Genetics Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - Alex Henderson
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Simon T Holden
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Tessa Homfray
- South West Thames Regional Genetics Centre, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Tracy Lester
- Oxford Regional Genetics Services, The Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rebecca A Lewis
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - Ruth Newbury-Ecob
- Department of Clinical Genetics, St Michael's Hospital, University Hospitals Bristol, Bristol, UK
| | - Katrina Prescott
- Chapel Allerton Hospital, Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Oliver W Quarrell
- Department of Clinical Genetics, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Eileen Roberts
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, Bristol, UK
| | - Dagmar Tapon
- Centre for Fetal Care, Queen Charlotte's and Chelsea Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Madeleine J Tooley
- Department of Clinical Genetics, St Michael's Hospital, University Hospitals Bristol, Bristol, UK
| | - Pradeep C Vasudevan
- Department of Clinical Genetics, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Astrid P Weber
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Diana G Wellesley
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Paul Westwood
- West of Scotland Genetics Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - Helen White
- Faculty of Medicine, University of Southampton, Southampton, UK; Wessex Regional Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Michael Parker
- The Ethox Centre, Nuffield Department of Population Health and Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, UK
| | - Denise Williams
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Lucy Jenkins
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Richard H Scott
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | - Mark D Kilby
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK; Centre for Women's and Newborn Health, Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Lyn S Chitty
- North East Thames Regional Genetics Service, UCL Great Ormond Street Institute of Child Health, Great Ormond Street NHS Foundation Trust, London UK
| | | | - Eamonn R Maher
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medical Genetics, University of Cambridge, Cambridge, UK; Cambridge Biomedical Research Centre, National Institute for Health Research, Cambridge, UK.
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Lepodise LM, Horvat J, Lewis RA. Superficial and Fundamental Correspondences in the Terahertz/IR (6-15 THz) Absorption Spectra of Aspirin and Benzoic Acid. J Phys Chem A 2018; 122:6886-6893. [PMID: 30060668 DOI: 10.1021/acs.jpca.8b05393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The terahertz absorption spectra of aspirin and benzoic acid have been measured in the range 200-500 cm-1 (6-15 THz). Density-functional theory (DFT) modeling has assigned fundamental vibrational modes to the observed absorption bands. Hydrogen bonds between the crystalline planes of aspirin resulted in better agreement between the experimental and modeled spectra than for benzoic acid. The similar structure of these two molecules suggests a similar absorption spectrum, which indeed was obtained experimentally. However, the detailed crystal structure and molecular differences result in some of the apparently common absorption bands being assigned to different vibrational modes through the DFT modeling. Thus, our study importantly reveals that even though crystalline forms of two similar molecules may have similar experimental terahertz spectra, the resemblance may be superficial rather than fundamental.
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Affiliation(s)
- L M Lepodise
- Botswana International University of Science and Technology , Palapye , Botswana.,School of Physics and Institute for Superconducting and Electronic Materials , University of Wollongong , Wollongong , NSW 2522 , Australia
| | - J Horvat
- School of Physics and Institute for Superconducting and Electronic Materials , University of Wollongong , Wollongong , NSW 2522 , Australia
| | - R A Lewis
- School of Physics and Institute for Superconducting and Electronic Materials , University of Wollongong , Wollongong , NSW 2522 , Australia
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Steele JA, Horvat J, Lewis RA, Henini M, Fan D, Mazur YI, Dorogan VG, Grant PC, Yu SQ, Salamo GJ. Mechanism of periodic height variations along self-aligned VLS-grown planar nanostructures. Nanoscale 2015; 7:20442-20450. [PMID: 26584058 DOI: 10.1039/c5nr06676j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this study we report in-plane nanotracks produced by molecular-beam-epitaxy (MBE) exhibiting lateral self-assembly and unusual periodic and out-of-phase height variations across their growth axes. The nanotracks are synthesized using bismuth segregation on the GaAsBi epitaxial surface, which results in metallic liquid droplets capable of catalyzing GaAsBi nanotrack growth via the vapor-liquid-solid (VLS) mechanism. A detailed examination of the nanotrack morphologies is carried out employing a combination of scanning electron and atomic force microscopy and, based on the findings, a geometric model of nanotrack growth during MBE is developed. Our results indicate diffusion and shadowing effects play significant roles in defining the interesting nanotrack shape. The unique periodicity of our lateral nanotracks originates from a rotating nucleation "hot spot" at the edge of the liquid-solid interface, a feature caused by the relative periodic circling of the non-normal ion beam flux incident on the sample surface, inside the MBE chamber. We point out that such a concept is divergent from current models of crawling mode growth kinetics and conclude that these effects may be utilized in the design and assembly of planar nanostructures with controlled non-monotonous structure.
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Affiliation(s)
- J A Steele
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia..
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Lepodise LM, Horvat J, Lewis RA. Terahertz (6-15 THz) Spectroscopy and Numerical Modeling of Intermolecular Vibrations in Benzoic Acid and Its Derivatives. Appl Spectrosc 2015; 69:590-596. [PMID: 25909770 DOI: 10.1366/14-07658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Terahertz spectroscopy of benzoic acid (BA) and two of its derivatives, 2-hydroxybenzoic acid (2OH-BA) and 3-hydroxybenzoic acid (3OH-BA), has been investigated in the spectral region 200 to 500 cm(-1) (6.06 to 15.15 THz). The spectra show distinct absorption features. There is agreement between some of the absorption lines observed for these compounds, despite a shift in energy, which is attributed to the differences in the molecular structures. Numerical modeling gave corresponding absorption lines, and this helped in the assignment. Temperature dependence studies revealed that most of the absorption lines are composite lines in this frequency region.
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Affiliation(s)
- Lucia M Lepodise
- School of Physics and Institute for Superconducting and Electronic Materials, University of Wollongong, NSW 2522, Australia
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Abstract
Previous THz spectroscopy of the TNT explosive precursor, 2,4-dinitrotoluene (DNT), has been restricted to room temperature (apart from one set of data at 11 K). Here, for the first time, we investigate the spectrum as the temperature is systematically varied, from 7 to 245 K. Many new features appear in the spectrum on cooling below room temperature. As well as the five absorption lines observed previously, we observe five additional lines. In addition, a new room-temperature line at 8.52 THz (281 cm(-1)) is observed. Six of the lines red-shift with temperature and four of them blue-shift. The blue shift is explained by interplay between intramolecular and intermolecular hydrogen bonds. The variation in line width and line intensity with temperature is not systematic, although a conspicuous decrease in line intensity with temperature is observed in all cases. Modeling with hybrid PBE0 and TPSSh functionals helps identify absorption modes.
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Affiliation(s)
- Lucia M Lepodise
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong , Wollongong, New South Wales 2522, Australia
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Nobile-Orazio E, Lewis RA. 7th International Immunoglobulin Conference: Neurology. Clin Exp Immunol 2014; 178 Suppl 1:45. [PMID: 25546757 DOI: 10.1111/cei.12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Data presented demonstrate the versatility of immunoglobulin (Ig) therapy for a variety of neurological disorders with different pathogenesis and presentations. In indications where the efficacy of Ig is well established, the neurology community is striving to improve the use of this valuable and limited resource by perfecting best practice guidelines, individualizing dosing schemes and investigating combination therapies to enhance treatment benefit. The data showing the efficacy of Ig therapy in conditions such as chronic pain and autoimmune encephalitis are promising. Future challenges for Ig use in neurological disorders were also outlined. Ongoing and upcoming randomized controlled trials will be pivotal to the use of Ig in the future, by identifying responder groups and elucidating the most effective administration practices. As our understanding and use of the therapy increases, it is essential that we collect data on the effects of long-term Ig treatment in neurological conditions, of which very little currently exists.
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Affiliation(s)
- E Nobile-Orazio
- Humanitas Clinical and Research Center, Milan University, Milan, Italy
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Steele JA, Lewis RA. Laser-induced oxidation kinetics of bismuth surface microdroplets on GaAsBi studied in situ by Raman microprobe analysis. Opt Express 2014; 22:32261-32275. [PMID: 25607191 DOI: 10.1364/oe.22.032261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report the cw-laser-induced oxidation of molecular-beam-epitaxy grown GaAsBi bismuth surface microdroplets investigated in situ by micro-Raman spectroscopy under ambient conditions as a function of irradiation power and time. Our results reveal the surface droplets are high-purity crystalline bismuth and the resultant Bi2O3 transformation to be β-phase and stable at room temperature. A detailed Raman study of Bi microdroplet oxidation kinetics yields insights into the laser-induced oxidation process and offers useful real-time diagnostics. The temporal evolution of new β-Bi2O3 Raman modes is shown to be well described by Johnson-Mehl-Avrami-Kolmogorov kinetic transformation theory and while this study limits itself to the laser-induced oxidation of GaAsBi bismuth surface droplets, the results will find application within the wider context of bismuth laser-induced oxidation and direct Raman laser processing.
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Abstract
Immunoglobulin (Ig) therapy has been used and studied as a treatment for a variety of neurological conditions for decades. In some of these disorders Ig therapy has a significant role as a first-line treatment. This session explores the use of Ig therapy in immune-mediated peripheral neuropathies and various central nervous system (CNS) diseases. Informative practice points relating to the management and treatment of these diseases are discussed. Potential future neurological indications for Ig therapy, as well as data on efficacy and possible mechanisms of action, are also presented. In peripheral immune-mediated neuropathies, data show good response rates to Ig therapy and it is often used as a first-line treatment. Intravenous immunoglobulin (IVIg) and subcutaneous immunoglobulin (SCIg) are both well tolerated, but dose and dosing frequency should be based on individual clinical responses. In Alzheimer's disease, although clinical data show no significant differences between IVIg and placebo, biomarker studies indicate that plasma-derived antibodies may be involved in clearance of amyloid aggregates from the brain. Data suggest that the use of high IVIg doses in early-stage Alzheimer's treatment may warrant further investigation. Ig therapy is considered a valuable option for autoimmune encephalitis, an antibody-mediated CNS disease. Combination treatment with IVIg and corticosteroids shows promising results and is proposed as a first-line treatment in these disorders. Until recently, very little was understood about the pathogenesis of chronic pain disorders. Data now indicate that perpetuation of the pain response may be underpinned by central immune activation. Some data suggest that Ig therapy may mitigate this effect, with good response rates in a number of studies, but these data need confirmation.
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Affiliation(s)
- E Nobile-Orazio
- Humanitas Clinical and Research Center, Milan UniversityRozzano, Milan, Italy
| | - R A Lewis
- Cedars-Sinai Medical CenterLos Angeles, CA, USA
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Steele JA, Lewis RA, Henini M, Lemine OM, Fan D, Mazur YI, Dorogan VG, Grant PC, Yu SQ, Salamo GJ. Raman scattering reveals strong LO-phonon-hole-plasmon coupling in nominally undoped GaAsBi: optical determination of carrier concentration. Opt Express 2014; 22:11680-11689. [PMID: 24921290 DOI: 10.1364/oe.22.011680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report room-temperature Raman scattering studies of nominally undoped (100) GaAs1−xBix epitaxial layers exhibiting Bi-induced (p-type) longitudinal-optical-plasmon-coupled (LOPC) modes for 0.018 ≤ x ≤ 0.048. Redshifts in the GaAs-like optical modes due to alloying are evaluated and are paralleled by strong damping of the LOPC. The relative integrated Raman intensities of LO(Γ) and LOPC ALO/ALOPC are characteristic of heavily doped p-GaAs, with a remarkable near total screening of the LO(Γ) phonon (ALO/ALOPC → 0) for larger Bi concentrations. A method of spectral analysis is set out which yields estimates of hole concentrations in excess of 5×1017cm−3 and correlates with the Bi molar fraction. These findings are in general agreement with recent electrical transport measurements performed on the alloy, and while the absolute size of the hole concentrations differ, likely origins for the discrepancy are discussed. We conclude that the damped LO-phonon-hole-plasmon coupling phenomena plays a dominant role in Raman scattering from unpassivated nominally undoped GaAsBi.
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Lepodise LM, Horvat J, Lewis RA. Collective librations of water molecules in the crystal lattice of rubidium bromide: experiment and simulation. Phys Chem Chem Phys 2013; 15:20252-61. [PMID: 24165585 DOI: 10.1039/c3cp53667j] [Citation(s) in RCA: 13] [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: 11/21/2022]
Abstract
Terahertz spectroscopy of RbBr reveals four prominent absorption lines at room temperature and a further 15 lines at 10 K. Via density-functional-theory (DFT) numerical modelling using the PBE0 hybrid GGA functional, all the absorptions are identified as correlated librations of water molecules in the RbBr lattice. Each libration mode is a combination of rocking, wagging and twisting motions of the water molecules. The number of libration lines and numerical modelling show that the C2v symmetry of water in RbBr is broken. Our modelling shows that the distribution of libration amplitudes and phases for different water molecules in the RbBr unit cell varies greatly between the different modes. All librational lines red-shift with increasing temperature. The rate of change for most lines is in the range 60-90 MHz K(-1) (or (2-3) × 10(-3) cm(-1) K(-1)). Two lines shift more rapidly with temperature, at rates of 240 and 300 MHz K(-1) (or (8 and 10) × 10(-3) cm(-1) K(-1)), respectively. Furthermore, the temperature dependence of the linewidth distinguishes two groups of lines. For one group, with weak linear temperature dependence of linewidth, cubic anharmonic terms in the RbBr crystal field are significant. This group is mainly associated with fully symmetric correlated librations. For the second group, with strong non-linear temperature dependence of the linewidth, quartic anharmonic terms in the RbBr crystal field are significant. However, the distribution of libration amplitudes, as well as the type of libration modes, influence the temperature dependence of the red shift, the linewidth, and the intensity, as well. Our combined experimental and theoretical investigation confirms the necessity of obtaining low-temperature data to observe all the calculated modes; moreover, the richness of detail in the temperature dependence of the data invites further modelling spanning a range of temperatures.
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Affiliation(s)
- L M Lepodise
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, Wollongong, New South Wales 2522, Australia.
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Lewis RA, Bruno-Alfonso A, de Souza GVB, Vickers REM, Colla JA, Constable E. Spherical, cylindrical and tetrahedral symmetries; hydrogenic states at high magnetic field in Si:P. Sci Rep 2013; 3:3488. [PMID: 24336145 PMCID: PMC3860012 DOI: 10.1038/srep03488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/26/2013] [Indexed: 11/09/2022] Open
Abstract
Phosphorous donors in silicon have an electronic structure that mimics the hydrogen atom, albeit on a larger length, smaller energy and smaller magnetic field scale. While the hydrogen atom is spherically symmetric, an applied magnetic field imposes cylindrical symmetry, and the solid-state analogue involves, in addition, the symmetry of the Si crystal. For one magnetic field direction, all six conduction-band valleys of Si:P become equivalent. New experimental data to high laboratory fields (30 T), supported by new calculations, demonstrate that this high symmetry field orientation allows the most direct comparison with free hydrogen.
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Affiliation(s)
- R A Lewis
- Institute for Superconducting and Electronic Materials, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - A Bruno-Alfonso
- Faculdade de Ciências, UNESP - Universidade Estadual Paulista, 17033-360, Bauru, SP, Brazil
| | - G V B de Souza
- POSMAT/UNESP - Universidade Estadual Paulista, 17033-360, Bauru, SP, Brazil
| | - R E M Vickers
- Institute for Superconducting and Electronic Materials, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J A Colla
- Institute for Superconducting and Electronic Materials, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - E Constable
- Institute for Superconducting and Electronic Materials, University of Wollongong, Wollongong, New South Wales 2522, Australia
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Du Rand IA, Barber PV, Goldring J, Lewis RA, Mandal S, Munavvar M, Rintoul RC, Shah PL, Singh S, Slade MG, Woolley A. Summary of the British Thoracic Society guidelines for advanced diagnostic and therapeutic flexible bronchoscopy in adults. Thorax 2011; 66:1014-5. [PMID: 22003155 DOI: 10.1136/thoraxjnl-2011-201052] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
This new guideline covers the rapidly advancing field of interventional bronchoscopy using flexible bronchoscopy. It includes the use of more complex diagnostic procedures such as endobronchial ultrasound, interventions for the relief of central airway obstruction due to malignancy and the recent development of endobronchial therapies for chronic obstructive pulmonary disease and asthma. The guideline aims to help all those who undertake flexible bronchoscopy to understand more about this important area. It also aims to inform respiratory physicians and other specialists dealing with lung cancer of the procedures possible in the management and palliation of central airway obstruction. The guideline covers transbronchial needle aspiration and endobronchial ultrasound-guided transbronchial needle aspiration, electrocautery/diathermy, argon plasma coagulation and thermal laser, cryotherapy, cryoextraction, photodynamic therapy, brachytherapy, tracheobronchial stenting, electromagnetic navigation bronchoscopy, endobronchial valves for emphysema and bronchial thermoplasty for asthma.
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Du Rand IA, Barber PV, Goldring J, Lewis RA, Mandal S, Munavvar M, Rintoul RC, Shah PL, Singh S, Slade MG, Woolley A. British Thoracic Society guideline for advanced diagnostic and therapeutic flexible bronchoscopy in adults. Thorax 2011; 66 Suppl 3:iii1-21. [PMID: 21987439 DOI: 10.1136/thoraxjnl-2011-200713] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Sidhu S, Falzon G, Hart SA, Fox JG, Lewis RA, Siu KKW. Classification of breast tissue using a laboratory system for small-angle x-ray scattering (SAXS). Phys Med Biol 2011; 56:6779-91. [DOI: 10.1088/0031-9155/56/21/002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Schaefer E, Zaloszyc A, Lauer J, Durand M, Stutzmann F, Perdomo-Trujillo Y, Redin C, Bennouna Greene V, Toutain A, Perrin L, Gérard M, Caillard S, Bei X, Lewis RA, Christmann D, Letsch J, Kribs M, Mutter C, Muller J, Stoetzel C, Fischbach M, Marion V, Katsanis N, Dollfus H. Mutations in SDCCAG8/NPHP10 Cause Bardet-Biedl Syndrome and Are Associated with Penetrant Renal Disease and Absent Polydactyly. Mol Syndromol 2011; 1:273-281. [PMID: 22190896 DOI: 10.1159/000331268] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2011] [Indexed: 11/19/2022] Open
Abstract
The ciliopathies are an expanding group of disorders caused by mutations in genes implicated in the biogenesis and function of primary cilia. Bardet-Biedl syndrome (BBS) is a model ciliopathy characterized by progressive retinal degeneration, obesity, polydactyly, cognitive impairment, kidney anomalies and hypogonadism. Mutations in SDCCAG8(NPHP10) were described recently in patients with nephronophthisis and retinal degeneration (Senior-Loken syndrome; SLS). Given the phenotypic and genetic overlap between known ciliopathy genes, we hypothesized that mutations in SDCCAG8 might also contribute alleles to more severe, multisystemic ciliopathies. We performed genetic and phenotypic analyses of 2 independent BBS cohorts. Subsequent to mutation screening, we made a detailed phenotypic analysis of 5 families mutated for SDCCAG8 (3 homozygous and 2 compound heterozygous mutations) and conducted statistical analyses across both cohorts to examine possible phenotype-genotype correlations with mutations at this locus. All patients with mutations in SDCCAG8 fulfilled the diagnostic criteria for BBS (retinal degeneration, obesity, cognitive defects, renal failure, hypogonadism). Interestingly, none of the patients with primary SDCCAG8 mutations had polydactyly, a frequent but not obligatory BBS feature. In contrast, the same patients displayed early-onset renal failure, obesity, as well as recurrent pulmonary and ENT infections. Comparison of the phenotypes of these families with our entire BBS cohort indicated that renal impairment and absent polydactyly correlated significantly with causal SDCCAG8 mutations. Thus, SDCCAG8 mutations are sufficient to cause BBS in 1-2% of our combined cohorts, and define this gene as the sixteenth BBS locus (BBS16). The absence of polydactyly and the concomitant, apparently fully penetrant association with early kidney failure represents the first significant genotype-phenotype correlation in BBS that potentially represents an indicator for phenotype-driven priority screening and informs specific patient management.
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Affiliation(s)
- E Schaefer
- Laboratoire de Génétique Médicale EA 3949, Equipe Avenir-Inserm, Faculté de Médecine de Strasbourg, Université de Strasbourg, Strasbourg
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Panov VP, Nagaraj M, Vij JK, Panarin YP, Kohlmeier A, Tamba MG, Lewis RA, Mehl GH. Spontaneous periodic deformations in nonchiral planar-aligned bimesogens with a nematic-nematic transition and a negative elastic constant. Phys Rev Lett 2010; 105:167801. [PMID: 21231015 DOI: 10.1103/physrevlett.105.167801] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Indexed: 05/16/2023]
Abstract
Hydrocarbon linked mesogenic dimers are found to exhibit an additional nematic phase below the conventional uniaxial nematic phase as confirmed by x-ray diffraction. The phase produces unusual periodic stripe domains in planar cells. The stripes are found to be parallel to the rubbing direction (in rubbed cells) with a well-defined period equal to double the cell gap. The stripes appear without external electromagnetic field, temperature or thickness gradients, rubbing or hybrid alignment treatments. Simple modeling proposes a negative sign for at least one of the two elastic constants: splay and twist, as a necessary condition for the observed pattern.
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Affiliation(s)
- V P Panov
- Department of Electronic and Electrical Engineering, Trinity College, University of Dublin, Dublin 2, Ireland
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England JD, Gronseth GS, Franklin G, Carter GT, Kinsella LJ, Cohen JA, Asbury AK, Szigeti K, Lupski JR, Latov N, Lewis RA, Low PA, Fisher MA, Herrmann D, Howard JF, Lauria G, Miller RG, Polydefkis M, Sumner AJ. Practice parameter: the evaluation of distal symmetric polyneuropathy: the role of autonomic testing, nerve biopsy, and skin biopsy (an evidence-based review). Report of the American Academy of Neurology, the American Association of Neuromuscular and Electrodiagnostic Medicine, and the American Academy of Physical Medicine and Rehabilitation. PM R 2009; 1:14-22. [PMID: 19627868 DOI: 10.1016/j.pmrj.2008.11.011] [Citation(s) in RCA: 40] [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] [Received: 11/24/2008] [Accepted: 11/24/2008] [Indexed: 11/17/2022]
Abstract
BACKGROUND Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of autonomic testing, nerve biopsy and skin biopsy for the assessment of polyneuropathy. METHODS A literature review using MEDLINE, EMBASE, Science Citation Index and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based upon the level of evidence. RESULTS AND CONCLUSIONS 1. Autonomic testing may be considered in the evaluation of patients with polyneuropathy to document autonomic nervous system dysfunction (Level B). Such testing should be considered especially for the evaluation of suspected autonomic neuropathy (Level B) and distal small fiber sensory polyneuropathy (SFSN) (Level C). A battery of validated tests is recommended to achieve the highest diagnostic accuracy (Level B). 2. Nerve biopsy is generally accepted as useful in the evaluation of certain neuropathies as in patients with suspected amyloid neuropathy, mononeuropathy multiplex due to vasculitis, or with atypical forms of chronic inflammatory demyelinating polyneuropathy (CIDP). However, the literature is insufficient to provide a recommendation regarding when a nerve biopsy may be useful in the evaluation of DSP (Level U). 3. Skin biopsy is a validated technique for determining intraepidermal nerve fiber (IENF) density and may be considered for the diagnosis of DSP, particularly SFSN (Level C). There is a need for additional prospective studies to define more exact guidelines for the evaluation of polyneuropathy.
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Affiliation(s)
- J D England
- Louisiana State University Health Sciences Center, New Orleans, USA
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England JD, Gronseth GS, Franklin G, Carter GT, Kinsella LJ, Cohen JA, Asbury AK, Szigeti K, Lupski JR, Latov N, Lewis RA, Low PA, Fisher MA, Herrmann DN, Howard JF, Lauria G, Miller RG, Polydefkis M, Sumner AJ. Practice parameter: the evaluation of distal symmetric polyneuropathy: the role of laboratory and genetic testing (an evidence-based review). Report of the American Academy of Neurology, the American Association of Neuromuscular and Electrodiagnostic Medicine, and the American Academy of Physical Medicine and Rehabilitation. PM R 2009. [PMID: 19627867 DOI: 10.1212/01.wnl.0000336370.51010.al] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of laboratory and genetic tests for the assessment of DSP. METHODS A literature review using MEDLINE, EMBASE, Science Citation Index and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based upon the level of evidence. RESULTS AND CONCLUSIONS 1. Screening laboratory tests may be considered for all patients with polyneuropathy (Level C). Those tests that provide the highest yield of abnormality are blood glucose, serum B12 with metabolites (methylmalonic acid with or without homocysteine) and serum protein immunofixation electrophoresis (Level C). If there is no definite evidence of diabetes mellitus by routine testing of blood glucose, testing for impaired glucose tolerance may be considered in distal symmetric sensory polyneuropathy (Level C). 2. Genetic testing is established as useful for the accurate diagnosis and classification of hereditary neuropathies (Level A). Genetic testing may be considered in patients with cryptogenic polyneuropathy who exhibit a hereditary neuropathy phenotype (Level C). Initial genetic testing should be guided by the clinical phenotype, inheritance pattern, and electrodiagnostic (EDX) features and should focus on the most common abnormalities which are CMT1A duplication/HNPP deletion, Cx32 (GJB1), and MFN2 mutation screening. There is insufficient evidence to determine the usefulness of routine genetic testing in patients with cryptogenic polyneuropathy who do not exhibit a hereditary neuropathy phenotype (Level U).
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Affiliation(s)
- J D England
- Louisiana State University Health Sciences Center, New Orleans, USA
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Abstract
An unusual concept for a simple and inexpensive terahertz source is presented: unpeeling adhesive tape. The observed spectrum of this terahertz radiation exhibits a peak at 2 THz and a broader peak at 18 THz. The radiation is not polarized. The mechanism of terahertz radiation is tribocharging of the adhesive tape and subsequent discharge, possibly bremsstrahlung with absorption or energy density focusing during the dielectric breakdown of a gas. The accompanying optical emission is also a consequence of tribocharging.
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Affiliation(s)
- J Horvat
- Institute for Superconducting and Electronic Materials, University of Wollongong, NSW 2522, Australia
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Abstract
OBJECTIVE The objective was to investigate the effect of intranasal phototherapy delivered by a phototherapy device (allergy reliever SN-206) on symptoms of hay fever (seasonal rhinitis) due to grass pollen in adults. This registered class IIA medical device had been on sale for 15 months with no adverse effects reported but there had been no assessment of efficacy. Previous research had indicated that phototherapy could alleviate symptoms of allergic rhinitis but no double-blind, placebo-controlled trails had been done. RESEARCH DESIGN AND METHODS The trial is a double-blind, placebo-controlled grass pollen challenge conducted out of the pollen season, on 101 adult male and female hay fever sufferers. Subjects were assigned to placebo or active groups by stratified random sampling using responses to a baseline questionnaire. All subjects used active or placebo devices three times a day for 14 days before pollen challenge. Subjects were monitored for 2.5 h after challenge. MAIN OUTCOME MEASURES Primary outcome measures were observed severity scores for sneezing, running eyes, running nose, and the amount of eosinophil cationic proteins (ECP) in nasal secretions. Secondary outcome measures were symptom scores by subject report (itching eyes, itching nose, itching throat, itching mouth/palate), and nasal peak inspiratory flow (PIFn) and peak expiratory flow (PEFn). RESULTS Significant reductions in severity of symptom scores were found for sneezing, running nose, running eyes and itchy mouth/palate (p < or = 0.05). No significant differences were found in the results for itchy eyes, itchy nose, itchy throat, ECPs, PIFn and PEFn. No adverse events occurred. CONCLUSIONS The results show that the device significantly reduced some hay fever symptoms. The study would have been improved if compliance was monitored electronically and if nasal congestion was monitored by report. The mode of action is unclear. The study does not consider long-term implications of the therapy.
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Affiliation(s)
- J C Emberlin
- National Pollen and Aerobiology Research Unit, University of Worcester, Worcester, UK.
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33
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England JD, Gronseth GS, Franklin G, Carter GT, Kinsella LJ, Cohen JA, Asbury AK, Szigeti K, Lupski JR, Latov N, Lewis RA, Low PA, Fisher MA, Herrmann D, Howard JF, Lauria G, Miller RG, Polydefkis M, Sumner AJ. Evaluation of distal symmetric polyneuropathy: the role of laboratory and genetic testing (an evidence-based review). Muscle Nerve 2009; 39:116-25. [PMID: 19086068 DOI: 10.1002/mus.21226] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of laboratory and genetic tests for the assessment of DSP. A literature review using MEDLINE, EMBASE, Science Citation Index, and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based on the level of evidence. (1) Screening laboratory tests may be considered for all patients with polyneuropathy (Level C). Those tests that provide the highest yield of abnormality are blood glucose, serum B(12) with metabolites (methylmalonic acid with or without homocysteine), and serum protein immunofixation electrophoresis (Level C). If there is no definite evidence of diabetes mellitus by routine testing of blood glucose, testing for impaired glucose tolerance may be considered in distal symmetric sensory polyneuropathy (Level C). (2) Genetic testing is established as useful for the accurate diagnosis and classification of hereditary neuropathies (Level A). Genetic testing may be considered in patients with cryptogenic polyneuropathy who exhibit a hereditary neuropathy phenotype (Level C). Initial genetic testing should be guided by the clinical phenotype, inheritance pattern, and electrodiagnostic (EDX) features and should focus on the most common abnormalities, which are CMT1A duplication/HNPP deletion, Cx32 (GJB1), and MFN2 mutation screening. There is insufficient evidence to determine the usefulness of routine genetic testing in patients with cryptogenic polyneuropathy who do not exhibit a hereditary neuropathy phenotype (Level U).
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Affiliation(s)
- J D England
- Louisiana State University Health Sciences Center, Baton Rouge, Louisiana, USA
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England JD, Gronseth GS, Franklin G, Carter GT, Kinsella LJ, Cohen JA, Asbury AK, Szigeti K, Lupski JR, Latov N, Lewis RA, Low PA, Fisher MA, Herrmann D, Howard JF, Lauria G, Miller RG, Polydefkis M, Sumner AJ. Evaluation of distal symmetric polyneuropathy: the role of autonomic testing, nerve biopsy, and skin biopsy (an evidence-based review). Muscle Nerve 2009; 39:106-15. [PMID: 19086069 DOI: 10.1002/mus.21227] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of autonomic testing, nerve biopsy, and skin biopsy for the assessment of polyneuropathy. A literature review using MEDLINE, EMBASE, Science Citation Index, and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based on the level of evidence. (1) Autonomic testing may be considered in the evaluation of patients with polyneuropathy to document autonomic nervous system dysfunction (Level B). Such testing should be considered especially for the evaluation of suspected autonomic neuropathy (Level B) and distal small fiber sensory polyneuropathy (SFSN) (Level C). A battery of validated tests is recommended to achieve the highest diagnostic accuracy (Level B). (2) Nerve biopsy is generally accepted as useful in the evaluation of certain neuropathies as in patients with suspected amyloid neuropathy, mononeuropathy multiplex due to vasculitis, or with atypical forms of chronic inflammatory demyelinating polyneuropathy (CIDP). However, the literature is insufficient to provide a recommendation regarding when a nerve biopsy may be useful in the evaluation of DSP (Level U). (3) Skin biopsy is a validated technique for determining intraepidermal nerve fiber (IENF) density and may be considered for the diagnosis of DSP, particularly SFSN (Level C). There is a need for additional prospective studies to define more exact guidelines for the evaluation of polyneuropathy.
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Affiliation(s)
- J D England
- Louisiana State University Health Sciences Center, Baton Rouge, Louisiana, USA
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35
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England JD, Gronseth GS, Franklin G, Carter GT, Kinsella LJ, Cohen JA, Asbury AK, Szigeti K, Lupski JR, Latov N, Lewis RA, Low PA, Fisher MA, Herrmann DN, Howard JF, Lauria G, Miller RG, Polydefkis M, Sumner AJ. Practice Parameter: evaluation of distal symmetric polyneuropathy: role of autonomic testing, nerve biopsy, and skin biopsy (an evidence-based review). Report of the American Academy of Neurology, American Association of Neuromuscular and Electrodiagnostic Medicine, and American Academy of Physical Medicine and Rehabilitation. Neurology 2008; 72:177-84. [PMID: 19056667 DOI: 10.1212/01.wnl.0000336345.70511.0f] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of autonomic testing, nerve biopsy, and skin biopsy for the assessment of polyneuropathy. METHODS A literature review using MEDLINE, EMBASE, and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based upon the level of evidence. RESULTS AND RECOMMENDATIONS 1) Autonomic testing should be considered in the evaluation of patients with polyneuropathy to document autonomic nervous system dysfunction (Level B). Such testing should be considered especially for the evaluation of suspected autonomic neuropathy (Level B) and distal small fiber sensory polyneuropathy (SFSN) (Level C). A battery of validated tests is recommended to achieve the highest diagnostic accuracy (Level B). 2) Nerve biopsy is generally accepted as useful in the evaluation of certain neuropathies as in patients with suspected amyloid neuropathy, mononeuropathy multiplex due to vasculitis, or with atypical forms of chronic inflammatory demyelinating polyneuropathy (CIDP). However, the literature is insufficient to provide a recommendation regarding when a nerve biopsy may be useful in the evaluation of DSP (Level U). 3) Skin biopsy is a validated technique for determining intraepidermal nerve fiber density and may be considered for the diagnosis of DSP, particularly SFSN (Level C). There is a need for additional prospective studies to define more exact guidelines for the evaluation of polyneuropathy.
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Affiliation(s)
- J D England
- American Academy of Neurology, St Paul, MN 55116, USA.
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36
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Crosbie JC, Svalbe I, Midgley SM, Yagi N, Rogers PAW, Lewis RA. A method of dosimetry for synchrotron microbeam radiation therapy using radiochromic films of different sensitivity. Phys Med Biol 2008; 53:6861-77. [DOI: 10.1088/0031-9155/53/23/014] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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37
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Kitchen MJ, Lewis RA, Morgan MJ, Wallace MJ, Siew ML, Siu KKW, Habib A, Fouras A, Yagi N, Uesugi K, Hooper SB. Dynamic measures of regional lung air volume using phase contrast x-ray imaging. Phys Med Biol 2008; 53:6065-77. [DOI: 10.1088/0031-9155/53/21/012] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Shy ME, Chen L, Swan ER, Taube R, Krajewski KM, Herrmann D, Lewis RA, McDermott MP. Neuropathy progression in Charcot-Marie-Tooth disease type 1A. Neurology 2008; 70:378-83. [PMID: 18227419 DOI: 10.1212/01.wnl.0000297553.36441.ce] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [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
OBJECTIVE To determine the rate of disease progression in Charcot-Marie-Tooth disease type 1A (CMT1A). BACKGROUND CMT1A is the most common inherited peripheral neuropathy, affecting approximately 1:5,000 people irrespective of ethnic background or gender. There is no cure for CMT1A. Clinical trials are being initiated that use the CMT Neuropathy Score (CMTNS), a composite score based on patient symptoms, signs, and neurophysiologic abnormalities, as the primary outcome variable. The sensitivity of the CMTNS or any other score to change over time, as a measure of CMT1A progression, has yet to be determined. METHODS We determined the CMTNS as well as the Neuropathy Impairment Score (NIS) on 72 patients followed for up to 8 years. The rate of disease progression was evaluated for the CMTNS and NIS using mixed effects linear regression models, adjusting for age and gender. RESULTS Both CMTNS and NIS showed changes over time. The CMTNS increased an average of 0.686 points per year (95% CI 0.461 to 0.911, p <or= 0.0001). The NIS increased 1.368 points per year on average (95% CI 0.616 to 2.121, p = 0.0005). There was a suggestion that the rate of progression increased with age. CONCLUSION Progression of CMT1A can be detected by both the CMT Neuropathy Score (CMTNS) and the Neuropathy Impairment Score (NIS). This supports the feasibility of clinical trials to detect a slowing of disease progression using either or both of these scales as outcome measures. Since the CMTNS combines symptoms, signs, and electrophysiology and the NIS is based solely on the neurologic examination, the two scales may be complementary.
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Affiliation(s)
- M E Shy
- Wayne State University, Department of Neurology, Center for Molecular Medicine and Genetics, 421 Ea Canfield, Detroit, MI 48201, USA.
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39
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Knott JC, Pond DC, Lewis RA. Metal-insulator transition and electroresistance in lanthanum/calcium manganites La1-xCa
x
MnO3 (x= 0–0.5) from voltage-current-temperature surfaces. ACTA ACUST UNITED AC 2008. [DOI: 10.1186/1754-0429-1-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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40
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Cheskin LJ, Mitchell AM, Jhaveri AD, Mitola AH, Davis LM, Lewis RA, Yep MA, Lycan TW. Efficacy of Meal Replacements Versus a Standard Food-Based Diet for Weight Loss in Type 2 Diabetes A Controlled Clinical Trial. Diabetes Educ 2008; 34:118-27. [DOI: 10.1177/0145721707312463] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Lawrence J. Cheskin
- Johns Hopkins Bloomberg School of Public Health, Department
of International Health, Center for Human Nutrition, Baltimore, Maryland,
| | - Amy M. Mitchell
- Johns Hopkins Bloomberg School of Public Health, Department
of International Health, Center for Human Nutrition, Baltimore, Maryland
| | - Ami D. Jhaveri
- Johns Hopkins Bloomberg School of Public Health, Department
of International Health, Center for Human Nutrition, Baltimore, Maryland
| | - Andrea H. Mitola
- Johns Hopkins Bloomberg School of Public Health, Department
of International Health, Center for Human Nutrition, Baltimore, Maryland
| | - Lisa M. Davis
- Johns Hopkins Bloomberg School of Public Health, Department
of International Health, Center for Human Nutrition, Baltimore, Maryland
| | - Rebecca A. Lewis
- Johns Hopkins Bloomberg School of Public Health, Department
of International Health, Center for Human Nutrition, Baltimore, Maryland
| | - Mary A. Yep
- Johns Hopkins Bloomberg School of Public Health, Department
of International Health, Center for Human Nutrition, Baltimore, Maryland
| | - Thomas W. Lycan
- Johns Hopkins Bloomberg School of Public Health, Department
of International Health, Center for Human Nutrition, Baltimore, Maryland
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41
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Abstract
OBJECTIVE The purpose of this study was to assess whether inert cellulose powder would reduce the response to nasal challenge with house dust mite antigens. The study aimed to investigate the efficacy of inert cellulose powder applied to the nose for the control of persistent allergic rhinitis in adults due to house dust mite allergy. The powder has been registered as a medical device since 1994 and is available in many countries as a remedy for hay fever. Anecdotal evidence reported that it reduced symptoms of persistent rhinitis but no scientific evidence exists for this. RESEARCH DESIGN AND METHODS A double blind, placebo-controlled cross over trial was conducted on 15 adult persistent rhinitis sufferers (diagnosed positive to Der p1 and/or Der f1 by SPT) and who had symptoms over the previous 2 years. The placebo was lactose powder. Challenge was by measured dose of homogenised allergenic dust. The study took place in the spring of 2006 before the main pollen seasons. MAIN OUTCOME MEASURES The primary outcome measures were observed severity scores for 3 symptom categories and the amount of ECP in nasal secretions. The secondary outcome measures were symptom scores by subject report (nasal blockage, itching of nose, throat and eyes), nasal peak inspiratory (PIFn) and expiratory flow (PEFn). RESULTS The results show significant differences for sneezing, itchy nose, runny nose and ECPs in nasal secretions. Some results are also significantly different between placebo and active for PIFn and for PEFn (all at p = 0.05). There were no adverse reactions. CONCLUSIONS The inert cellulose powder can have significant effects in reducing some symptoms of persistent rhinitis due to house dust mite allergy.
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Affiliation(s)
- J C Emberlin
- National Pollen and Aerobiology Research Unit, Institute of Health, University of Worcester, WR2 6AJ, UK.
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42
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Abstract
Analyser-based phase contrast imaging can provide radiographs of exceptional contrast at high resolution (<100 microm), whilst quantitative phase and attenuation information can be extracted using just two images when the approximations of geometrical optics are satisfied. Analytical phase retrieval can be performed by fitting the analyser rocking curve with a symmetric Pearson type VII function. The Pearson VII function provided at least a 10% better fit to experimentally measured rocking curves than linear or Gaussian functions. A test phantom, a hollow nylon cylinder, was imaged at 20 keV using a Si(1 1 1) analyser at the ELETTRA synchrotron radiation facility. Our phase retrieval method yielded a more accurate object reconstruction than methods based on a linear fit to the rocking curve. Where reconstructions failed to map expected values, calculations of the Takagi number permitted distinction between the violation of the geometrical optics conditions and the failure of curve fitting procedures. The need for synchronized object/detector translation stages was removed by using a large, divergent beam and imaging the object in segments. Our image acquisition and reconstruction procedure enables quantitative phase retrieval for systems with a divergent source and accounts for imperfections in the analyser.
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Affiliation(s)
- M J Kitchen
- School of Physics, Monash University, Victoria 3800, Australia.
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43
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Shy ME, Siskind C, Swan ER, Krajewski KM, Doherty T, Fuerst DR, Ainsworth PJ, Lewis RA, Scherer SS, Hahn AF. CMT1X phenotypes represent loss of GJB1 gene function. Neurology 2007; 68:849-55. [PMID: 17353473 DOI: 10.1212/01.wnl.0000256709.08271.4d] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [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: 11/15/2022] Open
Abstract
OBJECTIVE To investigate possible genotype-phenotype correlations and to evaluate the natural history of patients with Charcot-Marie-Tooth disease type 1X (CMT1X). BACKGROUND CMT1X is caused by over 260 distinct mutations in the gap junction beta 1 (GJB1) gene, located on the X chromosome, which encodes the gap junction protein connexin 32 (Cx32). The natural history of CMT1X is poorly understood, and it remains unknown whether particular mutations cause more severe neuropathies through abnormal gain-of-function mechanisms. METHODS We evaluated 73 male patients with CMT1X, who each have 1 of 28 different GJB1 mutations predicted to affect nearly all domains of Cx32. Disability was evaluated quantitatively by the CMT Neuropathy Score (CMTNS) as well as by the CMT Symptom Score (CMTSS) and the CMT Examination Score (CMTES), which are both based on the CMTNS. Patients were also evaluated by neurophysiology. RESULTS In all patients, disability increased with age, and the degree of disability was comparable with that observed in patients with a documented GJB1 deletion. Disability correlated with a loss of motor units as assessed by motor unit number estimates. CONCLUSIONS Taken together, these data suggest that most GJB1 mutations cause neuropathy by a loss of normal connexin 32 function. Therefore, treatment of male patients with Charcot-Marie-Tooth disease type 1X may prove amenable to gene replacement strategies.
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Affiliation(s)
- M E Shy
- Department of Neurology, Wayne State University, 421 E. Canfield, Detroit, MI 48201, USA.
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Abstract
Structure-based Drug Design (SBDD) is an essential part of the modern medicinal chemistry, and has led to the acceleration of many projects, and even to drugs on the market. Programs that perform docking and scoring of ligands to receptors are powerful tools in the drug designer's armoury that enhance the process of SBDD. They are even deployed on the desktop of many bench chemists. It is timely to review the state of the art, to understand how good our docking programs are, and what are the issues. In this review we would like to provide a guide around the reliable aspects of docking and scoring and the associated pitfalls aiming at an audience of medicinal chemists rather than modellers. For convenience, we will divide the review into two parts: docking and scoring. Docking concerns the preparation of the receptor and the ligand(s), the sampling of conformational space and stereochemistry (if appropriate). Scoring concerns the evaluation of all of the ligand-receptor poses generated by docking. The two processes are not truly independent, and this will be discussed here in detail. The preparation of the receptor and ligand(s) before docking requires great care. For the receptor, issues of protonation, tautomerisation and hydration are key, and we will discuss current approaches to these issues. Even more important is the degree of sampling: can the algorithms reproduce what is observed experimentally? If they can, are the scoring algorithms good enough to recognise this pose as the best? Do the scores correlate with observed binding affinity? How does local knowledge of the target (for example hinge-binding to a kinase) affect the accuracy of the predictions? We will review the key findings from several evaluation studies and present conclusions about when and how to interpret and trust the results of docking and scoring. Finally, we will present an outline of some of the latest developments in the area of scoring functions.
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Affiliation(s)
- B Coupez
- Computer-Aided Drug Discovery, Novartis Institute for Biomedical Research, Switzerland
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45
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Affiliation(s)
- R A Lewis
- Chemical Division, Medical Clinic, The Johns Hopkins University and Hospital, Baltimore
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46
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Lewis RA, Wilkins L. THE EFFECT OF ADRENOCORTICOTROPHIC HORMONE IN CONGENITAL ADRENAL HYPERPLASIA WITH VIRILISM AND IN CUSHING'S SYNDROME TREATED WITH METHYL TESTOSTERONE. J Clin Invest 2006; 28:394-400. [PMID: 16695689 PMCID: PMC439613 DOI: 10.1172/jci102082] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- R A Lewis
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore
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47
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Affiliation(s)
- G W Thorn
- Chemical Division, Medical Clinic, The Johns Hopkins University and Hospital, Baltimore
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48
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Shy ME, Blake J, Krajewski K, Fuerst DR, Laura M, Hahn AF, Li J, Lewis RA, Reilly M. Reliability and validity of the CMT neuropathy score as a measure of disability. Neurology 2006; 64:1209-14. [PMID: 15824348 DOI: 10.1212/01.wnl.0000156517.00615.a3] [Citation(s) in RCA: 282] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To determine the validity and reliability of the Charcot-Marie-Tooth disease (CMT) neuropathy score (CMTNS) in patients with inherited neuropathy. BACKGROUND Natural history studies and potential treatment trials for patients with various forms of CMT are limited by the lack of quantitative methodologies to monitor disease progression. Most cases of CMT can be considered length-dependent axonal neuropathies because disability for even the demyelinating forms correlates with length-dependent axonal degeneration. The total neuropathy score (TNS) is a validated composite measure of disability in length-dependent axonal neuropathies but is weighted toward predominantly sensory neuropathies. Thus, the authors have devised a CMTNS, modified from the TNS, to provide a single measure to quantify CMT disability. METHODS The authors measured inter- and intrainvestigator reliability of the CMTNS and performed a validation of the score with the Neuropathy Impairment Score (NIS), patient self-assessment scores, an ambulation index, and other measures of disability. RESULTS Inter- and intrainvestigator reliability was more than 95% in the 60 patients evaluated. Patients could be divided into mild (CMTNS, < or =10), moderate (CMTNS, 11 to 20), and severe (CMTNS, > or =21) categories and demonstrated excellent correlations among all measures of disability. CONCLUSION The Charcot-Marie-Tooth disease (CMT) neuropathy score is a validated measure of length-dependent axonal and demyelinating CMT disability and can be investigated as an end point for longitudinal studies and clinical trials of CMT.
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Affiliation(s)
- M E Shy
- Department of Neurology, Wayne State University, Detroit, MI 48201, USA.
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49
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Dolan MS, Weiss LA, Lewis RA, Pietrobelli A, Heo M, Faith MS. 'Take the stairs instead of the escalator': effect of environmental prompts on community stair use and implications for a national 'Small Steps' campaign. Obes Rev 2006; 7:25-32. [PMID: 16436100 DOI: 10.1111/j.1467-789x.2006.00219.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [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: 11/29/2022]
Abstract
The US government initiated a national health campaign targeting 100 'small step' lifestyle changes to combat obesity. Small Step #67 advocates stair instead of escalator usage in public settings. The aim of this study is to evaluate the effects of motivational signs prompting stair use over escalator use on pedestrians' stair usage in commuter settings. Eight studies, testing the effects of motivational prompts on stair vs. escalator usage in public settings, were reviewed. Participant and study attributes were descriptively coded. Effect size was calculated as the change in percent units of stair users during the intervention phases vs. the baseline phase. The average study included approximately 45,000 observations that were recorded across an average of 15 weeks of intervention. The mean +/- SD change in percent units of stair users was 2.8% +/- 2.4% (P < 0.001), and effects were twice as large in females (4.8%) as in males (2.4%). The number of stairs/building, baseline stair use, and total intervention weeks predicted change in stair use, although the effects were clinically miniscule. In a hypothetical city intervention, we projected that a 2.8% increase in stair usage would result in a weight loss and/or weight gain prevention of 300 g/person/year among new stair users. In sum, point-of-decision motivational signs may help communities attain Small Step #67. However, the singular impact of this community intervention on correcting energy imbalance may be minimal, having slight impact itself on reducing the national obesity prevalence.
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Affiliation(s)
- M S Dolan
- University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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Abstract
OBJECTIVE An inert cellulose powder has been on sale in the UK since 1994 as a remedy for hay fever but no scientific trials have been conducted previously. It is applied to the inside of the nose where it forms a gelatinous coating. The principal aim was to determine if there is a significant difference in the amount and type of rescue medication required for adult hay fever sufferers to control their symptoms while using either the inert cellulose powder or a placebo. The second objective was to see whether the cellulose powder resulted in an improvement in symptom control. RESEARCH DESIGN A double blind, placebo controlled study was conducted of 97 adult hay fever sufferers, over the grass pollen season of 2004. Participants (selectively recruited to be living within the catchment area of a 50-km radius from Worcester, UK) were assigned randomly to two groups (A, Active and B, Placebo) matched by age by decades and gender. Of those completing the trial, group A had 19 males and 28 females and group B had 21 males and 29 females. There were no significant differences between the groups in age distributions, severity of symptoms over the last 2 years or in medication taken. They completed daily symptom diary score cards and were allowed to take any medications they wished in addition to the inert cellulose powder or placebo because medication use was taken as an outcome measure. Results were analysed in relation to pollen counts. RESULTS Significant differences were found in the amounts of rescue medication taken by the active and placebo groups (p < 0.05). More people in the placebo group took rescue treatments than those in the active group. No significant differences were found (p < 0.01) between the active and placebo groups in Likert scores for any of the rhinitis nasal symptoms or in the total Likert symptom daily scores. No adverse events were reported during the study. CONCLUSIONS The amount of rescue medication taken by the placebo group was significantly more than that taken by the active group both overall, considering all types of medication, and also in the individual cases of antihistamines, nasal sprays and eye drops. These results provide evidence that the inert cellulose powder reduces the need to take rescue medication for the symptoms of hay fever.
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Affiliation(s)
- J C Emberlin
- National Pollen and Aerobiology Research Unit, Institute of Health, University of Worcester, Worcester, WR2 6AJ, UK.
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