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Heard M, Marmura H, Bryant D, Litchfield R, McCormack R, MacDonald P, Spalding T, Verdonk P, Peterson D, Bardana D, Rezansoff A, Getgood A. Corrigendum to 'No increase in adverse events with lateral extra-articular tenodesis augmentation of anterior cruciate ligament reconstruction - Results from the stability randomized trial' [Journal of ISAKOS 8 (2023) 246-254]. J ISAKOS 2023; 8:513. [PMID: 37845163 DOI: 10.1016/j.jisako.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Affiliation(s)
- M Heard
- Deparment of Surgery, University of Calgary, T2N 1N4, Canada; Banff Sport Medicine, T1W 0L5, Canada
| | - H Marmura
- Fowler Kennedy Sport Medicine Clinic, N6A 3K7, Canada; School of Physical Therapy, Western University, N6A 3K7, Canada
| | - D Bryant
- Fowler Kennedy Sport Medicine Clinic, N6A 3K7, Canada; School of Physical Therapy, Western University, N6A 3K7, Canada
| | - R Litchfield
- Fowler Kennedy Sport Medicine Clinic, N6A 3K7, Canada; Department of Surgery, Schulich School of Medicine and Dentistry, Western University, N6A 5C1, Canada
| | - R McCormack
- Department of Orthopaedics, University of British Columbia, V5Z 1M9, Canada; New West Orthopaedic & Sports Medicine Centre, V3L 5P5, Canada
| | - P MacDonald
- Department of Surgery, University of Manitoba, R3A 1R9, Canada; Pan Am Clinic, R3M 3E4, Canada
| | - T Spalding
- University Hospital Coventry and Warwickshire NHS Trust, CV2 2DX, UK
| | - P Verdonk
- Department of Physical Medicine and Orthopedics, Ghent University, 9000, Belgium; Antwerp Orthopedic Center, 2018, Belgium
| | - D Peterson
- Department of Surgery, McMaster University, L8S 4K1, Canada
| | - D Bardana
- Department of Surgery, Queen's University, K7L 2V7, Canada
| | - A Rezansoff
- Deparment of Surgery, University of Calgary, T2N 1N4, Canada; University of Calgary Sport Medicine Centre, T2N 1N4, Canada
| | - A Getgood
- Fowler Kennedy Sport Medicine Clinic, N6A 3K7, Canada; Department of Surgery, Schulich School of Medicine and Dentistry, Western University, N6A 5C1, Canada.
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Heard M, Marmura H, Bryant D, Litchfield R, McCormack R, MacDonald P, Spalding T, Verdonk P, Peterson D, Bardana D, Rezansoff A, Getgood A. No increase in adverse events with lateral extra-articular tenodesis augmentation of anterior cruciate ligament reconstruction - Results from the stability randomized trial. J ISAKOS 2023; 8:246-254. [PMID: 36646169 DOI: 10.1016/j.jisako.2022.12.001] [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: 08/10/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 01/15/2023]
Abstract
OBJECTIVES Results from the Stability Study suggest that adding a lateral extra-articular tenodesis (LET) to a hamstring tendon autograft reduces the rate of anterior cruciate ligament reconstruction (ACLR) failure in high-risk patients. The purpose of this study is to report adverse events over the 2-year follow-up period and compare groups (ACLR alone vs. ACLR + LET). METHODS Stability is a randomized clinical trial comparing hamstring tendon ACLR with and without LET. Patients aged 14-25 years with an ACL deficient knee were included. Patients were followed and adverse events documented (type, actions taken, resolution) with visits at 3, 6, 12, and 24 months postoperatively. Adverse events were categorized as none, minor medical, minor surgical, contralateral ACL rupture, or graft rupture. Patient reported outcome measures (PROMs) collected at each visit included the Knee Injury and Osteoarthritis Outcome Score (KOOS), International Knee Documentation Committee Score (IKDC), and ACL Quality of Life Questionnaire (ACL-QOL). RESULTS In total, 618 patients were randomized (mean age 18.9 years, 302 (49%) male). Forty-five patients (7%) suffered graft rupture; 34 (11%) in the ACLR group compared to 11 (4%) in the ACLR + LET group (RRR = 0.67, 95% CI 0.36 to 0.83, p < 0.001). There were no differences in effusion or infection rates between groups. The ACLR + LET group experienced an increased number of hardware removals (10 vs. 4). Overall, the rate of minor medical events (11%), minor surgical events (7%), and ipsilateral or contralateral ACL tears (10%) were low considering the high-risk patient profile. Increasing severity of adverse events was associated with lower PROMs at 24 months post-operative. Patients in the ACLR + LET group reported greater degree of pain at 3 months only. There were no clinically significant differences in range of motion between groups. CONCLUSIONS The addition of LET to hamstring tendon autograft ACLR in young patients at high risk of re-injury resulted in a statistically significant reduction in graft rupture. While the addition of LET may increase rates of hardware irritation, there was no significant increase in overall rates of minor medical adverse events, minor surgical events, or overall re-operation rates. The concerns regarding complications associated with a LET did not materialize in this study. LEVEL OF EVIDENCE Level I.
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Affiliation(s)
- M Heard
- Deparment of Surgery, University of Calgary, T2N 1N4, Canada; Banff Sport Medicine, T1W 0L5, Canada
| | - H Marmura
- Fowler Kennedy Sport Medicine Clinic, N6A 3K7, Canada; School of Physical Therapy, Western University, N6A 3K7, Canada
| | - D Bryant
- Fowler Kennedy Sport Medicine Clinic, N6A 3K7, Canada; School of Physical Therapy, Western University, N6A 3K7, Canada
| | - R Litchfield
- Fowler Kennedy Sport Medicine Clinic, N6A 3K7, Canada; Department of Surgery, Schulich School of Medicine and Dentistry, Western University, N6A 5C1, Canada
| | - R McCormack
- Department of Orthopaedics, University of British Columbia, V5Z 1M9, Canada; New West Orthopaedic & Sports Medicine Centre, V3L 5P5, Canada
| | - P MacDonald
- Department of Surgery, University of Manitoba, R3A 1R9, Canada; Pan Am Clinic, R3M 3E4, Canada
| | - T Spalding
- University Hospital Coventry and Warwickshire NHS Trust, CV2 2DX, UK
| | - P Verdonk
- Department of Physical Medicine and Orthopedics, Ghent University, 9000, Belgium; Antwerp Orthopedic Center, 2018, Belgium
| | - D Peterson
- Department of Surgery, McMaster University, L8S 4K1, Canada
| | - D Bardana
- Department of Surgery, Queen's University, K7L 2V7, Canada
| | - A Rezansoff
- Deparment of Surgery, University of Calgary, T2N 1N4, Canada; University of Calgary Sport Medicine Centre, T2N 1N4, Canada
| | - A Getgood
- Fowler Kennedy Sport Medicine Clinic, N6A 3K7, Canada; Department of Surgery, Schulich School of Medicine and Dentistry, Western University, N6A 5C1, Canada.
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James G, Bryant D. 1463 One Urology Unit’s Experience With Holmium Laser Enucleation Of The Prostate(Holep). Br J Surg 2021. [DOI: 10.1093/bjs/znab259.1110] [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: 11/14/2022]
Abstract
Abstract
Introduction
Holmium laser enucleation of the prostate (HoLEP) is a minimally invasive procedure for the management of Benign Prostatic Hyperplasia and Bladder Outlet Obstruction. The European Associations of Urologists (EAU) recommend HoLEP should be offered to patients with prostates measuring >30cc or who are anticoagulated
Aim
To review the outcomes of one-unit HoLEP procedures. Comparing the first third of patients to the final third of patients in a 183-patient cohort.
Method
We collected data retrospectively over 44-month period from 183 patients using electronic patient records. Outcomes measured; length of stay (los), length of time for catheter. Length of time of procedure. comparing the 1st 61 patient with the last 61 patients and reviewed rates of complications from HoLEP using the Clavien-Dindo classification
Results
The mean size of prostate was 83cc. 149 (81%) of patients had a LOS of £ 1 day. The mean length of catheter time 3.44 days. Mean length of operating time – 71 minutes. Length of time for the 1st 61 patients was 70.2 minutes compared with 73.1 minutes for last 61 patients. With regards to complications, 8 patient had Grade 3 however 0 patients had grade 4 or 5.
Conclusions
Patients undergo HoLEP procedure with Prostate size in keeping with EAU. This unit has a short length of stay post-op with low complication rate. HoLEP has a short post op catheter time.
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Affiliation(s)
- G James
- Sunderland Royal Hospital, Sunderland, United Kingdom
| | - D Bryant
- Sunderland Royal Hospital, Sunderland, United Kingdom
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Yousefzadeh C, Van Rynbach A, Bryant D, Bos P. High-efficiency, tunable, fringe-field switching-mode beam steering based on a liquid crystal Pancharatnam phase. Appl Opt 2020; 59:10706-10718. [PMID: 33361890 DOI: 10.1364/ao.404603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
We have fabricated, characterized, and analyzed a recently proposed non-mechanical beam steering device based on the Pancharatnam-Berry phase in a liquid crystal. The architecture of our proposed device employs a linear array of phase control elements (PCEs) to locally control the orientation of the liquid crystal director into a cycloidal pattern to deflect transmitted light. The PCEs are comprised of a fringe-field switching electrode structure that can provide a variable in-plane electric field. Detailed optimization of the director configuration is in a good agreement with experimental results showing that the half-wave retardation condition has been uniformly achieved across the aperture. Moreover, efficiency simulations using a finite-difference time-domain algorithm verify a high beam steering efficiency for the proposed device.
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Feldsine PT, Falbo-Nelson MT, Brunelle SL, Forgey RL, Al-Hasani S, Ball C, Beatty S, Blanchfield B, Bowen B, Bremer N, Brookman D, Brookman S, Brushaber M, Bryant J, Bryant D, Bryant R, Chlebowski ET, Copeland F, Culak DA, Dalley E, Destro C, Finkenbiner D, Frissora R, Fung DYC, Garcia GR, Gray MR, Hagen CJ, Harshavardhan T, Hart-Thakur R, Inami G, Johnson S, Kandakai LV, Lessard D, Lin S, Liu V, Matiuck S, McAteer L, Miller L, Moon B, Nasri H, Pack L, Pilot K, Price C, Pruett P, Ramirez C, Richter D, Schmieg JA, Schultz G, Sloan EM, Sprague DM, Tebay D, Tomer J, Tuncan E, Warburton D, Watson M, West D. Assurance Enzyme Immunoassay for Detection of Enterohemorrhagic Escherichia coli 0157:H7 in Selected Foods: Collaborative Study. J AOAC Int 2020. [DOI: 10.1093/jaoac/80.3.530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Five foods types were analyzed by the Assurance EHEC (Escherichia coli 0157:H7) enzyme immunoassay (EIA) and by the Bacteriological Analytical Manual (BAM) culture method. Each sample of each food type at each inoculation level was simultaneously analyzed by both methods. A total of 21 laboratories representing state and federal government agencies and private industry in the United States and Canada participated. Samples were inoculated with E. coli 0157:H7, except for one lot of poultry that was naturally contaminated. A total of 1304 samples and controls were analyzed and confirmed, of which 473 were positive and 818 were negative by both methods. Thirteen samples were positive by BAM but negative by EIA. Because of the study design, it was not possible for the BAM method to produce false-negative or falsepositive results. The Assurance method for detection of E. coli OI57:H7 in selected foods has been adopted first action by AOAC INTERNATIONAL.
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Affiliation(s)
| | | | | | - Robin L Forgey
- BioControl Systems, Inc., 19805 N. Creek Parkway, Bothell, WA 98011
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Entis P, Bryant D, Bryant J, Bryant RG, Inami G, Cholensky JS, Garcia GR, Ramsey SM, Courtney T, Pruett WP, Dagdag EB, Davis-DeBella PE, San D, Humes LM, Lau D, Watson J, Erickson J, Hayes M, Ingham S, Sage J, Jirele K, Zuroski K, Kelley G, Lerner I, Patel DR, Peery DA, Simpso S, Zachary C. Direct 24-Hour Presumptive Enumeration of Escherichia coli 0157:H7 in Foods Using Hydrophobic Grid Membrane Filter Followed by Serological Confirmation: Collaborative Study. J AOAC Int 2020. [DOI: 10.1093/jaoac/81.2.403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
abstract
Fifteen laboratories took part in a collaborative study to validate a method for enumerating Escherichia coli 0157:H7. The method is based on use of a hydrophobic grid membrane filter and consists of 24 h presumptive enumeration on SD-39 Agar and serological confirmation to yield a confirmed E. coli 0157:H7 count. Six food products were analyzed: pasteurized apple cider, pasteurized 2% milk, cottage cheese, cooked ground pork, raw ground beef, and frozen whole egg. The test method produced significantly higher confirmed count results than did the reference method for milk, pork, and beef. Test method results were numerically higher than but statistically equivalent to reference method results for cheese, cider, and egg. The test method produced lower repeatability and reproducibility values than did the reference method for most food/inoculation level combinations and values very similar to those of the reference method for the remaining combinations. Overall, 94% of presumptive positive isolates from the test method were confirmed serologically as E. coli 0157:H7, and 98% of these were also biochemically typical of E. coli 0157:H7 (completed test). Corresponding rates for the reference method were 69 and 98%, respectively. On the basis of the results of this collaborative study and the precollaborative study that preceded it, it is recommended that this method be adopted official first action for enumeration of E. coli 0157:H7 in meats, poultry, dairy foods, infant formula, liquid eggs, mayonnaise, and apple cider
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Affiliation(s)
- Phyllis Entis
- QA Life Sciences, Inc., 6645 Nancy Ridge Dr, San Diego, CA 92121
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Feldsine PT, Albo-Nelson MT, Brunelle SL, Forgey RL, Al-Hasani S, Ball C, Beatty S, Blanchfield B, Bowen B, Bremer N, Brookman D, Brookman S, Brushaber M, Bryant J, Bryant D, Bryant R, Chlebowski ET, Copeland F, Culak DA, Dalley E, Destro C, Finkenbiner D, Frissora R, Fung DYC, Garcia GR, Gray MR, Hagen CJ, Harshavardhan T, Hart-Thakur R, Inami G, Johnson S, Kandakai LV, Lessard D, Lin S, Liu V, Matiuck S, McAteer L, Miller L, Moon B, Nasri H, Pack L, Pilot K, Price C, Pruett P, Ramirez C, Richter D, Schmieg JA, Schultz G, Sloan EM, Sprague DM, Tebay D, Tomer J, Tuncan E, Warburton D, Watson M, West D. Visual Immunoprecipitate Assay (VIP) for Detection of Enterohemorrhagic Escherichia coli (EHEC) 0157:H7 in Selected Foods: Collaborative Study. J AOAC Int 2020. [DOI: 10.1093/jaoac/80.3.517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Five foods representative of a variety of food products were analyzed by the Visual Immunoprecipitate Assay (VIP) and the Bacteriological Analytical Manual (BAM) culture method for the presence of Escherichia coli 0157: H7. A total of 21 laboratories representing state and federal government agencies, as well as private industry, in the United States and Canada participated. Food types were inoculated with strains of E. coli 0157:H7, with the exception of one lot of poultry, which was naturally contaminated. During this study, a total of 1377 samples and controls were analyzed and confirmed, of which 508 were positive and 867 were negative by both methods. Two samples were positive by BAM and negative by VIP. Because of the study design, it was not possible for the BAM method to produce false-negative or false-positive results. The VIP assay for detection of EHEC in selected foods has been adopted first action by AOAC INTERNATIONAL.
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Affiliation(s)
| | | | | | - Robin L Forgey
- BioControl Systems, Inc., 19805 N. Creek Parkway, Bothell, WA 98011
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Hughes D, Dailianis AE, Hill L, Curiale MS, Gangar V, Arnold D, Barrat C, Baxter T, Bell J, Brooks R, Bryant D, Burke K, Burnie A, Cliffard D, Danisavich T, Daniels K, Deiss K, D’Onorio A, Faucher K, Finkenbiner D, Gasanov U, Gebler J, Gerry A, Graham D, Graham T, Harris P, Hetrick S, Jurgens J, Keating KJ, Klokman R, Le C, Matrozza M, McCarthy R, McCawley C, Munyard S, Pye V, Rajkowski K, Ristov K, Rosinko J, Schneider K, Schubert MJ, Sloan E, Souter, Wilson M, Zuroski K. Salmonella in Foods: New Enrichment Procedure for TECRA Salmonella Visual Immunoassay Using a Single RV(R10) Only, TT Only, or Dual RV(R10) and TT Selective Enrichment Broths (AOAC Official Method 998.09): Collaborative Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/86.4.775] [Citation(s) in RCA: 6] [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: 11/13/2022]
Abstract
Abstract
A collaborative study was conducted to compare a new enrichment procedure for the TECRA® Salmonella Visual Immunoassay (TSVIA) with the reference method given in the U.S. Food and Drug Administration's Bacteriological Analytical Manual (7th Ed.). Three food types (milk powder, pepper, and soy flour) were analyzed in Australia and 3 food types (milk chocolate, dried egg, and raw turkey) were analyzed in the United States. Thirty-eight collaborators participated in the study. The TECRA method was evaluated using both Rappaport-Vassiliadis R10 (RV(R10)) and tetrathionate (TT) broths for selective enrichment. M broth cultures arising from each of the 2 selective enrichment broths were tested in the TSVIA using 2 individual wells, one for each selective broth, and a single well to test the pooled selective enrichment broths. The results for the pooled enrichment broths were reported elsewhere. This study presents the results for the use of single enrichment broths, i.e., RV(R10) only or TT only, with the TSVIA. No significant differences (p > 0.05) were observed for the pairwise comparison of the proportion of positive samples for either RV(R10) or TT used as a single enrichment broth for the TSVIA with that for the reference method.
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Affiliation(s)
- Denise Hughes
- TECRA International, 13 Rodborough Rd, Frenchs Forest, NSW 2086, Australia
| | - Angela E Dailianis
- TECRA International, 13 Rodborough Rd, Frenchs Forest, NSW 2086, Australia
| | - Louise Hill
- TECRA International, 13 Rodborough Rd, Frenchs Forest, NSW 2086, Australia
| | - Michael S Curiale
- Silliker Laboratories Group, Research Services, Halsted St, Chicago Heights, IL 60430
| | - Vidhya Gangar
- Silliker Laboratories Group, Research Services, Halsted St, Chicago Heights, IL 60430
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Hughes D, Dailianis A, Duncan L, Briggs J, McKintyre DA, Silbernagel K, Anderson G, Anderson J, Bannach B, Barratt C, Booyens C, Briggs J, Brooks R, Bryant D, Burnie A, Carver C, Chambers D, Chong J, Clarke D, Coates E, Comontofski G, Deiss K, Destro C, Dillon J, Duncan L, Dundas M, Dymond N, Dziedziczak D, Eglezos S, Gasanov U, Gebler J, Graham T, Haley E, Johnson L, Kurien S, Maczuga J, Matera J, Matthew K, Munyard S, Ramine A, Reed J, Remes A, Subasinghe N, Tan A, Tan J, Tatum M, Taylor M, Torrance H, Twohy C, Vialpando M, Watts K. Modification of Enrichment Protocols for TECRA Listeria Visual Immunoassay Method 995.22: Collaborative Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/86.2.340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
A collaborative study was conducted to validate new enrichment methods for the TECRA Listeria Visual Immunoassay (TLVIA). These new methods incorporate a newly formulated medium, TECRA Listeria Enrichment Broth, which does not contain the highly toxic antifungal agent, cycloheximide. The new procedures will provide an alternative to the enrichment procedures described in AOAC Method 995.22. Three food types (raw ground beef, lettuce, and ice cream) were analyzed in the United States, and 2 food types (cooked turkey and cooked fish fillets) were analyzed in Australasia. Thirty collaborators participated in the study, 16 in Australasia and 14 in the United States. With the exception of one batch of ground beef, comparison of the proportion of positive test portions (p ≥ 0.05) showed no significant difference between the TLVIA and the reference method for the 5 foods at 3 inoculation levels. For the one batch of naturally contaminated raw ground beef, the TLVIA gave significantly more confirmed positive results than the reference method.
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Affiliation(s)
- Denise Hughes
- TECRA International, 13 Rodborough Rd, French’s Forest, NSW 2086, Australia
| | - Angela Dailianis
- TECRA International, 13 Rodborough Rd, French’s Forest, NSW 2086, Australia
| | - Louise Duncan
- TECRA International, 13 Rodborough Rd, French’s Forest, NSW 2086, Australia
| | - Julie Briggs
- TECRA International, 13 Rodborough Rd, French’s Forest, NSW 2086, Australia
| | | | - Karen Silbernagel
- rtech laboratories, Lexington Ave, N. Arden Hills, Minneapolis, MN 55126
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10
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Lindberg KG, Lindberg KG, Kinneberg KM, Lindberg KG, Batterson D, Bobb R, Boleszczuk P, Brudvig S, Bryant D, Bryce J, Buckner K, Bulthaus M, DeJesus J, Ellis K, Finkenbiner D, Fleming S, Follni-Lieder E, Harper C, Ihrke P, Johnson K, King J, Langridge M, Maycock L, McAteer L, McCann T, Otten N, Robbins R, Sass A, Saunders L, Schop R, Strand S, Tebay D, VanWinkle J, Wolowski C. Dry Rehydratable Film Method for Rapid Enumeration of Coliforms in Foods (3M™ Petrifilm™ Rapid Coliform Count Plate): Collaborative Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/85.1.56] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
A rehydratable dry-film plating method for coliforms in foods, the 3M™ Petrifilm™ Rapid Coliform Count plate method, was compared with the U.S. Food and Drug Administration's Bacteriological Analytical Manual method for nondairy foods and the American Public Health Association's Standard Methods for the Examination of Dairy Products (SMEDP) method for dairy foods. Six food types, vanilla ice cream, cheddar cheese, fresh refrigerated uncooked pasta, wheat flour, prepared frozen macaroni and cheese, and frozen hash browns, were analyzed for coliforms by 11 collaborating laboratories. For each food product tested, the collaborators received 8 blind samples consisting of a control sample and 3 levels of inoculated sample, each in duplicate. The mean log counts for the methods were comparable. The repeatability and reproducibility variances of the Petrifilm Rapid Coliform Count method at 14 and 24 h were not significantly different from those of the standard methods.
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Bird CB, Hoerner RJ, Restaino L, Anderson G, Birbari W, Bodra L, Brookman D, Bryant D, Campbell C, Degraft-Hanson J, Fetviet D, Forde R, Goins D, Hajkowski S, Haley E, Holland R, Jones J, Joseph JM, Kallewaard N, Keckeissen J, Kirkbride T, Kusch S, Noel D, Nutsch A, Okolo C, Parks K, Raines D, Remes A, Roach V, Robbins R, Rodrick G, Shelef L, Theissen H, Vasavada PC, Wang T. Comparison of the Reveal 20-Hour Method and the BAM Culture Method for the Detection of Escherichia coli O157:H7 in Selected Foods and Environmental Swabs: Collaborative Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/84.3.737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Four different food types along with environmental swabs were analyzed by the Reveal for E. coli O157:H7 test (Reveal) and the Bacteriological Analytical Manual (BAM) culture method for the presence of Escherichia coli O157:H7. Twenty-seven laboratories representing academia and private industry in the United States and Canada participated. Sample types were inoculated with E. coli O157:H7 at 2 different levels. Of the 1095 samples and controls analyzed and confirmed, 459 were positive and 557 were negative by both methods. No statistical differences (p <0.05) were observed between the Reveal and BAM methods.
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Affiliation(s)
| | | | - Lawrence Restaino
- R&F Laboratories, 245 W. Roosevelt Rd, Bldg 3, Unit 17, West Chicago, IL 60185
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Bird CB, Hoerner RJ, Restaino L, Anderson G, Birbari W, Bodra L, Brookman D, Bryant D, Campbell C, Degraft-Hanson J, Fetviet D, Forde R, Goins D, Hajkowski S, Haley E, Holland R, Jones J, Joseph JM, Kallewaard N, Keckeissen J, Kirkbride T, Kusch S, Noel D, Nutsch A, Okolo C, Parks K, Raines D, Remes A, Roach V, Robbins R, Rodrick G, Shelef L, Theissen H, Vasavada PC, Wang T. Reveal 8-Hour Test System for Detection of Escherichia coli O157:H7 in Raw Ground Beef, Raw Beef Cubes, and Iceberg Lettuce Rinse: Collaborative Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/84.3.719] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Five different food types were analyzed by the Reveal for E. coli O157:H7 8-Hour Test System (Reveal 8) and either the U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM) culture method or the U.S. Department of Agriculture Food Safety Inspection Service (FSIS) culture method for the presence of E. coli O157:H7. A total of 27 laboratories representing academia and private industry in the United States and Canada participated. Food types were inoculated with E. coli O157:H7 at 2 different levels: a high level where predominantly positive results were expected, and a low level where fractional recovery was anticipated. During this study, 1110 samples and controls were analyzed by both the Reveal 8 and by BAM or FSIS by each of the collaborators (2220 samples in total). For each set of samples, 740 were artificially inoculated with E. coli O157:H7, and 370 were uninoculated controls. The Reveal 8 detected 528 presumptive positives of which 487 were confirmed positive by the BAM culture method. In comparison, BAM and FSIS detected 489 of the 740 artificially contaminated samples as positive. In an additional in-house study performed only on chilled and frozen raw ground beef, 240 artificially inoculated samples were analyzed by both the Reveal 8 and by FSIS. The Reveal 8 detected and confirmed 104 samples as positive compared to 79 confirmed positive by FSIS.
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Affiliation(s)
| | | | - Lawrence Restaino
- R&F Laboratories, 245 W. Roosevelt Rd, Bldg 3, Unit 17, West Chicago, IL 60185
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13
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Seselgyte R, Bryant D, Demetriou C, Ishida M, Peskett E, Moreno N, Morrogh D, Sell D, Lees M, Farrall M, Moore GE, Sommerlad B, Pauws E, Stanier P. Disruption of FOXF2 as a Likely Cause of Absent Uvula in an Egyptian Family. J Dent Res 2019; 98:659-665. [PMID: 30917284 DOI: 10.1177/0022034519837245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This study investigated the genetic basis of an unusual autosomal dominant phenotype characterized by familial absent uvula, with a short posterior border of the soft palate, abnormal tonsillar pillars, and velopharyngeal insufficiency. Cytogenetic analysis and single-nucleotide polymorphism-based linkage analysis were investigated in a 4-generation family with 8 affected individuals. Whole exome sequencing data were overlaid, and segregation analysis identified a single missense variant, p.Q433P in the FOXF2 transcription factor, that fully segregated with the phenotype. This was found to be in linkage disequilibrium with a small 6p25.3 tandem duplication affecting FOXC1 and GMDS. Notably, the copy number imbalances of this region are commonly associated with pathologies that are not present in this family. Bioinformatic predictions with luciferase reporter studies of the FOXF2 missense variant indicated a negative impact, affecting both protein stability and transcriptional activation. Foxf 2 is expressed in the posterior mouse palate, and knockout animals develop an overt cleft palate. Since mice naturally lack the structural equivalent of the uvula, we demonstrated FOXF2 expression in the developing human uvula. Decipher also records 2 individuals with hypoplastic or bifid uvulae with copy number variants affecting FOXF2. Nevertheless, given cosegregation with the 6p25.3 duplications, we cannot rule out a combined effect of these gains and the missense variant on FOXF2 function, which may account for the rare palate phenotype observed.
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Affiliation(s)
- R Seselgyte
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - D Bryant
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - C Demetriou
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - M Ishida
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - E Peskett
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - N Moreno
- 2 Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - D Morrogh
- 3 NE Thames Regional Genetics Service Laboratory, Great Ormond Street Hospital NHS Trust, London, UK
| | - D Sell
- 4 North Thames Cleft Centre, St Andrew's Centre, Broomfield Hospital, Chelmsford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - M Lees
- 4 North Thames Cleft Centre, St Andrew's Centre, Broomfield Hospital, Chelmsford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,5 Department of Clinical Genetics, Great Ormond Street Hospital NHS Trust, London, UK
| | - M Farrall
- 6 Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - G E Moore
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - B Sommerlad
- 4 North Thames Cleft Centre, St Andrew's Centre, Broomfield Hospital, Chelmsford, UK; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - E Pauws
- 2 Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - P Stanier
- 1 Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
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14
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Beattie WS, Wijeysundera DN, Chan MTV, Peyton PJ, Leslie K, Paech MJ, Sessler DI, Wallace S, Myles PS, Galagher W, Farrington C, Ditoro A, Baulch S, Sidiropoulos S, Bulach R, Bryant D, O’Loughlin E, Mitteregger V, Bolsin S, Osborne C, McRae R, Backstrom M, Cotter R, March S, Silbert B, Said S, Halliwell R, Cope J, Fahlbusch D, Crump D, Thompson G, Jefferies A, Reeves M, Buckley N, Tidy T, Schricker T, Lattermann R, Iannuzzi D, Carroll J, Jacka M, Bryden C, Badner N, Tsang MWY, Cheng BCP, Fong ACM, Chu LCY, Koo EGY, Mohd N, Ming LE, Campbell D, McAllister D, Walker S, Olliff S, Kennedy R, Eldawlatly A, Alzahrani T, Chua N, Sneyd R, McMillan H, Parkinson I, Brennan A, Balaji P, Nightingale J, Kunst G, Dickinson M, Subramaniam B, Banner-Godspeed V, Liu J, Kurz A, Hesler B, Fu AY, Egan C, Fiffick AN, Hutcherson MT, Turan A, Naylor A, Obal D, Cooke E. Implication of Major Adverse Postoperative Events and Myocardial Injury on Disability and Survival. Anesth Analg 2018. [DOI: 10.1213/ane.0000000000003310] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Varahra A, Rodrigues IB, MacDermid JC, Bryant D, Birmingham T. Exercise to improve functional outcomes in persons with osteoporosis: a systematic review and meta-analysis. Osteoporos Int 2018; 29:265-286. [PMID: 29306984 DOI: 10.1007/s00198-017-4339-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 12/04/2017] [Indexed: 11/29/2022]
Abstract
UNLABELLED Osteoporosis affects many aspects of daily life. The aim of this systematic review was to assess the effects of exercise interventions on functional outcomes in persons with osteoporosis, in comparison with controls. METHODS Four databases were searched and yielded 1587 citations. Two reviewers independently determined study eligibility, rated risk of bias, appraised methodological quality of studies, and resolved discordance by consensus. RESULTS A total of 28 studies examining 2113 participants met inclusion criteria; 25 studies were suitable for meta-analyses. Four categories of exercise were identified using the ProFaNE taxonomy. After removing studies with high risk of bias and sorting them into intervention sub-types, we were able to sufficiently reduce the heterogeneity. The standardized mean difference (SMD) favored multicomponent exercise for mobility (- 0.56, 95% CI [- 0.81, - 0.32], p = 0.06, I2 = 51%); balance (0.50, 95% CI [0.27, 0.74], p = 0.28, I2 = 21%); and self-reported measures of functioning (- 0.69, 95% CI [- 1.04, - 0.34], p = 0.02, I2 = 61%). Trials were judged at low or unclear risk of selection bias, indicating inadequate reporting and at high risk of performance bias due to lack of participant blinding. The mean methodological quality rating of the studies was 63.5% indicating moderate quality. CONCLUSIONS A multicomponent exercise program of high-speed training combined with simulated functional tasks is promising to enhance functional outcomes. Due to substantial clinical heterogeneity of the target groups and specific demands of exercise modes, it is unclear which exercise program is optimal.
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Affiliation(s)
- A Varahra
- University of Western Ontario Health and Rehabilitation Sciences, 1151 Richmond St., London, ON, N6A 3K7, Canada.
| | - I B Rodrigues
- University School of Rehabilitation Science, 1400 Main Street W, IAHS 308, Hamilton, ON, L8S 4K1, Canada
| | - J C MacDermid
- School of Physical Therapy, 1151 Richmond St., London, ON, N6A 3K7, Canada
| | - D Bryant
- School of Physical Therapy, 1151 Richmond St., London, ON, N6A 3K7, Canada
| | - T Birmingham
- School of Physical Therapy, 1151 Richmond St., London, ON, N6A 3K7, Canada
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16
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VanBuren R, Wai CM, Ou S, Pardo J, Bryant D, Jiang N, Mockler TC, Edger P, Michael TP. Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla. Nat Commun 2018; 9:13. [PMID: 29296019 PMCID: PMC5750206 DOI: 10.1038/s41467-017-02546-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/08/2017] [Indexed: 01/10/2023] Open
Abstract
Plant genome size varies by four orders of magnitude, and most of this variation stems from dynamic changes in repetitive DNA content. Here we report the small 109 Mb genome of Selaginella lepidophylla, a clubmoss with extreme desiccation tolerance. Single-molecule sequencing enables accurate haplotype assembly of a single heterozygous S. lepidophylla plant, revealing extensive structural variation. We observe numerous haplotype-specific deletions consisting of largely repetitive and heavily methylated sequences, with enrichment in young Gypsy LTR retrotransposons. Such elements are active but rapidly deleted, suggesting "bloat and purge" to maintain a small genome size. Unlike all other land plant lineages, Selaginella has no evidence of a whole-genome duplication event in its evolutionary history, but instead shows unique tandem gene duplication patterns reflecting adaptation to extreme drying. Gene expression changes during desiccation in S. lepidophylla mirror patterns observed across angiosperm resurrection plants.
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Affiliation(s)
- Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA.
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Shujun Ou
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Jeremy Pardo
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Doug Bryant
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Patrick Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
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17
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Birmingham TB, Moyer R, Leitch K, Chesworth B, Bryant D, Willits K, Litchfield R, Fowler PJ, Giffin JR. Changes in biomechanical risk factors for knee osteoarthritis and their association with 5-year clinically important improvement after limb realignment surgery. Osteoarthritis Cartilage 2017; 25:1999-2006. [PMID: 28888904 DOI: 10.1016/j.joca.2017.08.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 07/18/2017] [Accepted: 08/30/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To evaluate 5-year outcomes after lower limb realignment and test the hypothesis that surgery-induced changes in selected biomechanical risk factors for medial knee osteoarthritis (OA) are associated with clinically important improvements. DESIGN We prospectively evaluated patient-reported outcomes, full-limb standing radiographs and gait biomechanics before, 6 months (surgery-induced change) and 5 years after medial opening wedge high tibial osteotomy (HTO) in 170 patients (46.4 ± 8.9 years, 135 males) with knee OA and varus alignment. Logistic regression tested the associations of 6-month changes in mechanical axis angle and knee adduction moment with achieving an increase of ≥10 points in the Knee injury and Osteoarthritis Outcome Score (KOOS)4 at 5 years, with and without adjusting for covariates. Gait data were also compared to existing data from healthy controls. RESULTS Mean 5-year changes (95% confidence interval (CI)) were: KOOS4: +14.2 (10.8, 17.6); mechanical axis angle: +8.21° (7.58, 8.83); knee adduction moment: -1.49 %BW*Ht (-1.35, -1.63). The postoperative knee adduction moments were typically lower than values for healthy controls. When divided into quartiles, although all strata improved significantly, patients with reductions in knee adduction moment of 1.14-1.74 %BW*Ht (neither largest nor smallest changes) had highest 5-year KOOS4 scores. The 6-month change in knee adduction moment (odds ratios (OR) = 0.38; 95% CI: 0.22, 0.67), preoperative KOOS4 (OR = 0.96; 95% CI: 0.94, 0.99) and preoperative medial tibiofemoral narrowing grade (OR = 0.62; 95% CI: 0.37, 1.00) were negatively associated with having a 5-year clinically important improvement (C-statistic = 0.70). CONCLUSIONS Substantial improvements in biomechanical risk factors and patient-reported outcomes are observed 5 years after medial opening wedge HTO. The surgery-induced change in load distribution during walking is significantly associated with long-term clinically important improvement.
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Affiliation(s)
- T B Birmingham
- School of Physical Therapy, Faculty of Health Sciences, University of Western Ontario, Canada; Fowler Kennedy Sport Medicine Clinic, London Health Sciences Centre, Ontario, Canada; Bone and Joint Institute, University of Western Ontario, Canada.
| | - R Moyer
- School of Physiotherapy, Faculty of Health Professions, Dalhousie University, Canada; Fowler Kennedy Sport Medicine Clinic, London Health Sciences Centre, Ontario, Canada; Bone and Joint Institute, University of Western Ontario, Canada.
| | - K Leitch
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, University of Western Ontario, Canada; Fowler Kennedy Sport Medicine Clinic, London Health Sciences Centre, Ontario, Canada; Bone and Joint Institute, University of Western Ontario, Canada.
| | - B Chesworth
- School of Physical Therapy, Faculty of Health Sciences, University of Western Ontario, Canada; Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, University of Western Ontario, Canada; Fowler Kennedy Sport Medicine Clinic, London Health Sciences Centre, Ontario, Canada; Bone and Joint Institute, University of Western Ontario, Canada.
| | - D Bryant
- School of Physical Therapy, Faculty of Health Sciences, University of Western Ontario, Canada; Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, University of Western Ontario, Canada; Fowler Kennedy Sport Medicine Clinic, London Health Sciences Centre, Ontario, Canada; Bone and Joint Institute, University of Western Ontario, Canada.
| | - K Willits
- Department of Surgery, Schulich School of Medicine and Dentistry, University of Western Ontario, Canada; Fowler Kennedy Sport Medicine Clinic, London Health Sciences Centre, Ontario, Canada; Bone and Joint Institute, University of Western Ontario, Canada.
| | - R Litchfield
- Department of Surgery, Schulich School of Medicine and Dentistry, University of Western Ontario, Canada; Fowler Kennedy Sport Medicine Clinic, London Health Sciences Centre, Ontario, Canada; Bone and Joint Institute, University of Western Ontario, Canada.
| | - P J Fowler
- Department of Surgery, Schulich School of Medicine and Dentistry, University of Western Ontario, Canada; Fowler Kennedy Sport Medicine Clinic, London Health Sciences Centre, Ontario, Canada; Bone and Joint Institute, University of Western Ontario, Canada.
| | - J R Giffin
- Department of Surgery, Schulich School of Medicine and Dentistry, University of Western Ontario, Canada; Fowler Kennedy Sport Medicine Clinic, London Health Sciences Centre, Ontario, Canada; Bone and Joint Institute, University of Western Ontario, Canada.
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18
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VanBuren R, Wai CM, Zhang Q, Song X, Edger PP, Bryant D, Michael TP, Mockler TC, Bartels D. Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomaeum. Plant Cell Environ 2017; 40:2292-2306. [PMID: 28730594 DOI: 10.1111/pce.13027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 03/09/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 05/24/2023]
Abstract
Resurrection plants desiccate during periods of prolonged drought stress, then resume normal cellular metabolism upon water availability. Desiccation tolerance has multiple origins in flowering plants, and it likely evolved through rewiring seed desiccation pathways. Oropetium thomaeum is an emerging model for extreme drought tolerance, and its genome, which is the smallest among surveyed grasses, was recently sequenced. Combining RNA-seq, targeted metabolite analysis and comparative genomics, we show evidence for co-option of seed-specific pathways during vegetative desiccation. Desiccation-related gene co-expression clusters are enriched in functions related to seed development including several seed-specific transcription factors. Across the metabolic network, pathways involved in programmed cell death inhibition, ABA signalling and others are activated during dehydration. Oleosins and oil bodies that typically function in seed storage are highly abundant in desiccated leaves and may function for membrane stability and storage. Orthologs to seed-specific LEA proteins from rice and maize have neofunctionalized in Oropetium with high expression during desiccation. Accumulation of sucrose, raffinose and stachyose in drying leaves mirrors sugar accumulation patterns in maturing seeds. Together, these results connect vegetative desiccation with existing seed desiccation and drought responsive pathways and provide some key candidate genes for engineering improved drought tolerance in crop plants.
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Affiliation(s)
- Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48823, USA
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
| | - Qingwei Zhang
- IMBIO, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Xiaomin Song
- IMBIO, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48823, USA
| | - Doug Bryant
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Dorothea Bartels
- IMBIO, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany
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19
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VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, Rowley ER, Priest HD, Michael TP, Lyons E, Filichkin SA, Dossett M, Finn CE, Bassil NV, Mockler TC. The genome of black raspberry (Rubus occidentalis). Plant J 2016; 87:535-47. [PMID: 27228578 DOI: 10.1111/tpj.13215] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 01/05/2016] [Revised: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 05/02/2023]
Abstract
Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the US Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae and Rubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein-coding genes, we identified 290 very recent small-scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberry F. vesca, which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed to Verticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and other Rubus cultivars.
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Affiliation(s)
- Robert VanBuren
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Doug Bryant
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Jill M Bushakra
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA
| | - Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
| | - Erik R Rowley
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Henry D Priest
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | | | - Eric Lyons
- CyVerse, BIO5, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Sergei A Filichkin
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University Corvallis, Corvallis, OR, 97331, USA
| | - Michael Dossett
- B.C. Blueberry Council (in Partnership with Agriculture and Agri-Food Canada) - Agassiz Research and Development Centre, Agassiz, BC, VOM 1A0, Canada
| | - Chad E Finn
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR, 97330, USA
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
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Kazimierczuk F, Bryant D. The Social Determinants of Obesity: Examining The Intersections of Race, Class, and Gender in African American Women. J Acad Nutr Diet 2016. [DOI: 10.1016/j.jand.2016.06.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E, Freeling M, Bartels D, Ten Hallers B, Hastie A, Michael TP, Mockler TC. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 2015; 527:508-11. [PMID: 26560029 DOI: 10.1038/nature15714] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/10/2015] [Indexed: 12/20/2022]
Abstract
Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (>16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.
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Affiliation(s)
- Robert VanBuren
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Doug Bryant
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA.,Department of Horticulture, Michigan State University, East Lansing, Michigan 48823, USA
| | - Haibao Tang
- iPlant Collaborative, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.,Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Diane Burgess
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA
| | | | | | - Richard Hall
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Jenny Gu
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Eric Lyons
- iPlant Collaborative, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA
| | | | | | - Alex Hastie
- BioNano Genomics, San Diego, California 92121, USA
| | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
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Urbanic J, Case D, Baez-Diaz L, Brown D, Strasser J, Enevold G, Naughton M, Weaver K, Baglan K, Bryant D, Langefeld C, Lad T, Lee L, Rine G, Curtis A, Koprowski C, Tomlinson W, Lesser G, Shaw E, Hu J. Late Breast Toxicity Rates in a Prospective Evaluation of Radiation Therapy (RT) in a Multiracial/Ethnic Population of Breast Cancer (BC) Patients. Int J Radiat Oncol Biol Phys 2015. [DOI: 10.1016/j.ijrobp.2015.07.670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Gatalica Z, Vranic S, Basu G, Bryant D, Lynch H. Thymidylate Synthase Over-Expression Underlies the Observed Lack of 5-Fu Therapy Benefit for Msi-H Colorectal Cancers. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu333.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, Manzaneda AJ, Barry K, Garvin DF, Budak H, Tuna M, Mitchell-Olds T, Pfender WF, Juenger TE, Mockler TC, Vogel JP. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J 2014; 79:361-74. [PMID: 24888695 DOI: 10.1111/tpj.12569] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [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: 11/07/2013] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 05/08/2023]
Abstract
Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.
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Affiliation(s)
- Sean P Gordon
- USDA-ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710, USA
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Li L, Bryant D, Van Heugten T, Bos PJ. Speed, optical power, and off-axis imaging improvement of refractive liquid crystal lenses. Appl Opt 2014; 53:1124-1131. [PMID: 24663311 DOI: 10.1364/ao.53.001124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/14/2014] [Indexed: 06/03/2023]
Abstract
Two design approaches (multicell and addition of phase resets in single cell) are introduced to optimize the performances of tunable refractive liquid crystal lenses, including improvements on the switching speed, optical power, and the off-axis, wide-angle imaging performance. Key parameters and advantages for each method are discussed, and their effects on the performance are demonstrated in detail with numerical calculations.
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Li L, Bryant D, Van Heugten T, Bos PJ. Near-diffraction-limited and low-haze electro-optical tunable liquid crystal lens with floating electrodes. Opt Express 2013; 21:8371-8381. [PMID: 23571926 DOI: 10.1364/oe.21.008371] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A near-diffraction-limited, low-haze and tunable liquid crystal (LC) lens is presented. Building on an understanding of the key factors that have limited the performance of lenses based on liquid crystals, we show a simple design whose optical quality is similar to a high quality glass lens. It uses 'floating' electrodes to provide a smooth, controllable applied potential profile across the aperture to manage the phase profile.
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Affiliation(s)
- Liwei Li
- Liquid Crystal Institute, Kent State University, Kent, OH 44240, USA
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Li L, Bryant D, van Heugten T, Bos PJ. Physical limitations and fundamental factors affecting performance of liquid crystal tunable lenses with concentric electrode rings. Appl Opt 2013; 52:1978-1986. [PMID: 23518745 DOI: 10.1364/ao.52.001978] [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] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 02/11/2013] [Indexed: 06/01/2023]
Abstract
A comprehensive analysis of fundamental factors and their effects on the performance of liquid crystal (LC)-based lenses is given. The analysis adopts numerical LC director and electric field simulation, as well as scalar diffraction theory for calculating the lens performance considering different variable factors. A high-efficiency LC lens with concentric electrode rings is fabricated for verifying and enriching the analysis. The measurement results are in close agreement with the analysis, and a summary of key factors is given with their quantitative contributions to the efficiency.
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Affiliation(s)
- Liwei Li
- Liquid Crystal Institute, Kent State University, Kent, Ohio 44240, USA
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Bourdeaux C, Thomas M, Gould T, Evans Z, Bryant D. Validation of a computerised system to calculate the sequential organ failure assessment score. Crit Care 2010. [PMCID: PMC2934079 DOI: 10.1186/cc8477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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29
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Breeze J, Bryant D. Current Concepts in the Epidemiology and Management of Battlefield Head, Face and Neck trauma. J ROY ARMY MED CORPS 2009; 155:274-8. [DOI: 10.1136/jramc-155-04-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Grubbs SS, Gonzalez M, Krasna M, Siegel R, Bryant D, Tschetter L, Hayenga L, Duggan B, St. Germaine D, Denicoff A. Tracking clinical trial accrual strategies and barriers via a Web-based screening tool. J Clin Oncol 2009. [DOI: 10.1200/jco.2009.27.15_suppl.6586] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
6586 Background: The National Cancer Institute Community Cancer Centers Program (NCCCP) has developed a web based tracking tool to monitor screening of patients for clinical trial participation. The system is designed to collect data from multiple research sites throughout the geographically diverse group. The log blindly collects patient demographics, successful trial entry, and reasons for trial enrollment failure. Methods: Seven NCCCP sites utilized the log during the 60 day open accrual period for the Wake Forrest WFU 07–02–03 cancer control trial (chronic lymphocytic leukemia COLD- fX) in Novermber 2008 and December 2008. Results: 327 chronic lymphocytic leukemia patients were screened mostly by chart review. 162 (50%) were eligible for study entry. 45 (14%) entered the trial. 103 (31%) eligible patients declined entry. Of the 103, 72 (70%) did not wish to participate in research, 15 (15%) had travel constraints, 5 (5%) perceived excess toxicity, 9 (9%) gave no reason. 14 (3%) eligible had their physician decline entry. Overall, 28% of eligible patients entered the trial. 165 (50%) were trial ineligible. 82 (50%) for prior therapy, 30 (18%) for co morbid conditions, 10 (6%) missed an entry time requirement, 39 (24%) have incomplete data. Conclusions: The NCCCP trial screening log successfully captures real time clinical trial participation data from a diverse network of clinical trial sites. This data base will allow future analysis of individual clinical trial and site accrual barriers and empower strategies to increase trial participation. No significant financial relationships to disclose.
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Affiliation(s)
- S. S. Grubbs
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
| | - M. Gonzalez
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
| | - M. Krasna
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
| | - R. Siegel
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
| | - D. Bryant
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
| | - L. Tschetter
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
| | - L. Hayenga
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
| | - B. Duggan
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
| | - D. St. Germaine
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
| | - A. Denicoff
- Helen F. Graham Cancer Center, Newark, DE; St. Joseph Hospital, Orange, CA; St. Joseph Medical Center, Towson, MD; Hartford Hospital, Hartford, CT; Our Lady of the Lake Regional Medical Center, Baton Rouge, LA; Sanford USD Medical Center, Sioux Falls, SD; St. Vincent Indianapolis Hospital, Indianapolis, IN; NCI CBIIT Community Informatics Program, Rockville, MD; NCI Division of Cancer Prevention, Bethesda, MD; NCI CTEP, Bethesda, MD
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Hunt MA, Birmingham TB, Bryant D, Jones I, Giffin JR, Jenkyn TR, Vandervoort AA. Lateral trunk lean explains variation in dynamic knee joint load in patients with medial compartment knee osteoarthritis. Osteoarthritis Cartilage 2008; 16:591-9. [PMID: 18206395 DOI: 10.1016/j.joca.2007.10.017] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 10/29/2007] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To test the hypothesis that selected gait kinematics, particularly lateral trunk lean, observed in patients with medial compartment knee osteoarthritis explain variation in dynamic knee joint load. METHOD In this cross-sectional observational study, 120 patients with radiographically confirmed varus gonarthrosis underwent three-dimensional gait analysis at their typical walking speed. We used sequential (hierarchical) linear regression to examine the amount of variance in dynamic knee joint load (external knee adduction moment) explained by static lower limb alignment (mechanical axis angle) and gait kinematics determined a priori based on their proposed effect on knee load (walking speed, toe-out angle, and lateral trunk lean angle). RESULTS Approximately 50% of the variation in the first peak external knee adduction moment was explained by mechanical axis angle (25%), Western Ontario and McMaster Universities Osteoarthritis Index pain score (1%), gait speed (1%), toe-out angle (12%), and lateral trunk lean angle (13%). There was no confounding or interaction with Kellgren and Lawrence grade of severity. CONCLUSIONS Gait kinematics, particularly lateral trunk lean, explain substantial variation in dynamic knee joint load in patients with medial compartment knee osteoarthritis. While largely ignored in previous gait studies, the effect of lateral trunk lean should be considered in future research evaluating risk factors and interventions for progression of knee osteoarthritis.
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Affiliation(s)
- M A Hunt
- Fowler Kennedy Sport Medicine Clinic, University of Western Ontario, London, Ontario, Canada
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Vist GE, Hagen KB, Devereaux PJ, Bryant D, Kristoffersen DT, Oxman AD. Outcomes of patients who participate in randomised controlled trials compared to similar patients receiving similar interventions who do not participate. Cochrane Database Syst Rev 2007:MR000009. [PMID: 17443630 DOI: 10.1002/14651858.mr000009.pub3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Some people believe that patients who take part in randomised controlled trials (RCTs) face risks that they would not face if they opted for non-trial treatment. Others think that trial participation is beneficial and the best way to ensure access to the most up to date physicians and treatments. OBJECTIVES To assess the effects of patient participation in RCTs ('trial effects') independent both of the effects of the clinical treatments being compared ('treatment effects') and any differences between patients who participated in RCTs and those who did not. SEARCH STRATEGY In May 2001, we searched The Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, The Cochrane Methodology Register, SciSearch and PsycINFO for potentially relevant studies. Our search yielded over 10,000 references. In addition, we reviewed the reference lists of relevant articles and wrote to over 250 investigators to try to obtain further information. SELECTION CRITERIA Randomised studies and cohort studies with data on clinical outcomes of RCT participants and similar patients who received similar treatment outside of RCTs. DATA COLLECTION AND ANALYSIS At least two reviewers independently assessed studies for inclusion, assessed study quality and extracted data. Study authors were contacted for additional information. MAIN RESULTS We included five randomised studies (yielding 6 comparisons) and 50 non-randomised cohort studies (85 comparisons), with 31,140 patients treated in RCTs and 20,380 patients treated outside RCTs. In the randomised studies, patients were invited to participate in an RCT or not; these comparisons provided limited information because of small sample sizes (a total of 412 patients) and the nature of the questions they addressed. There was statistically significant heterogeneity (P < 0.002, I(2) = 36.2%) among the 73 dichotomous outcome comparisons; none of the potential explanatory factors we investigated helped to explain this heterogeneity. No statistically significant differences were found for 63 of the 73 comparisons. Eight comparisons reported statistically significant better outcomes for patients treated within RCTs, and two comparisons reported statistically significant worse outcomes for patients treated within RCTs. There were no statistically significant differences in heterogeneity (P = 0.53, I(2) = 0%) or in outcomes (SMD 0.01, 95% CI -0.10 to 0.12) of patients treated within and outside RCTs in the 18 comparisons which had used continuous outcomes. AUTHORS' CONCLUSIONS This review indicates that participation in RCTs is not associated with greater risks than receiving the same treatment outside RCTs. These results challenge the assertion that the results of RCTs are not applicable to usual practice.
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Affiliation(s)
- G E Vist
- Norwegian Knowledge Centre for Health Services, PO Box 7004, St Olavs Plass, Oslo, Norway, 0130.
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Vist GE, Hagen KB, Devereaux PJ, Bryant D, Kristoffersen DT, Oxman AD. Outcomes of patients who participate in randomised controlled trials compared to similar patients receiving similar interventions who do not participate. THE COCHRANE DATABASE OF SYSTEMATIC REVIEWS 2004. [DOI: 10.1002/14651858.mr000009.pub2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Burns A, Bryant D, Clark S. An aid to accurate skin closure. Laryngoscope 2002; 112:412-3. [PMID: 11889409 DOI: 10.1097/00005537-200202000-00041] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Charlwood J, Bryant D, Skehel JM, Camilleri P. Analysis of N-linked oligosaccharides: progress towards the characterisation of glycoprotein-linked carbohydrates. Biomol Eng 2001; 18:229-40. [PMID: 11911090 DOI: 10.1016/s1389-0344(01)00098-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The covalent attachment of carbohydrate to proteins is a very common co- or post-translational event in the biosynthesis of glycoproteins. The type and heterogeneity of these oligosaccharides can affect a range of physico-chemical and biological properties of a glycoprotein. Thus the development of sensitive, reliable and robust analytical methods for carbohydrate analysis is important in the pharmaceutical industry, especially in the recombinant production of experimental and therapeutic glycoproteins. In this report we have reviewed methodology for the in-gel enzymatic release of N-linked oligosaccharides from glycoproteins separated by electrophoresis. These oligosaccharides are derivatised by reductive amination using 3-acetamido-6-aminoacridine (AA-Ac), a novel, highly fluorescent probe. A major advantage of this technique is that glycan derivatives are amenable to analysis by an array of chromatographic and mass spectrometric methods, allowing the resolution and characterisation of a wide variety of glycan structures. It is hoped that in due course the methodology described will be applied to proteomics studies, especially in identifying the role of carbohydrate in protein function and disease.
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Affiliation(s)
- J Charlwood
- SmithKline Beecham Pharmaceuticals, New Frontiers Science Park North), Harlow, Essex, UK
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Affiliation(s)
- O Gascuel
- Département Informatique Fondamentale et Applications, L.I.R.M.M., 161 rue Ada, 34392, Montpellier, France.
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Abstract
The present study was designed to assess both the prevalence and structure of antisocial behavior in a normative sample of preschoolers. Prevalence estimates suggested that 40% of preschoolers exhibit at least one antisocial behavior each day. Furthermore, 10% of preschoolers exhibit six or more antisocial behaviors each day. Consistent with research based on older children, factor analyses provided support for conceptualizing antisocial behavior in early childhood as consisting of both overt and covert dimensions. While both overt and covert behaviors had acceptable test-retest reliability, only overt behaviors had acceptable interrater reliability. Finally both overt and covert dimensions of antisocial behavior were uniquely related to general measures of conduct problems, hyperactivity, and adult and peer conflict in the classroom setting. Findings are discussed with regard to early assessment and the developmental course of antisocial behavior.
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Affiliation(s)
- M Willoughby
- Department of Psychology, University of North Carolina at Chapel Hill, 27599-3270, USA.
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Abstract
The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the "median problem for breakpoints"; this solution can then be incorporated into a routine for estimating optimal gene orders for all the ancestral genomes in a fixed phylogeny. For the difficult (and most prevalent) case where the genomes contain partially different sets of genes, we present a general heuristic for the median problem for induced breakpoints. A fixed-phylogeny optimization based on this is applied in a phylogenetic study of a set of completely sequenced protist mitochondrial genomes, confirming some of the recent sequence-based groupings which have been proposed and, conversely, confirming the usefulness of the breakpoint method as a phylogenetic tool even for small genomes.
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Affiliation(s)
- D Sankoff
- Centre de recherches mathématiques, Université de Montréal, Québec.
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Abstract
The influence of expertise and task factors on age differences in a simulated pilot-Air Traffic Control (ATC) communication task was examined. Young, middle-aged, and older pilots and nonpilots listened to ATC messages that described a route through an airspace, during which they referred to a chart of this airspace. Participants read back each message and then answered a probe question about the route. It was found that pilots read back messages more accurately than nonpilots, and younger participants were more accurate than older participants. Age differences were not reduced for pilots. Pilots and younger participants also answered probes more accurately, suggesting that they were better able to interpret the ATC messages in terms of the chart in order to create a situation model of the flight. The findings suggest that expertise benefits occur for adults of all ages. High levels of flying experience among older pilots (as compared with younger pilots) helped to buffer age-related declines in cognitive resources, thus providing evidence for the mediating effects of experience on age differences.
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Affiliation(s)
- D G Morrow
- Department of Psychology, University of New Hampshire, Durham 03824, USA.
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Abstract
OBJECTIVE To compare the demographic and intrapartum factors of term pregnancies in which early-onset neonatal seizures developed with the characteristics of a large, unselected control population. STUDY DESIGN Pregnancies delivered at term (gestational age > or = 37 weeks) in one birthing unit between 1984 and 1995 with a discharge diagnosis of neonatal seizures were identified. Maternal and neonatal charts of these patients were reviewed to confirm the diagnosis of early-onset seizure (EOS) which was defined as a clinical or EEG-diagnosed seizure within 72 hours of life. Demographic and intrapartum factors were compared between these EOS cases and all singleton term pregnancies delivered over the same time period in which there was no EOS. A regression model was then developed to determine factors predictive of EOS. RESULTS Of 80,561 total deliveries during the 11-year study period, there were 64,340 control and 62 EOS (0.1%) deliveries. Regression modeling identified NICU admission, depressed 1- and 5-minute Apgar scores, and neonatal intubation as predictors of EOS, but not operative vaginal, vaginal breech, or cesarean delivery. CONCLUSION Depressed condition at birth and/or the requirement for NICU care was the most important risk associated with early seizures in term infants.
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Affiliation(s)
- Y Sorokin
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Hutzel Hospital, Detroit Medical Center, Wayne State University, Detroit, MI, USA
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Buchman AL, Sohel M, Moukarzel A, Bryant D, Schanler R, Awal M, Burns P, Dorman K, Belfort M, Jenden DJ, Killip D, Roch M. Plasma choline in normal newborns, infants, toddlers, and in very-low-birth-weight neonates requiring total parenteral nutrition. Nutrition 2001; 17:18-21. [PMID: 11165882 DOI: 10.1016/s0899-9007(00)00472-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Choline deficiency is associated with hepatic abnormalities in adult volunteers and patients administered total parenteral nutrition (TPN). Preliminary investigation has suggested that plasma-free choline concentration (PFCh) is greater in neonatal animals, including humans, than in adults. The aims of this study were to determine the normal PFCh and phospholipid-bound choline concentration (PPLBCh) for newborns, infants, and toddlers and to determine the change during TPN. We also sought to determine the degree of fetal choline extraction, the relation between maternal and newborn plasma choline concentrations, and the relation between plasma choline status and normal newborn length, weight, and gestational age. Blood samples were obtained from 104 full-term newborns in two centers (Ben Taub and Maimonides), 25 mothers, 21 normal infants aged 20.3 +/- 11.8 wk, 12 normal infants aged 62.4 +/- 3.9 wk, and 14 preterm infants (gestational age = 28.9 +/- 2.2 wk) who required TPN. The vein PFChs were 28.1 +/- 13.0 nmol/mL (Ben Taub) and 68.1 +/- 16.9 nmol/mL (Maimonides). The artery PFChs were 27.1 +/- 13.0 nmol/mL (Ben Taub) and 57.9 +/- 11.6 nmol/mL (Maimonides). The vein PPLChs were 1004.7 +/- 246.6 nmol/mL (Ben Taub) and 1121.2 +/- 289.6 nmol/mL (Maimonides). The artery PPLChs were 1065.7 +/- 469.3 nmol/mL (Ben Taub) and 1106.9 +/- 285.8 nmol/mL (Maimonides). The vein-minus-artery differences for PFCh were 1.0 +/- 9.7 nmol/mL (Ben Taub) and 10.2 +/- 10.9 nmol/mL (Maimonides). The vein-minus-artery differences for PPLCh were -51.9 +/- 398.2 nmol/mL (Ben Taub General Hospital, Houston, Texas) and 14.4 +/- 254.3 nmol/mL (Maimonides, New York, New York). Maternal venous PFCh was 8.4 +/- 3.1 nmol/mL. Maternal venous PPLCh was 2592.1 +/- 584.0 nmol/mL (range = 1227.8-3729.0). Maternal venous PFCh correlated with newborn arterial PFCh (r = 0.53, P < 0.05) but not with newborn venous PFCh. No correlation was seen between maternal venous and newborn PPLCh. No significant differences were seen in PPLCh or choline extraction in Ben Taub versus Maimonides patients, although PFCh was significantly greater in the newborns from Maimonides (P < 0.05). The mean venous PFCh and PPLCh in the preterm infants before beginning TPN was 21.2 +/- 6.3 and 1366.8 +/- 339.1 nmol/mL, respectively. Just before initiation of tube feeding (4.0 +/- 2.7 d after TPN had been started), mean venous PFCh and PPLCh was 18.4 +/- 5.3 and 2251.8 +/- 686.9 nmol/mL, respectively. When TPN was discontinued and tube feeding increased to goal, after 10.8 +/- 10.4 d, venous PFCh and PPLCh was 22.6 +/- 8.7 and 2072.5 +/- 540.6 nmol/mL, respectively. Venous PFCh and PPLCh was 13.4 +/- 2.5 and 1827.5 +/- 327.0 nmol/mL, respectively in the older infant group. In conclusion, newborn PFCh is significantly greater than PFCh in adults but falls to adult levels within the first year of life. Low maternal PFCh may be associated with low newborn PFCh. Normal newborn plasma choline status has no bearing on intrauterine growth, although the role of maternal choline deficiency in underweight newborns is unknown. Newborn PPLCh is substantially below that of adults, which suggests its use in membrane synthesis during growth.
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Affiliation(s)
- A L Buchman
- Division of Gastroenterology, Hepatology, and Nutrition, University of Texas Houston Health Science Center, Houston, Texas, USA
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Affiliation(s)
- D Bryant
- Brigham and Women's Hospital, Boston, Mass., USA
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Malin DH, Lake JR, Moon WD, Moy D, Montellano AL, Moy E, Campbell TD, Bell MV, Bryant D, Harrison LM, Grandy DK. Nociceptin/orphanin FQ (N/OFQ) induces a quasi-morphine abstinence syndrome in the rat. Psychopharmacology (Berl) 2000; 151:344-50. [PMID: 11026741 DOI: 10.1007/s002130000473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 10/27/2022]
Abstract
Nociceptin/orphanin FQ (N/OFQ) is a neuropeptide that exerts antiopiate effects under some circumstances, and there is evidence that it contributes to opiate tolerance. This raises the question, might N/OFQ also contribute to opiate dependence and abstinence? Twenty-two male Sprague-Dawley rats were cannulated in the third ventricle and challenged 7 days later by third ventricle injection of 50, 200 or 1,000 ng N/OFQ or saline alone. Each rat was observed under "blind" conditions for 30 min beginning 15 min after onset of the third ventricle injection. There was a significant positive linear trend of signs as a function of N/OFQ dose. Subjects receiving saline had 18.0+/-2.0 (mean+/-SEM) overall abstinence-like signs, whereas subjects receiving 50, 200 or 1000 ng N/OFQ had 35.2+/-3.6, 49.8+/-2.6 and 63.5+/-9.7 signs, respectively. In 16 additional rats, abstinence-like signs induced by 1000 ng N/OFQ were significantly attenuated by low SC doses of morphine or clonidine. These results raise the possibility that N/OFQ might contribute to opiate dependence and subsequent abstinence syndrome. On the other hand, N/OFQ over a wide dose range induced abstinence signs with similar potency in morphine dependent and non-dependent rats.
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Affiliation(s)
- D H Malin
- University of Houston-Clear Lake, TX 77058, USA.
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Virmani AK, Rathi A, Zöchbauer-Müller S, Sacchi N, Fukuyama Y, Bryant D, Maitra A, Heda S, Fong KM, Thunnissen F, Minna JD, Gazdar AF. Promoter methylation and silencing of the retinoic acid receptor-beta gene in lung carcinomas. J Natl Cancer Inst 2000; 92:1303-7. [PMID: 10944551 DOI: 10.1093/jnci/92.16.1303] [Citation(s) in RCA: 270] [Impact Index Per Article: 11.3] [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: 11/14/2022] Open
Abstract
BACKGROUND Retinoic acid plays an important role in lung development and differentiation, acting primarily via nuclear receptors encoded by the retinoic acid receptor-beta (RARbeta) gene. Because receptor isoforms RARbeta2 and RARbeta4 are repressed in human lung cancers, we investigated whether methylation of their promoter, P2, might lead to silencing of the RARbeta gene in human lung tumors and cell lines. METHODS Methylation of the P2 promoter from small-cell lung cancer (SCLC) and non-small-cell lung cancer (NSCLC) cell lines and tumor samples was analyzed by the methylation-specific polymerase chain reaction (PCR). Expression of RARbeta2 and RARbeta4 was analyzed by reverse transcription-PCR. Loss of heterozygosity (LOH) was analyzed by PCR amplification followed by electrophoretic separation of PCR products. Statistical differences were analyzed by Fisher's exact test with continuity correction. RESULTS The P2 promoter was methylated in 72% (63 of 87) of SCLC and in 41% (52 of 127) of NSCLC tumors and cell lines, and the difference was statistically significant (two-sided P:<.001). By contrast, in 57 of 58 control samples, we observed only the unmethylated form of the gene. Four tumor cell lines with unmethylated promoter regions expressed both RARbeta2 and RARbeta4. Four tumor lines with methylated promoter regions lacked expression of these isoforms, but demethylation by exposure to 5-aza-2'-deoxycytidine restored their expression. LOH at chromosome 3p24 was observed in 100% (13 of 13) of SCLC lines and 67% (12 of 18) of NSCLC cell lines, and the difference was statistically significant (two-sided P: =.028). CONCLUSIONS Methylation of the RARbeta P2 promoter is one mechanism that silences RARbeta2 and RARbeta4 expression in many lung cancers, particularly SCLC. Chemical demethylation is a potential approach to lung cancer therapy.
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Affiliation(s)
- A K Virmani
- Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas 75390-8593, USA
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Abstract
We have recently shown that phototactic movement in the unicellular cyanobacterium Synechocystis sp. PCC6803 requires type IV pilins. To elucidate further type IV pilus-dependent motility, we inactivated key genes implicated in pilus biogenesis and function. Wild-type Synechocystis sp. PCC6803 cells have two morphologically distinct pilus types (thick and thin pili). Of these, the thick pilus morphotype, absent in a mutant disrupted for the pilin-encoding pilA1 gene, appears to be required for motility. The thin pilus morphotype does not appear to be altered in the pilA1 mutant, raising the possibility that thin pili have a function distinct from that of motility. Mutants disrupted for pilA2, which encodes a second pilin-like protein, are still motile and exhibit no difference in morphology or density of cell-surface pili. In contrast, inactivation of pilD (encoding the leader peptidase) or pilC (encoding a protein required for pilus assembly) abolishes cell motility, and both pilus morphotypes are absent. Thus, the PilA1 polypeptide is required for the biogenesis of the thick pilus morphotype which, in turn, is necessary for motility (hence we refer to them as type IV pili). Furthermore, PilA2 is critical neither for motility nor for pilus biogenesis. Two genes encoding proteins with similarity to PilT, which is considered to be a component of the motor essential for type IV pilus-dependent movement, were also inactivated. A pilT1 mutant is (i) non-motile, (ii) hyperpiliated and (iii) accumulates higher than normal levels of the pilA1 transcript. In contrast, pilT2 mutants are motile, but are negatively phototactic under conditions in which wild-type cells are positively phototactic.
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Affiliation(s)
- D Bhaya
- The Carnegie Institution of Washington, Department of Plant Biology, Stanford, CA 94305, USA.
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Thompson M, Kliewer A, Maass D, Becker L, White DJ, Bryant D, Arteaga G, Horton J, Giroir BP. Increased cardiomyocyte intracellular calcium during endotoxin-induced cardiac dysfunction in guinea pigs. Pediatr Res 2000; 47:669-76. [PMID: 10813595 DOI: 10.1203/00006450-200005000-00019] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [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: 11/06/2022]
Abstract
Septic shock is a complex pathophysiologic state characterized by circulatory insufficiency, multiple system organ dysfunction, and frequent mortality. Although profound cardiac dysfunction occurs during sepsis, the pathogenesis of this dysfunction remains poorly understood. To determine whether abnormalities in intramyocyte calcium accumulation might contribute to the development of cardiac dysfunction, we measured myocyte intracellular calcium during peak cardiac dysfunction after an endotoxin challenge. Intraperitoneal administration of Escherichia coli lipopolysaccharide 4 mg/kg to adult guinea pigs resulted in significantly impaired cardiac performance (Langendorff preparation) 18 h after challenge compared with control. This included diminished left ventricular pressure development (56 +/- 7 versus 95 +/- 4 mm Hg, p < 0.05), maximal rate of left ventricular pressure rise (998 +/- 171 versus 1784 +/- 94 mm Hg/s, p < 0.05) and left ventricular pressure fall (1014 +/- 189 versus 1621 +/- 138 mm Hg/s, p < 0.05). Assay of intracellular calcium in fura-2AM-loaded cardiac myocytes demonstrated increased intracellular calcium concentration in myocytes obtained from lipopolysaccharide-challenged animals compared with controls (234 +/- 18 versus 151 +/- 6 nM, p < 0.05). Inhibition of calcium-release channel (ryanodine receptor) opening by administration of dantrolene prevented the increase in intracytoplasmic calcium (159 +/- 8 versus 234 +/- 18 nM, p < 0.05) and partially ameliorated systolic and diastolic ventricular dysfunction. These data indicate that abnormalities of intracellular calcium contribute to the development of endotoxin-induced myocardial dysfunction.
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Affiliation(s)
- M Thompson
- Crystal Charity Ball Center for Pediatric Critical Care Research, Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas 75235-9063, USA
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Burchinal MR, Roberts JE, Riggin R, Zeisel SA, Neebe E, Bryant D. Relating quality of center-based child care to early cognitive and language development longitudinally. Child Dev 2000; 71:339-57. [PMID: 10834469 DOI: 10.1111/1467-8624.00149] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.3] [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: 11/30/2022]
Abstract
How quality of center-based child care relates to early cognitive and language development was examined longitudinally from 6 to 36 months of age in a sample of 89 African American children. Both structural and process measures of quality of child care were collected through observation of the infant classroom. Results indicated that higher quality child care was related to higher measures of cognitive development (Bayley Scales of Infant Development), language development (Sequenced Inventory of Communication Development), and communication skills (Communication and Symbolic Behavior Scales) across time, even after adjusting for selected child and family characteristics. In addition, classrooms that met professional recommendations regarding child:adult ratios tended to have children with better language skills. Classrooms that met recommendations regarding teacher education tended to have girls with better cognitive and receptive language skills. These findings, in conjunction with the growing child-care literature, provide further evidence that researchers and policymakers should strive to improve the quality of child care to enhance early development of such vulnerable children.
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Maitra A, Tavassoli FA, Albores-Saavedra J, Behrens C, Wistuba II, Bryant D, Weinberg AG, Rogers BB, Saboorian MH, Gazdar AF. Molecular abnormalities associated with secretory carcinomas of the breast. Hum Pathol 1999; 30:1435-40. [PMID: 10667421 DOI: 10.1016/s0046-8177(99)90165-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [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: 10/26/2022]
Abstract
Secretory carcinomas (SCAs) represent a unique histological variant of invasive breast carcinomas, occurring predominantly in patients younger than 30 years of age. Data from limited series have shown SCAs to have a favorable prognosis in patients younger than 20 years of age, whereas the clinical course tends to parallel the more common in filtrating ductal carcinomas (IDCs) in patients older than 20 years. There are no reports on the molecular abnormalities associated with this unusual tumor. Microdissected archival formalin-fixed tissue from 10 SCAs collected from 2 institutions were used to determine the frequencies of allelic loss at 13 chromosomal regions with 19 microsatellite markers, using multiplex polymerase chain reaction (PCR)-based techniques. The results of loss of heterozygosity (LOH) and microsatellite alterations (MAs) analyses were compared with 20 cases of IDCs. P53 gene mutation analysis was also performed on the 10 SCAs using single-strand conformation polymorphism (SSCP) analysis, followed by sequencing of abnormal bands. LOH at multiple regions of chromosome 3p were the most common abnormality in both SCAs (55%) and IDCs (50%), followed by LOH at 17q21 (BRCA1 locus), 13q14 (retinoblastoma gene locus), and 8p21-23. No significant differences were seen in the frequencies of LOH at any chromosomal region except for 17p13 (p53 gene locus), where allelic losses were absent in SCAs, but evident in 46% of IDCs (P < .05). The 2 histological entities were similar in the fractional regional loss (FRL) index (0.26 v 0.24), fractional allelic loss (FAL) index (0.23 v 0.27), as well as in the frequency of MAs (0.015 v 0.005), P > .05. P53 gene missense mutation (G:C::A:T) was detected in 1 of 10(10%) SCAs. Based on the considerable similarities in the molecular abnormalities associated with both tumors, the formation of secondary lumina in both the in situ and the invasive components, as well as suggestions from limited series that the clinical behavior in adult patients parallels that of IDCs, SCA most likely reflects a secretory variant of IDCs.
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MESH Headings
- Adult
- Aged
- Alleles
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/therapy
- Carcinoma, Ductal, Breast/genetics
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 3
- Chromosomes, Human, Pair 8
- Female
- Genes, p53
- Humans
- Loss of Heterozygosity
- Microsatellite Repeats
- Middle Aged
- Mutation
- Polymerase Chain Reaction
- Polymorphism, Single-Stranded Conformational
- Prognosis
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Affiliation(s)
- A Maitra
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, USA
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Wistuba II, Bryant D, Behrens C, Milchgrub S, Virmani AK, Ashfaq R, Minna JD, Gazdar AF. Comparison of features of human lung cancer cell lines and their corresponding tumors. Clin Cancer Res 1999; 5:991-1000. [PMID: 10353731] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Although human lung tumor-derived cell lines play an important role in the investigation of lung cancer biology and genetics, there is no comprehensive study comparing the genotypic and phenotypic properties of lung cancer cell lines with those of the individual tumors from which they were derived. We compared a variety of properties of 12 human non-small cell lung carcinoma (NSCLC) cell lines (cultured for a median period of 39 months; range, 12-69) and their corresponding archival tumor tissues. There was, in general, an excellent concordance between the lung tumor cell lines and their corresponding tumor tissues for morphology (100%), the presence of aneuploidy (100%), immunohistochemical expression of HER2/neu (100%) and p53 proteins (100%), loss of heterozygosity at 13 chromosomal regions analyzed (97%) using 37 microsatellite markers, microsatellite alterations (MAs, 75%), TP53 (67%), and K-ras (100%) gene mutations. In addition, there was 100% concordance for the parental allele lost in all 115 comparisons of allelic losses. Some discrepancies were found; more aneuploid subpopulations of cells were detected in the cell lines as well as higher incidences of TP53 mutations (4 of 10 mutations not found in the tumors) and microsatellite alterations (two cell lines with MAs not detected in the tumors). Similar loss of heterozygosity frequencies by chromosomal regions and mean fractional allelic loss index were detected between successfully cultured and 40 uncultured lung tumors (0.45 and 0.49, respectively), indicating that both groups were similar. Our findings indicate that the NSCLC cell lines in the large majority of instances retain the properties of their parental tumors for lengthy culture periods. NSCLC cell lines appear very representative of the lung cancer tumor from which they were derived and thus provide suitable model systems for biomedical studies of this important neoplasm.
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Affiliation(s)
- I I Wistuba
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas 75235, USA
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Abstract
The Fort Bragg Demonstration and evaluation was designed to test the cost-effectiveness of a continuum of care model of service delivery for children and adolescents. A crucial aspect of the evaluation was the measurement of the quality of services provided in the Demonstration. Two key service components were examined: intake assessment and case management. It was concluded that these key components of the continuum of care were implemented with sufficient quality to have the theoretically predicted effects on mental health.
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Affiliation(s)
- L Bickman
- Vanderbilt Institute for Public Policy Studies, Vanderbilt University, Nashville, TN 37212, USA
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