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Wilson NM, Norton A, Young FP, Collins DW. Airborne transmission of severe acute respiratory syndrome coronavirus-2 to healthcare workers: a narrative review. Anaesthesia 2020; 75:1086-1095. [PMID: 32311771 PMCID: PMC7264768 DOI: 10.1111/anae.15093] [Citation(s) in RCA: 219] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
Abstract
Healthcare workers are at risk of infection during the severe acute respiratory syndrome coronavirus‐2 pandemic. International guidance suggests direct droplet transmission is likely and airborne transmission occurs only with aerosol‐generating procedures. Recommendations determining infection control measures to ensure healthcare worker safety follow these presumptions. Three mechanisms have been described for the production of smaller sized respiratory particles (‘aerosols’) that, if inhaled, can deposit in the distal airways. These include: laryngeal activity such as talking and coughing; high velocity gas flow; and cyclical opening and closure of terminal airways. Sneezing and coughing are effective aerosol generators, but all forms of expiration produce particles across a range of sizes. The 5‐μm diameter threshold used to differentiate droplet from airborne is an over‐simplification of multiple complex, poorly understood biological and physical variables. The evidence defining aerosol‐generating procedures comes largely from low‐quality case and cohort studies where the exact mode of transmission is unknown as aerosol production was never quantified. We propose that transmission is associated with time in proximity to severe acute respiratory syndrome coronavirus‐1 patients with respiratory symptoms, rather than the procedures per se. There is no proven relation between any aerosol‐generating procedure with airborne viral content with the exception of bronchoscopy and suctioning. The mechanism for severe acute respiratory syndrome coronavirus‐2 transmission is unknown but the evidence suggestive of airborne spread is growing. We speculate that infected patients who cough, have high work of breathing, increased closing capacity and altered respiratory tract lining fluid will be significant producers of pathogenic aerosols. We suggest several aerosol‐generating procedures may in fact result in less pathogen aerosolisation than a dyspnoeic and coughing patient. Healthcare workers should appraise the current evidence regarding transmission and apply this to the local infection prevalence. Measures to mitigate airborne transmission should be employed at times of risk. However, the mechanisms and risk factors for transmission are largely unconfirmed. Whilst awaiting robust evidence, a precautionary approach should be considered to assure healthcare worker safety.
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Affiliation(s)
- N M Wilson
- Department of Intensive Care Medicine, Prince of Wales Hospital, Sydney, NSW, Australia
| | - A Norton
- Emergency Department, Oamaru Hospital, New Zealand
| | - F P Young
- Department of Intensive Care Medicine, Prince of Wales Hospital, Sydney, NSW, Australia
| | - D W Collins
- Department of Intensive Care Medicine, Prince of Wales Hospital, Sydney, NSW, Australia
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Reichle RH, De Lannoy GJM, Liu Q, Koster RD, Kimball JS, Crow WT, Ardizzone JV, Chakraborty P, Collins DW, Conaty AL, Girotto M, Jones LA, Kolassa J, Lievens H, Lucchesi RA, Smith EB. Global Assessment of the SMAP Level-4 Surface and Root-Zone Soil Moisture Product Using Assimilation Diagnostics. J Hydrometeorol 2017; 18:3217-3237. [PMID: 30364509 DOI: 10.1175/jhm-d-17-0063.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Soil Moisture Active Passive (SMAP) mission Level-4 Soil Moisture (L4_SM) product provides 3-hourly, 9-km resolution, global estimates of surface (0-5 cm) and root-zone (0-100 cm) soil moisture and related land surface variables from 31 March 2015 to present with ~2.5day latency. The ensemble-based L4_SM algorithm assimilates SMAP brightness temperature (Tb) observations into the Catchment land surface model. This study describes the spatially distributed L4_SM analysis and assesses the observation-minus-forecast (O-F) Tb residuals and the soil moisture and temperature analysis increments. Owing to the climatological rescaling of the Tb observations prior to assimilation, the analysis is essentially unbiased, with global mean values of ~0.37 K for the O-F Tb residuals and practically zero for the soil moisture and temperature increments. There are, however, modest regional (absolute) biases in the O-F residuals (under ~3 K), the soil moisture increments (under ~0.01 m3 m-3), and the surface soil temperature increments (under ~1 K). Typical instantaneous values are ~6 K for O-F residuals, ~0.01 (~0.003) m3 m-3 for surface (root-zone) soil moisture increments, and ~0.6 K for surface soil temperature increments. The O-F diagnostics indicate that the actual errors in the system are overestimated in deserts and densely vegetated regions and underestimated in agricultural regions and transition zones between dry and wet climates. The O-F auto-correlations suggest that the SMAP observations are used efficiently in western North America, the Sahel, and Australia, but not in many forested regions and the high northern latitudes. A case study in Australia demonstrates that assimilating SMAP observations successfully corrects short-term errors in the L4_SM rainfall forcing.
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Affiliation(s)
- Rolf H Reichle
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | | | - Qing Liu
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Randal D Koster
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | | | - Wade T Crow
- USDA ARS Hydrology and Remote Sensing Laboratory, Beltsville, MD, USA
| | - Joseph V Ardizzone
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Purnendu Chakraborty
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Douglas W Collins
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Austin L Conaty
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Manuela Girotto
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- GESTAR, Universities Space Research Association, Columbia, MD, USA
| | | | - Jana Kolassa
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- GESTAR, Universities Space Research Association, Columbia, MD, USA
| | - Hans Lievens
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Laboratory of Hydrology and Water Management, Ghent University, Ghent, Belgium
| | - Robert A Lucchesi
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Edmond B Smith
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
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Reichle RH, De Lannoy GJM, Liu Q, Koster RD, Kimball JS, Crow WT, Ardizzone JV, Chakraborty P, Collins DW, Conaty AL, Girotto M, Jones LA, Kolassa J, Lievens H, Lucchesi RA, Smith EB. Global Assessment of the SMAP Level-4 Surface and Root-Zone Soil Moisture Product Using Assimilation Diagnostics. J Hydrometeorol 2017; 18:3217-3237. [PMID: 30364509 PMCID: PMC6196324 DOI: 10.1175/jhm-d-17-0130.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The Soil Moisture Active Passive (SMAP) mission Level-4 Soil Moisture (L4_SM) product provides 3-hourly, 9-km resolution, global estimates of surface (0-5 cm) and root-zone (0-100 cm) soil moisture and related land surface variables from 31 March 2015 to present with ~2.5day latency. The ensemble-based L4_SM algorithm assimilates SMAP brightness temperature (Tb) observations into the Catchment land surface model. This study describes the spatially distributed L4_SM analysis and assesses the observation-minus-forecast (O-F) Tb residuals and the soil moisture and temperature analysis increments. Owing to the climatological rescaling of the Tb observations prior to assimilation, the analysis is essentially unbiased, with global mean values of ~0.37 K for the O-F Tb residuals and practically zero for the soil moisture and temperature increments. There are, however, modest regional (absolute) biases in the O-F residuals (under ~3 K), the soil moisture increments (under ~0.01 m3 m-3), and the surface soil temperature increments (under ~1 K). Typical instantaneous values are ~6 K for O-F residuals, ~0.01 (~0.003) m3 m-3 for surface (root-zone) soil moisture increments, and ~0.6 K for surface soil temperature increments. The O-F diagnostics indicate that the actual errors in the system are overestimated in deserts and densely vegetated regions and underestimated in agricultural regions and transition zones between dry and wet climates. The O-F auto-correlations suggest that the SMAP observations are used efficiently in western North America, the Sahel, and Australia, but not in many forested regions and the high northern latitudes. A case study in Australia demonstrates that assimilating SMAP observations successfully corrects short-term errors in the L4_SM rainfall forcing.
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Affiliation(s)
- Rolf H. Reichle
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | | | - Qing Liu
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Randal D. Koster
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | | | - Wade T. Crow
- USDA ARS Hydrology and Remote Sensing Laboratory, Beltsville, MD, USA
| | - Joseph V. Ardizzone
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Purnendu Chakraborty
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Douglas W. Collins
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Austin L. Conaty
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Manuela Girotto
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- GESTAR, Universities Space Research Association, Columbia, MD, USA
| | | | - Jana Kolassa
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- GESTAR, Universities Space Research Association, Columbia, MD, USA
| | - Hans Lievens
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Laboratory of Hydrology and Water Management, Ghent University, Ghent, Belgium
| | - Robert A. Lucchesi
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
| | - Edmond B. Smith
- Global Modeling and Assimilation Office, NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Science Systems and Applications, Inc., Lanham, MD, USA
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Collins DW, Downs CS, Katz SG, Gatt SP, Marsland C, Abrahams N, Turner RJ. Airway management on placental support (AMPS)--the anaesthetic perspective. Anaesth Intensive Care 2002; 30:647-59. [PMID: 12413268 DOI: 10.1177/0310057x0203000518] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Neonatal airway obstruction has been reported to have a high mortality. Antenatal diagnosis of this condition is now possible. Anaesthetic and surgical techniques have been developed that allow neonatal airway obstruction to be managed at delivery, while the fetus remains oxygenated via the placental circulation. Three case studies are presented, and the anaesthetic issues for mother and fetus/neonate are discussed with reference to previously published cases of airway management on placental support. In particular, techniques for uterine relaxation and maintenance of placental circulation are explored. The history of these procedures and issues of planning and logistics are also discussed.
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Affiliation(s)
- D W Collins
- Department of Anaesthesia, Sydney Children's Hospital Randwick, NSW, Australia
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Abstract
The volatile anaesthetic agents are known to influence uterine muscle tone. All of the agents studied to date have been found to produce uterine relaxation. This property has been used to produce therapeutic uterine relaxation for difficult obstetric deliveries and the Ex Utero Intrapartum Treatment (EXIT) procedure. This study describes the effects of sevoflurane on isolated human myometrium at concentrations of 0.1, 0.25, 0.5, 0.75, 1.0, 1.5, 2.5 and 3.5 MAC. Sevoflurane produces dose-dependent depression of uterine muscle contractility with an ED50 of 0.94 MAC. Frequency of contraction was increased at concentrations of 2.5 MAC and greater. At concentrations of 3.5 MAC and above, uterine activity was virtually abolished.
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Affiliation(s)
- R J Turner
- Department of Anaesthesia, The University of New South Wales, Prince of Wales Hospital, Sydney, NSW, Australia
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Abstract
The neuropsychological assets and deficits of several types of pediatric neurological disease, disorder, and dysfunction are described. These are examined from the perspective of the syndrome of nonverbal learning disabilities (NLD) and the "white matter model" designed to explain its complex manifestations. It is concluded that children with some of these diseases exhibit the NLD phenotype, whereas others do not. For the most part, the diseases in which the NLD phenotype is particularly evident are those wherein it has been demonstrated that perturbations of white matter (long myelinated fibers) are particularly prominent.
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Affiliation(s)
- B P Rourke
- Department of Psychology, University of Windsor, Windsor, Ontario, Canada.
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Kahrilas PJ, Falk GW, Johnson DA, Schmitt C, Collins DW, Whipple J, D'Amico D, Hamelin B, Joelsson B. Esomeprazole improves healing and symptom resolution as compared with omeprazole in reflux oesophagitis patients: a randomized controlled trial. The Esomeprazole Study Investigators. Aliment Pharmacol Ther 2000; 14:1249-58. [PMID: 11012468 DOI: 10.1046/j.1365-2036.2000.00856.x] [Citation(s) in RCA: 235] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The pharmacologic profile of the new proton pump inhibitor esomeprazole has demonstrated advantages over omeprazole that suggest clinical benefits for patients with acid-related disease. METHODS 1960 patients with endoscopy-confirmed reflux oesophagitis (RO) were randomized to once daily esomeprazole 40 mg (n=654) or 20 mg (n=656), or omeprazole 20 mg (n=650), the standard recommended dose for RO, for up to 8 weeks in a US, multicentre, double-blind trial. The primary efficacy variable was the proportion of patients healed at week 8. Secondary variables included healing and heartburn resolution at week 4, time to first resolution and sustained resolution of heartburn, and per cent of heartburn-free days and nights. Safety and tolerability were also evaluated. RESULTS Significantly more patients were healed at week 8 with esomeprazole 40 mg (94.1%) and 20 mg (89.9%) vs. omeprazole 20 mg (86.9%), using cumulative life table estimates, ITT analysis (each P < 0.05). Esomeprazole 40 mg was also significantly more effective than omeprazole for healing at week 4 and for all secondary variables evaluating heartburn resolution. The most common adverse events in all treatment groups were headache, abdominal pain and diarrhoea. CONCLUSION Esomeprazole was more effective than omeprazole in healing and symptom resolution in GERD patients with reflux oesophagitis, and had a tolerability profile comparable to that of omeprazole.
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Affiliation(s)
- P J Kahrilas
- Department of Gastroenterology and Hepatology, Northwestern University Medical School, Chicago, IL 60611-3008, USA.
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Abstract
In yeast, the Rad51-related proteins include Rad55 and Rad57, which form a heterodimer that interacts with Rad51. Five human Rad51 paralogs have been identified (XRCC2, XRCC3, Rad51B/Rad51L1, Rad51C/Rad51L2, and Rad51D/Rad51L3), and each interacts with one or more of the others. Previously we reported that HsRad51 interacts with XRCC3, and Rad51C interacts with XRCC3, Rad51B, and HsRad51. Here we report that in the yeast two-hybrid system, Rad51D interacts with XRCC2 and Rad51C. No other interactions, including self-interactions, were found, indicating that the observed interactions are specific. The yeast Rad51 interacts with human Rad51 and XRCC3, suggesting Rad51 conservation since the human yeast divergence. Data from yeast three-hybrid experiments indicate that a number of the pairs of interactions between human Rad51 paralogs can occur simultaneously. For example, Rad51B expression enhances the binding of Rad51C to XRCC3 and to HsRad51D, and Rad51C expression allows the indirect interaction of Rad51B with Rad51D. Experiments using 6xHis-tagged proteins in the baculovirus system confirm several of our yeast results, including Rad51B interaction with Rad51D only when Rad51C is simultaneously expressed and Rad51C interaction with XRCC2 only when Rad51D is present. These results suggest that these proteins may participate in one complex or multiple smaller ones.
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Affiliation(s)
- D Schild
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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Dosanjh MK, Collins DW, Fan W, Lennon GG, Albala JS, Shen Z, Schild D. Isolation and characterization of RAD51C, a new human member of the RAD51 family of related genes. Nucleic Acids Res 1998; 26:1179-84. [PMID: 9469824 PMCID: PMC147393 DOI: 10.1093/nar/26.5.1179] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.2] [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: 02/06/2023] Open
Abstract
The yeast and human RAD51 genes encode strand-transfer proteins that are thought to be involved in both recombinational repair of DNA damage and meiotic recombination. In yeast, the Rad51 family of related proteins also includes Rad55, Rad57 and Dmc1. In mammalian cells, five genes in this family have been identified (HsRAD51, XRCC2, XRCC3, RAD51B/hREC2 and HsDMC1), and here we report the isolation of the sixth member, RAD51C. RAD51C was originally identified by a computer screen of the EST database. A full-length approximately 1.3 kb cDNA clone has been isolated that encodes a protein of 376 aa, having a 18-26% aa identity with other human Rad51 family members. RAD51C includes a previously mapped sequenced-tagged site location near the end of chromosome 17q. The RAD51C transcript is expressed in various human tissues, with highest level of expression in testis, followed by heart muscle, spleen and prostate. Yeast two-hybrid experiments indicate that the Rad51C protein binds to two other members of the Rad51 protein family (Xrcc3 and Rad51B) but not to itself. These findings suggest that Rad51C may function similarly to the yeast Rad55 or Rad57 proteins, rather than as a Rad51 functional homolog.
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Affiliation(s)
- M K Dosanjh
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Abstract
Mental rotation tests require participants to identify rotated versions of a target stimulus. The Vandenberg Mental Rotations Test depicts rotations in 3-D space and typically yields one of the largest established cognitive sex differences favoring males. It is presently unclear whether this male advantage is related to the nature of rotations depicted in 3-D space or to the high level of difficulty of this task. The present study developed a new test depicting picture plane, or 2-D, rotations. When task difficulty within this 2-D test was varied, a male advantage as large as that seen on the Vandenberg test was found for the difficult component. These findings suggest that processing in 3 dimensions is not a necessary condition for a large sex difference on tests of mental rotation.
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Affiliation(s)
- D W Collins
- Department of Psychology, University of Western Ontario, London, Canada.
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Collins DW. Conflict resolution: a short description of the mediation process for health care professionals. Colo Nurse 1997; 97:9-10. [PMID: 9355321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Abstract
Mental rotation tests require participants to identify rotated versions of a target stimulus. The Vandenberg Mental Rotations Test depicts rotations in 3-D space and typically yields one of the largest established cognitive sex differences favoring males. It is presently unclear whether this male advantage is related to the nature of rotations depicted in 3-D space or to the high level of difficulty of this task. The present study developed a new test depicting picture plane, or 2-D, rotations. When task difficulty within this 2-D test was varied, a male advantage as large as that seen on the Vandenberg test was found for the difficult component. These findings suggest that processing in 3 dimensions is not a necessary condition for a large sex difference on tests of mental rotation.
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Affiliation(s)
- D W Collins
- Department of Psychology, University of Western Ontario, London, Canada.
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Abstract
Protein-coding sequences of 337 human genes were compared with those of homologous genes from rodent (mouse or rat). A composite alignment containing 477,189 nucleotide positions was constructed, and 21,570 amino acid replacements were inferred. The rates of transitional and transversional silent substitutions in fourfold degenerate sites are estimated as 1.71 x 10(-9) and 1.22 x 10(-9) site -1 year -1, respectively. Rates of substitutions in replacement sites, subject to selective constraints mediated by the genetic code, are lower, but also reflect a transitional bias. The amino acid exchange rejected least often during evolution is Asp/Glu, which is fixed at 30% the rate of transversions in silent sites. The most mutable amino acids in this survey are threonine and serine; serine coded by AGY is more mutable than serine coded by TCN. A scoring matrix for evaluating amino acid similarity was derived from this study.
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Affiliation(s)
- D W Collins
- Space Sciences Laboratory, University of California at Berkeley, Oakland 94608
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Collins DW, Coroneo MT. Removal of corneal foreign bodies: an instructional model. Ophthalmic Surg 1994; 25:99-101. [PMID: 8183522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A simple method for inflicting corneal foreign body injuries on bovine eyes is described and illustrated. The subsequent use of these eyes for teaching corneal and rust-ring removal is demonstrated. This method is suitable for instruction of large numbers of students and could be included in an undergraduate curriculum.
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Affiliation(s)
- D W Collins
- Department of Ophthalmolgy, University of New South Wales, Prince of Wales Hospital, Randwick, Australia
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Collins DW. FISH: a guide to protein-coding DNA sequences in the GenBank database. Comput Appl Biosci 1993; 9:337-42. [PMID: 8324634 DOI: 10.1093/bioinformatics/9.3.337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
FISH (Fast Index Search for Homologous coding sequences) consists of a database and associated software and is intended to function as a directory of protein-coding gene sequences. The FISH index contains descriptions of 22,361 DNA sequences from release 69.0 of the GenBank genetic sequence database. Complete coding sequences are represented numerically with counts of nucleotides and synonymous codons, and with GenBank LOCUS names and short descriptions. The software permits the database to be queried by GenBank LOCUS name, sequence length (expressed as total number of codons), or by comparison with a DNA sequence. In the latter case, the numerical descriptions are compared with simple distance measures in place of actual DNA sequences. The FISH package can be used to rapidly assemble lists of similar coding sequences, without regard to functional annotation or sequence alignments. Typical search times are well under a minute on widely available IBM-compatible microcomputers.
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Affiliation(s)
- D W Collins
- Space Sciences Laboratory, Oakland, CA 94608
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17
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Abstract
We have investigated the relationship between the G + C content of silent (synonymous) sites in codons and the amino acid composition of encoded proteins for approximately 1,600 human genes. There are positive correlations between silent site G + C and the proportions of codons for Arg, Pro, Ala, Trp, His, Gln, and Leu and negative ones for Tyr, Phe, Asn, Ile, Lys, Asp, Thr, and Glu. The median proteins coded by groups of genes that differ in silent-site G + C content also differ in amino acid composition, as do some proteins coded by homologous genes. The pattern of compositional change can be largely explained by directional mutation pressure, the genetic code, and differences in the frequencies of accepted amino acid substitutions; the shifts in protein composition are likely to be selectively neutral.
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Affiliation(s)
- D W Collins
- Space Sciences Laboratory, University of California, Berkeley
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Abstract
This paper describes the main elements of the Western Australian retinitis pigmentosa register including details of the data stored on the register, aspects of the coding systems used and some description of the tests employed in diagnosis of retinitis pigmentosa. The register is family based and contains data on affected individuals and on their unaffected relatives. As at November 1991, the register contained data for 391 individuals from 207 separate families. Of the 391 individuals, 240 had definite or probable retinitis pigmentosa and 26 were possibly affected. The remainder were unaffected family members. In many cases, both affected and unaffected family members are being studied serially and the register is designed to store and easily retrieve serial data to allow study of disease progression for individuals and within families.
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Affiliation(s)
- E Chelva
- Department of Biophysics, Sir Chalres Gairdner Hospital, Perth, Western Australia
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19
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Abstract
DNA sequences coding for protein may be represented by counts of nucleotides or codons. A complete reading frame may be abbreviated by its base count, e.g. A76C158G121T74, or with the corresponding codon table, e.g. (AAA)0(AAC)1(AAG)9 ... (TTT)0. We propose that these numerical designations be used to augment current methods of sequence annotation. Because base counts and codon tables do not require revision as knowledge of function evolves, they are well-suited to act as cross-references, for example to identify redundant GenBank entries. These descriptors may be compared, in place of DNA sequences, to extract homologous genes from large databases. This approach permits rapid searching with good selectivity.
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Affiliation(s)
- D W Collins
- Space Sciences Laboratory, University of California, Berkeley 94720
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Wallace K, Chelva E, Collins DW, Black JL. The role of electrophysiology in the diagnosis and assessment of retinitis pigmentosa. Australas Phys Eng Sci Med 1985; 8:103-9. [PMID: 4096671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Abstract
This paper describes a study on pacemaker longevity carried out on 65 subjects using mostly the Telectronics model 171 and model 173 pacemakers and based on an analysis of pacing rate reduction as a function of time since implant. Three different modes of rundown were observed. The shortest predicted lifetime was 23 months for a model 171 unit. This study was undertaken after the manufacturer and battery companies clearly delineated the existence of the problem and steps to be taken in the follow-up of patients. Careful analysis of medical records of the patients did not yield any correlation between sex, age, indications for implantation, initial pacing threshold, or amount of use of the pacemaker, and the early rundown of these pacemakers. Our study indicated that, in general, the model 173 had a shorter expected lifetime than the model 171. Using a reduction in pacing rate of 5.5 bpm from the rate at implant as the end-of-life indicator, the study showed that 16% of the model 173 pacemakers would need to be replaced within 3 years of implant and 78% within 6 years of implant. In the case of the model 171 units, 10% would need to be replaced within 3 years of implant and 48% within 6 years. Follow-up of patients with these units should be scheduled to monitor closely the rate of rundown in order to predict replacement dates.
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Black JL, Collins DW, De Roach JN, Zubrick S. A detailed study of sequential saccadic eye movements for normal- and poor-reading children. Percept Mot Skills 1984; 59:423-34. [PMID: 6514491 DOI: 10.2466/pms.1984.59.2.423] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This paper presents the results of an in-depth study of parameters characterizing sequenced saccadic eye movements for a group of dyslexic children and a comparative normal control group with ages in the range greater than 8.0 yr. and less than 13.0 yr. No parameters were statistically different for the two groups, which supports the findings of Brown, et al. and contradicts the findings of Pavlidis. Our results indicate that sequenced saccadic eye movements are not diagnostically useful for early detection of dyslexia.
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Abstract
This paper describes a detailed study of horizontal eye movements associated with visual tracking of a smoothly moving target. Essentially all children, even at target velocities as low as 5 degrees/sec., show some saccadic eye movements superimposed on smooth tracking movements. Detailed analysis of pursuit eye-movements from a group of 26 poor readers and 34 normal controls (8 to 13 yr.) showed that about 25% of poor readers have an abnormally raised saccadic component in smooth pursuit. This suggests that studies of eye movements during tracking of smoothly moving targets at low velocity, combined with a quantitative approach to data analysis, may be useful for early detection of a significant proportion of poor-reading children.
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McLaren T, Black JL, Collins DW. Quantitative electroneurography: assessment of facial nerve palsy. Australas Phys Eng Sci Med 1984; 7:104-7. [PMID: 6517769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Abstract
This paper describes an extensive study of the parameters of saccadic eye movement in a group of 28 poor-reading children and a comparative normally reading group of 31 children. Ages ranged from 6.0 to 16.9 yr. Poor readers had normal intelligence but were lagging by at least two years in reading ability as compared to their peer age group. Parameters studied in refixation eye movements included saccadic latency, accuracy, velocity, and acceleration, as well as differences in latency for abduct and adduct movements. Shapes of saccades were also studied. It was shown that eye-movement performance in simple saccadic refixation was not distinguishably different for poor readers and normal readers, even though in reading, which requires higher processing, eye-movement characteristics are quite different. Maturational changes for various saccadic eye-movement parameters were also examined for the normal and poor reading groups.
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Knezevic W, Mastaglia FL, Black JL, Collins DW. Brainstem auditory evoked responses and quantitative saccade studies in multiple sclerosis: a comparative evaluation. Clin Exp Neurol 1984; 20:175-9. [PMID: 6568939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Brainstem auditory evoked responses (BAERs) and quantitative saccadic eye movement studies provide information on the integrity of pathways traversing the brainstem. To compare the relative yield of abnormalities with the two techniques, the findings in a group of 46 patients with clinically definite, probable or suspected multiple sclerosis, in whom both procedures were performed, were analysed. BAERs were abnormal in 18 cases (39%), the abnormalities being subclinical in 10 (22%). One or more saccade parameters (reaction time, velocity, accuracy) were abnormal in 31 cases (67%), the abnormalities being subclinical in 19 (41%). When the results of both procedures were taken into account, the overall incidence of abnormalities was 76% and the overall incidence of subclinical abnormalities was 52%. Abnormalities were found with both techniques in 15 cases and with neither technique in 12 cases. Sixteen cases with normal BAERs had an abnormal saccade study, but only three cases with a normal saccade study had abnormal BAERs. It is concluded that BAERs and quantitative saccade studies have a complementary role in the investigation of patients with multiple sclerosis.
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Cala LA, Thickbroom GW, Black JL, Collins DW, Mastaglia FL. Brain density and cerebrospinal fluid space size: CT of normal volunteers. AJNR Am J Neuroradiol 1981; 2:41-7. [PMID: 6784549 PMCID: PMC8331815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
This study attempted to establish normal values for cerebral white and deep gray matter density and total brain density, and to discover how much dilatation of the cerebrospinal fluid--containing spaces occurs with advancing age up to 40 years. The 53 female and 62 male healthy volunteers, 15-40 years old, had been screened to exclude individuals with neurologic disease, previous head trauma, congenital or acquired heart disease, chronic pulmonary disease and other systemic illness, and those who consumed more than small amounts of alcoholic beverages. The computed tomography scan data for the 115 subjects were scored subjectively for the severity of atrophy. It was found that in both genders there was an increasing frequency with advancing age of sulcal widening of the frontal lobes and cerebellar vermis starting in the teens. A ventriculo-internal cranial ratio was calculated for 93 subjects who had been examined on the EMI CT 1010, the mean value being 0.31 +/- 0.08 for females and 0.33 +/- 0.06 for males. The ratio did not change significantly with age up to 40 years. On the same 93 subjects, mean values and standard deviations were obtained for normal white matter (30.1 +/- 3.5 Hounsfield units (H) for females and 29.8 +/- 3.3 H for males) and for normal deep gray matter (33.0 +/- 3.3 H for females; 33.2 +/- 2.6 H for males) and for total brain density (33.9 +/- 2.7 H for females; 33.6 +/- 2.6 H for males).
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Bajada S, Mastaglia FL, Black JL, Collins DW. Effects of induced hyperthermia on visual evoked potentials and saccade parameters in normal subjects and multiple sclerosis patients. J Neurol Neurosurg Psychiatry 1980; 43:849-52. [PMID: 7420109 PMCID: PMC490679 DOI: 10.1136/jnnp.43.9.849] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A convenient method for raising body temperature has been developed and used to evaluate temperature effects on visual evoked potentials and saccade reaction time and velocity in five normal subjects and five patients with multiple sclerosis.
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Abstract
Ocular movements were studied in 108 patients with established or suspected multiple sclerosis using an on-line computer-based electro-oculographic technique. In one group of patients peak eye movement velocities alone were measured during horizontal refixation saccades. In a second group saccade reaction times and accuracies were measured in addition to velocities, while in a subgroup a quantitative analysis of horizontal pursuit eye movements was also carried out. With the saccade velocity test abnormalities were present in 44 per cent of cases studied and were subclinical in 18 per cent. Abnormalities were found in 57 per cent of cases in whom the detailed saccade analysis was performed, including 48 per cent of patients with clinically normal eye movements. Saccade reaction time and accuracy were more sensitive parameters than saccade velocity, and the highest yield of abnormalities was obtained when all three were taken into consideration. Abnormalities of pursuit movements were found in 71 per cent of cases studied and were frequently subclinical. Abnormalities of saccadic and pursuit movements were not always present together in the same patient, and the overall yield of abnormalities was higher when the results of both types of study were taken into account. The yield of abnormalities with the eye movement studies was somewhat lower than with the pattern-reversal VEP in the clinically definite multiple sclerosis group, but was higher in patients in the other categories. Subclinical abnormalities of eye movement were found in a significant number of patients with normal VEPs. The finding of such an abnormality in patients with spinal cord syndromes allowed reclassification of 14 patients to a category with a higher degree of diagnostic certainty. It is concluded that quantitative electro-oculography is a valuable adjunct to the clinical evaluation of eye movements and has an important role in the investigation of patients suspected of multiple sclerosis.
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Abstract
The design and use of an on-line PDP 11/40-based system for quantitative study of ocular kinetics are described. The system can be used in neurophysiological or ophthalmological applications. Two different techniques are presented. In one, horizontal, vertical or oblique eye motion can be studied, in the other horizontal eye motion only. Several parameters of eye motion can be measured including saccadic velocity, eye movement latency and accuracy of refixation. For ophthalmological EOG applications the system allows measurement of the absolute voltage excursion corresponding to a horizontal eye movement of a specific amplitude. The system consists of five software programs and supporting signal processing equipment. The software package runs under the RSX11M executive.
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Abstract
Averaged cortical evoked potentials from single clicks were recorded from 51 patients and controls. The patient group consisted of 40 subjects with a diagnosis of 'nuclear' schizophrenia, and 11 subjects with diagnoses including mania, anxiety neurosis and personality disorder. Changes in auditory evoked cortical responses (AECR's) were most marked in clinically stable, dysphoric, chronic schizophrenics. These subjects showed reproducible, low amplitude, 'untidy' responses in which the amplitude of the primary peak was lower than the amplitude of later peaks. Chronic schizophrenics who were rated as being depressed, showed a more 'normal' AECR. AECR changes during the memorising of nonsense syllables demonstrated a functional separation between early and later peaks of the AECR. It was postulated that the AECR changes in schizophrenia and during memorising result from pathological patterns of cortical desynchronisation produced by altered mid-brain activity different from that of anxious arousal, and that the clinical 'steady-state' of chronic schizophrenia is reflected in the 'steady-state' desynchronisation changes in the AECR.
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Thompson GH, Black JL, Collins DW. A quantitative review of the performance of implanted cardiac pacemakers, Medtronic Model No. 5944. Aust N Z J Med 1978; 8:255-8. [PMID: 279320 DOI: 10.1111/j.1445-5994.1978.tb04519.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
One of the service functions of the Sir Charles Gairdner Hospital Department of Biophysics since 1972 has been the routine performance testing of pacemakers implanted by the Hospital's Cardiologists. This service was set up to measure pacemaker pulse parameters with a view to detecting battery depletion. It was also found to be of great help in showing lead insulation deterioration, intermittent capture and movement of the catheter tip within the right ventricle, information that is frequently of help to the Cardiologists in planning acute or elective pacemaker replacement.
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Abstract
A detailed method of analysis of the pattern-reversal visual evoked potential is presented. This method takes into account a number of parameters in addition to the latency of the major surface-positive component (P2) and has been tested in a group of 50 normal subjects and in 98 patients with established or suspected multiple sclerosis (MS). It was found that this more detailed form of analysis improved the detection rate of abnormal responses in the MS subjects particularly in those classified in the suspected category. The potential value of this form of analysis, particularly in clinical neurophysiology laboratories where the recording of visual evoked potentials is the only technique employed in the investigation of patients with suspected MS, is discussed.
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Abstract
The design and use of an on-line PDP 11/40 based vector cardiographic pacemaker assessment system is described. The system has been designed for comprehensive, automated testing of either fixed rate or demand implanted cardiac pacemakers. It is accurate and can be operated by a laboratory assistant without special training. Pacemaker parameters extracted are pulse height, width, rate, energy index and the frontal plane vector length and angle at maximum inspiration and during quiet breathing. In addition, a graphical representation of the patient's ECG and the pacemaker pulse is obtained on a computer graphics terminal. Patient data are written to cartridge disk for permanent record following the test. At each subsequent test of the implanted pacemaker, the data on disk are addended with the latest quantitative results. A separate off-line FORTRAN program can interrogate disk files for detailed analysis of patient data and display of parameter trends since implantation.
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Mastaglia FL, Black JL, Cala LA, Collins DW. Evoked potentials, saccadic velocities, and computerized tomography in diagnosis of multiple sclerosis. Br Med J 1977; 1:1315-7. [PMID: 861595 PMCID: PMC1607177 DOI: 10.1136/bmj.1.6072.1315] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
One hundred and two patients with suspected or established multiple sclerosis (MS) were investigated by one or more of the following techniques: measurement of visual evoked potentials (VEP); measurement of cervical and cortical somatosensory evoked potentials (SEP); measurement of horizontal saccadic eye movement velocities (SV); and computerised axial tomography of the cranium and orbits (CT). Each of the techniques was valuable in detecting abnormalities, some of which were subclinical, in many patients. More abnormalities were found in patients studied by more than one technique, the most being detected in patients who were studied by all five techniques. We conclude that the techniques have a complementary role in investigating suspected MS.
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Collins DW, Cookingham RE, Lewis A. Continuously tunable optical filter for use in resonance Raman spectroscopy. Appl Opt 1977; 16:252-254. [PMID: 20168462 DOI: 10.1364/ao.16.000252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A tunable optical filter is described for removing undesired emissions from laser beams for use in resonance Raman and fluorescence spectroscopy. The bandpass is 1 nm, and the filter is tunable from 400 nm to 750 nm. The degree of polarization of the dye laser beam is improved by the filter. Two independent controls tune the filter to the selected frequency, while the input and output beam directions remain fixed.
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Abstract
The design and use of a PDP 11/40 based automated on-line cardiac pacemaker assessment system is described. One program has been developed for testing pacemakers on the bench and another for implanted pacemaker tests. Either fixed rate or demand pacemakers can be tested. The on-line system is easy and fast to use and is also highly accurate. Parameters extracted are pulse width, rate and pulse energy. In addition, a graphical representation of the patient's ECG and the pacemaker pulse is obtained on a computer graphics terminal.
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Collins DW. Ulnar deviation splints. Hand 1971; 3:21-2. [PMID: 5098334 DOI: 10.1016/0072-968x(71)90007-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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