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Xiong X, Stagnitti F, Peterson J, Allinson G, Turoczy N. Heavy metal contamination of pasture soils by irrigated municipal sewage. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2001; 67:535-540. [PMID: 11779068 DOI: 10.1007/s001280156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Young TL, Atwood LD, Ronan SM, Dewan AT, Alvear AB, Peterson J, Holleschau A, King RA. Further refinement of the MYP2 locus for autosomal dominant high myopia by linkage disequilibrium analysis. Ophthalmic Genet 2001; 22:69-75. [PMID: 11449316 DOI: 10.1076/opge.22.2.69.2233] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
INTRODUCTION High myopia (>-6.00 diopters) is a complex common disorder that predisposes individuals to retinal detachment, glaucoma, macular degeneration, and premature cataracts. A recent linkage analysis of seven families with autosomal dominant high myopia has identified one locus (MYP2) for high myopia on chromosome 18p11.31 (Young et al.: Am J Hum Genet 1998;63:109-119). Haplotype analysis revealed an initial interval of 7.6 centimorgans (cM). METHODS Transmission disequilibrium tests (TDT) with both the Statistical Analysis for Genetic Epidemiology (SAGE) 3.1 TDTEX and GENEHUNTER 2 (GH2) programs were performed using chromosome 18p marker alleles for this interval. RESULTS Using SAGE analysis, the following p values were obtained for markers in marker order in this region: D18S1146 (p = 0.227), D18S481 (p = 0.001), D18S63 (p = 0.062), D18S1138 (p = 0.0004), D18S52 (p = 1.79 x 10(-6)), and D18S62 (p = 0.141). GH2 TDT analysis revealed the following p values for the best allele for the markers: D18S1146 (p = 0.083), D18S481 (p = 0.108), D18S63 (p = 0.034), D18S1138 (p = 0.011), D18S52 (p = 0.007), and D18S62 (p = 0.479). CONCLUSION These data suggest that the gene for 18p11.31-linked high myopia is most proximal to marker D18S52, with a likely interval of 0.8 cM between markers D18S63 and D18S52. Due to the contraction of the interval size by TDT, these results provide a basis for focused positional cloning and candidate gene analysis at the MYP2 locus.
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Salzberg SL, White O, Peterson J, Eisen JA. Microbial genes in the human genome: lateral transfer or gene loss? Science 2001; 292:1903-6. [PMID: 11358996 DOI: 10.1126/science.1061036] [Citation(s) in RCA: 227] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The human genome was analyzed for evidence that genes had been laterally transferred into the genome from prokaryotic organisms. Protein sequence comparisons of the proteomes of human, fruit fly, nematode worm, yeast, mustard weed, eukaryotic parasites, and all completed prokaryote genomes were performed, and all genes shared between human and each of the other groups of organisms were collected. About 40 genes were found to be exclusively shared by humans and bacteria and are candidate examples of horizontal transfer from bacteria to vertebrates. Gene loss combined with sample size effects and evolutionary rate variation provide an alternative, more biologically plausible explanation.
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Coleman J, Wrzosek T, Roman R, Peterson J, McAllister P. Setting system suitability criteria for detectability in high-performance liquid chromatography methods using signal-to-noise ratio statistical tolerance intervals. J Chromatogr A 2001; 917:23-7. [PMID: 11403474 DOI: 10.1016/s0021-9673(01)00669-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
For pharmaceutical products, one approach developed to assure that different chromatographic systems are capable of generating valid results is the system suitability test. Typically, a system suitability test involves numerical limits for predefined chromatographic parameters such as theoretical plates, tailing factor, injector reproducibility, etc. An estimation of the ratio of signal compared to baseline is one way to measure system performance, according to a valid method, independent of the instrument. However, since this comparison relates the height of the signal to the height of the noise, it is difficult to relate to the peak area measurements that are typically used for quantification of samples. Additionally, although peak area and peak height may be highly correlated over a wide region, peak area at very low concentrations can be more sensitive to all components of noise due to peak shape. To establish a system suitability criterion, one can use the ratio of the area signal to the baseline noise for replicate injections for samples prepared at concentration equal to the limit of quantitation during the validation studies. A lower limit for this ratio can be derived using statistical tolerance intervals. This lower limit can be applied as a system suitability criterion to measure that any system is performing adequately for measuring low level components in the sample for all future use of the method.
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Husni E, Welch V, Simon L, Shea B, Peterson J, Tugwell P, Wells G. Opioid therapy for treating osteoarthritis pain. Hippokratia 2001. [DOI: 10.1002/14651858.cd003115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
AIM The aim of this paper is to establish an outcome standard for the assessment of healing radiographically after resurgery of persistent periradicular lesions by systematically reviewing the results from published studies. METHODOLOGY The systematic review process requires the definition of predetermined criteria delineating the inclusion parameters of studies reviewed. Of 42 papers that were reviewed, eight qualified for inclusion. A weighted-average was calculated from the results taken from the eight eligible, peer-reviewed studies, published between 1970 and 1997. RESULTS Three hundred and thirty patients out of 2375 (14%) from the included studies underwent resurgery for failure of healing as determined radiographically. Of this population, 35.7% healed successfully after resurgery, 26.3% healed with uncertain results and 38% did not heal at the one-year follow-up. CONCLUSIONS Although there is nearly equal distribution of results between all categories, a 35.7% rate of healing as assessed radiographically is essentially equivalent to the 38% failure rate. This paper will allow an evaluation of current research results to establish an outcome standard and enable techniques and filling materials to be evaluated and compared. Furthermore, the outcome standard can assist in defining demographic and aetiological factors that contribute to the potential outcome of resurgery cases.
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Pearce LL, Epperly MW, Greenberger JS, Pitt BR, Peterson J. Identification of respiratory complexes I and III as mitochondrial sites of damage following exposure to ionizing radiation and nitric oxide. Nitric Oxide 2001; 5:128-36. [PMID: 11292362 DOI: 10.1006/niox.2001.0338] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In 32D cl 3 hematopoietic progenitor cells, the overexpression of manganese superoxide dismutase (MnSOD, SOD2), the enzyme normally found in mitochondria, protects against the damaging effects of ionizing radiation. In the presence of a nitric oxide donor, which exacerbates the damage, inhibition of mitochondrial function can be demonstrated to be associated with respiratory complexes I (NADH dehydrogenase) and III (cytochrome c reductase), but not II (succinate dehydrogenase), IV (cytochrome c oxidase), or V (ATP synthase). The same pattern of inhibition is observed in the case of isolated bovine heart mitochondria exposed to ionizing radiation and the nitric oxide donor. The addition of authentic peroxynitrite (ONO2(-)) to isolated mitochondria also results in damage to complexes I and III (but not II, IV, and V), as shown by assays of electron-transfer activities and electron paramagnetic resonance (EPR) spectroscopic measurements, suggesting ONO2(-) to be responsible for most of the observed radiation damage in both the cultured cell lines and isolated mitochondria. It is argued that, in general, production of ONO2(-) is an important contributor to radiation damage in biological systems and the implications of these findings in relation to possible mechanisms of oxidant-linked apoptosis are briefly considered.
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Penny WF, Ben-Yehuda O, Kuroe K, Long J, Bond A, Bhargava V, Peterson JF, McDaniel M, Juliano J, Witztum JL, Ross J, Peterson KL. Improvement of coronary artery endothelial dysfunction with lipid-lowering therapy: heterogeneity of segmental response and correlation with plasma-oxidized low density lipoprotein. J Am Coll Cardiol 2001; 37:766-74. [PMID: 11693750 DOI: 10.1016/s0735-1097(00)01180-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVES This study assessed coronary artery endothelial function in patients with hypercholesterolemia before and after lipid lowering, using quantitative angiography to examine the acetylcholine (Ach) response along the entire analyzable vessel. BACKGROUND Lipid lowering reverses endothelial dysfunction, but whether improvement occurs only in some segments and not others has not been established. Statistical correlation of improvement with specific lipid moieties remains undefined. METHODS Quantitative angiography was performed after Ach (10(-6), 10(-5), 10(-4) M) in 29 patients with coronary atherosclerosis before and 18 +/- 5.2 months after lipid-lowering treatment (statins, bile sequestrant resins). Standard lipid moieties and markers of oxidized low density lipoprotein (LDL) (immunoglobulin G and M autoantibody titers to malondialdehyde-LDL, E06 epitope) were measured serially. RESULTS Pre-treatment of the vessel diameters at control and with 10(-6)M, 10(-5) M and 10(-4) M Ach were 2.108 +/- 0.085, 2.086 +/- 0.087, 2.069 +/- 0.084 and 1.963 +/- 0.097 mm (M +/- SE), respectively, and increased at follow-up to 2.139 +/- 0.094, 2.119 +/- 0.086, 2.127 +/- 0.084 and 2.080 +/- 0.085 mm (p < 0.0001). Improvement in the most constricted and modest declination in the more dilated segments were observed. Change in the E06 and Apolipoprotein A-1 titers correlated with improved vasomotion (p = 0.027 and 0.005, respectively). The pre- and post-treatment levels of the E06 epitope, as well as the post-treatment IgM autoantibody titer to MDA-low density lipoprotein, also correlated (p < 0.028, < 0.001 and p < 0.004, respectively). CONCLUSIONS Drug treatment reverses endothelial dysfunction, but the effect is heterogeneous. Most coronary segments show enhancement, while others show declination of dilation, underscoring the importance of assessing the entire analyzable artery. Improvement in vasomotion correlates most significantly with markers of plasma-oxidized low-density lipoprotein.
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Peterson JF, Bates DW. Preventable medication errors: identifying and eliminating serious drug interactions. JOURNAL OF THE AMERICAN PHARMACEUTICAL ASSOCIATION (WASHINGTON, D.C. : 1996) 2001; 41:159-60. [PMID: 11297326 DOI: 10.1016/s1086-5802(16)31243-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921. [PMID: 11237011 DOI: 10.1038/35057062] [Citation(s) in RCA: 14634] [Impact Index Per Article: 636.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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Kalaria VG, Mendelsohn A, Peterson J, Ling FS. Double-chambered right ventricle in an adult patient. THE JOURNAL OF INVASIVE CARDIOLOGY 2001; 13:111-3. [PMID: 11176019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A 65-year-old male was referred for to our facility for right and left heart catheterization and coronary angiography for evaluation of a ventricular septal defect and to rule out significant coronary artery disease. During the procedure, the patient was diagnosed with a double-chambered right ventricle (DCRV). Most DCRV cases are diagnosed at a young age; presentation in an adult is extremely rare.
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Lee SR, Peterson J, Niven P, Bahl C, Page E, DeLeys R, Giordano-Schmidt D, Baggett D, Green G. Efficacy of a hepatitis C virus core antigen enzyme-linked immunosorbent assay for the identification of 'window-phase' blood donations. Vox Sang 2001; 80:19-23. [PMID: 11339063 DOI: 10.1046/j.1423-0410.2001.00008.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND OBJECTIVES Recent studies have suggested that potentially infectious donations provided during the antibody-negative 'window' phase of hepatitis C virus (HCV) infection may be identified by testing for viral RNA or HCV core protein. We therefore evaluated the performance of an HCV antigen enzyme-linked immunosorbent assay (ELISA) for identification of window-phase donations and for prospective screening of blood donors. MATERIALS AND METHODS One-hundred and twenty-eight archived plasma donations containing HCV RNA, but lacking antibody to HCV (anti-HCV), were tested by using the HCV antigen ELISA, together with 9951 freshly collected serum and plasma specimens from blood donors. RESULTS HCV core antigen was detected in 94% (120/128) of window-phase plasma donations. Overall specificity in freshly collected blood donor specimens was 99.74%. Two putative window-phase donations containing HCV core protein and viral RNA were identified from paid plasma donors by prospective testing with the HCV antigen ELISA. CONCLUSION These results indicate that an HCV antigen ELISA can identify almost all (94%) of viraemic donations given during the seronegative window phase of infection. The performance of the HCV antigen ELISA appears to be suitable for large-scale screening of blood donations.
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Welch V, Brosseau L, Peterson J, Shea B, Tugwell P, Wells G. Therapeutic ultrasound for osteoarthritis of the knee. Cochrane Database Syst Rev 2001:CD003132. [PMID: 11687038 DOI: 10.1002/14651858.cd003132] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Therapeutic ultrasound is one of several physical therapy modalities suggested for the management of pain and loss of function due to OA. OBJECTIVES To assess the effectiveness of therapeutic ultrasound therapy for treating OA. SEARCH STRATEGY We searched the Cochrane Musculoskeletal Group trials register, and MEDLINE, up to the end of December 2000, using the sensitive search strategy developed by the Cochrane Collaboration. The search was complemented with bibliography searching of the reference list of the trials retrieved from the electronic search. Key experts in the area were contacted for further published and unpublished articles. SELECTION CRITERIA All randomized controlled trials (RCTs) and controlled clinical trials (CCTs) comparing therapeutic ultrasound against placebo or another active intervention in patients with OA were selected. DATA COLLECTION AND ANALYSIS Two reviewers determined the studies to be included based on inclusion and exclusion criteria (LB, VW). Data were independently abstracted by two reviewers (VW, LB), and checked by a third reviewer (BS) using a pre-developed adapted form for the OA sub-group of the Cochrane Musculoskeletal Group. The same two reviewers, using a validated scale, assessed the methodological quality of the RCTs and CCTs independently. OA outcome measures were extracted from the publications. The pooled analysis was performed using weighted mean differences (WMDs) for joint counts, pain, global and functional assessments. A chi-square test was used to assess heterogeneity among trials. Fixed effects models were used throughout and random effects for outcomes showing heterogeneity. MAIN RESULTS Three trials, including 294 patients with knee OA were included. Only one trial (n=74) compared therapeutic ultrasound to placebo. This trial showed no difference in range of motion, pain or gait velocity after 4 weeks of therapeutic ultrasound. Two trials compared therapeutic ultrasound to an active therapy (n=220). These trials showed no statistical difference between galvanic current or short wave diathermy for the outcomes of pain and patient-assessed improvement. REVIEWER'S CONCLUSIONS Ultrasound therapy appears to have no benefit over placebo or short wave diathermy for patients with knee OA. These conclusions are limited by the poor reporting of the characteristics of the device, of the population, of the OA,and therapeutic application of the ultrasound and low methodological quality of the trials included. No conclusions can be drawn about the use of ultrasound in smaller joints such as the wrists or hands.
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Theologis A, Ecker JR, Palm CJ, Federspiel NA, Kaul S, White O, Alonso J, Altafi H, Araujo R, Bowman CL, Brooks SY, Buehler E, Chan A, Chao Q, Chen H, Cheuk RF, Chin CW, Chung MK, Conn L, Conway AB, Conway AR, Creasy TH, Dewar K, Dunn P, Etgu P, Feldblyum TV, Feng J, Fong B, Fujii CY, Gill JE, Goldsmith AD, Haas B, Hansen NF, Hughes B, Huizar L, Hunter JL, Jenkins J, Johnson-Hopson C, Khan S, Khaykin E, Kim CJ, Koo HL, Kremenetskaia I, Kurtz DB, Kwan A, Lam B, Langin-Hooper S, Lee A, Lee JM, Lenz CA, Li JH, Li Y, Lin X, Liu SX, Liu ZA, Luros JS, Maiti R, Marziali A, Militscher J, Miranda M, Nguyen M, Nierman WC, Osborne BI, Pai G, Peterson J, Pham PK, Rizzo M, Rooney T, Rowley D, Sakano H, Salzberg SL, Schwartz JR, Shinn P, Southwick AM, Sun H, Tallon LJ, Tambunga G, Toriumi MJ, Town CD, Utterback T, Van Aken S, Vaysberg M, Vysotskaia VS, Walker M, Wu D, Yu G, Fraser CM, Venter JC, Davis RW. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature 2000; 408:816-20. [PMID: 11130712 DOI: 10.1038/35048500] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genome of the flowering plant Arabidopsis thaliana has five chromosomes. Here we report the sequence of the largest, chromosome 1, in two contigs of around 14.2 and 14.6 megabases. The contigs extend from the telomeres to the centromeric borders, regions rich in transposons, retrotransposons and repetitive elements such as the 180-base-pair repeat. The chromosome represents 25% of the genome and contains about 6,850 open reading frames, 236 transfer RNAs (tRNAs) and 12 small nuclear RNAs. There are two clusters of tRNA genes at different places on the chromosome. One consists of 27 tRNA(Pro) genes and the other contains 27 tandem repeats of tRNA(Tyr)-tRNA(Tyr)-tRNA(Ser) genes. Chromosome 1 contains about 300 gene families with clustered duplications. There are also many repeat elements, representing 8% of the sequence.
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Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blöcker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomènech P, De Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quétier F, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D'Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Löhnert TH, Nordsiek G, Reichelt J, Scharfe M, Schön O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwälder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz JP, Cottet A, Casacuberta E, Monfort A, Argiriou A, flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KF, Kaul S, Town CD, Koo HL, Tallon LJ, Jenkins J, Rooney T, Rizzo M, Walts A, Utterback T, Fujii CY, Shea TP, Creasy TH, Haas B, Maiti R, Wu D, Peterson J, Van Aken S, Pai G, Militscher J, Sellers P, Gill JE, Feldblyum TV, Preuss D, Lin X, Nierman WC, Salzberg SL, White O, Venter JC, Fraser CM, Kaneko T, Nakamura Y, Sato S, Kato T, Asamizu E, Sasamoto S, Kimura T, Idesawa K, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature 2000; 408:820-2. [PMID: 11130713 DOI: 10.1038/35048706] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.
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Asplund K, Gustafson Y, Jacobsson C, Bucht G, Wahlin A, Peterson J, Blom JO, Angquist KA. Geriatric-based versus general wards for older acute medical patients: a randomized comparison of outcomes and use of resources. J Am Geriatr Soc 2000; 48:1381-8. [PMID: 11083312 DOI: 10.1111/j.1532-5415.2000.tb02626.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND The effects of residence in an acute geriatrics-based ward (AGW) with emphasis on early rehabilitation and discharge planning for older patients with acute medical illnesses were assessed. Outcome and use of resources were compared with those of patients treated in general medical wards (MWs). A per-protocol rather than intention-to-treat analysis was performed. METHODS A randomized trial with 3-months follow-up. A total of 190 patients aged 70 years and older were randomized to an acute geriatrics-based ward, and 223 patients were randomized to general medical wards. RESULTS The two groups were comparable at inclusion. However, after care in the AGW, 71% of patients could be discharged directly home compared with 64% of those treated in MWs (relative risk 1.17; 95% CI, 0.93-1.49). The length of stay was shorter in the AGW (mean 5.9 vs 7.3 days; P = .002). The proportion of patients in geriatric or other hospital wards or in nursing homes did not differ, but the proportion of AGW patients in sheltered living tended to be lower (P = .085). At the follow-up, case fatality, ADL function, psychological well-being, need for daily personal assistance, drug consumption, need for readmission to hospital, and total health care costs after discharge did not differ between the two groups. Poor global outcome was observed in 37% of AGW and 34% of MW patients. CONCLUSIONS A geriatric approach with greater emphasis on early rehabilitation and discharge planning in the AGW shortened the length of hospital stay and may have reduced the need for long-term institutional living. This occurred despite patients in an acute geriatric ward not having better medical or functional outcome than older acute patients treated in general medical wards.
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Peterson J. Heart and soul of spiritual care. Should nurses provide spiritual care?.. THE KANSAS NURSE 2000; 75:8-9. [PMID: 11998668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Maher JE, Peterson J, Hastings K, Dahlberg LL, Seals B, Shelley G, Kamb ML. Partner violence, partner notification, and women's decisions to have an HIV test. J Acquir Immune Defic Syndr 2000; 25:276-82. [PMID: 11115959 DOI: 10.1097/00126334-200011010-00012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Reports of partner violence against HIV-positive women after they have disclosed their serostatus have led some to reassess partner notification strategies and to speculate that fear of partner violence following partner notification may influence women's HIV testing decisions. We studied whether associations exist between women's declining to have an HIV test and history of partner violence, fear of partner violence, previous experience with partner notification, or beliefs about partner notification. METHODS In this cross-sectional study, we interviewed women seen at Newark and Miami sexually transmitted disease clinics. The women were at least 18 years old, not known to be HIV positive, not tested for HIV in the previous 3 months, and offered HIV testing during the clinic visit. Women who declined testing were compared with women who accepted. RESULTS Of 490 participants (89% of eligible women), 16% reported partner violence in the past year, and 28% declined HIV testing. Declining the test was not significantly (p >.05) associated with history or fear of partner violence, previous experience with partner notification, or beliefs about partner notification. When specifically asked, only 2 women responded that their declining the test was related to fear that their partner or partners might harm them if the women tested positive. CONCLUSIONS Among women seen at these clinics, we did not find evidence that declining the HIV test was strongly influenced by partner violence, previous experience with partner notification, or beliefs about partner notification. However, many women reported partner violence. Therefore, providers should assess the potential for partner violence and be prepared to make appropriate referrals.
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Tugwell P, Wells G, Shea B, Peterson J, Cranney A, Henry D, O'Connell D, Robertson J, Gillespie WG. Hormone replacement therapy for osteoporosis in postmenopausal women. THE COCHRANE DATABASE OF SYSTEMATIC REVIEWS 2000. [DOI: 10.1002/14651858.cd000354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Peterson J, Moodie D. Aortic dissection late after repair of congenital aortic coarctation. Cardiol Young 2000; 10:405-8. [PMID: 10950339 DOI: 10.1017/s1047951100009720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Aortic dissection is one of several complications that can be seen late after repair of aortic coarctation. We report an unusual presentation of this complication, and review the pertinent literature.
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Chang A, Nishiyama A, Peterson J, Prineas J, Trapp BD. NG2-positive oligodendrocyte progenitor cells in adult human brain and multiple sclerosis lesions. J Neurosci 2000; 20:6404-12. [PMID: 10964946 PMCID: PMC6772992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Multiple sclerosis (MS) is characterized by multifocal loss of myelin, oligodendrocytes, and axons. Potential MS therapies include enhancement of remyelination by transplantation or manipulation of endogenous oligodendrocyte progenitor cells. Characteristics of endogenous oligodendrocyte progenitors in normal human brain and in MS lesions have not been studied extensively. This report describes the distribution of cells in sections from normal adult human brain and MS lesions by using antibodies directed against NG2, an integral membrane chondroitin sulfate proteoglycan expressed by oligodendrocyte progenitor cells. Stellate-shaped NG2-positive cells were detected in the white and gray matter of normal adult human brain and appeared as abundant as, but distinct from, astrocytes, oligodendrocytes, and microglia. Stellate-shaped or elongated NG2-positive cells also were detected in chronic MS lesions. A subpopulation of the elongated NG2-positive cells expressed the putative apoptotic signaling molecule p75(NTR). TUNEL-positive cells in three active, nine chronic active, and four chronic inactive lesions, however, were p75(NTR)-negative. These studies identify cells with phenotypic markers of endogenous oligodendrocyte progenitors in the mature human CNS and suggest that functional subpopulations of NG2-positive cells exist in MS lesions. Endogenous oligodendrocyte progenitor cells may represent a viable target for future therapies intended to enhance remyelination in MS patients.
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Peterson J, Green G, Iida K, Caldwell B, Kerrison P, Bernich S, Aoyagi K, Lee SR. Detection of hepatitis C core antigen in the antibody negative 'window' phase of hepatitis C infection. Vox Sang 2000; 78:80-5. [PMID: 10765142 DOI: 10.1159/000031155] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND AND OBJECTIVES Despite improvements in assays for anti-HCV, there remains a significant delay before the appearance of antibodies following infection, during which, circulating viral RNA is present. We have evaluated a prototype assay for the serological detection of hepatitis C virus (HCV) core antigen with specimens derived from the early phase of HCV infection. MATERIALS AND METHODS Serial specimens from 24 individuals undergoing HCV seroconversion were tested for the presence of anti-HCV, HCV RNA and HCV core antigen. RESULTS HCV antigen was detected at the same time as HCV RNA in 83% (20/24) cases. The mean time to the first detection of HCV antigen was approximately 1 day later than HCV RNA. Overall, 87% of HCV-RNA-positive specimens contained detectable HCV core antigen. CONCLUSION These results indicate that HCV core antigen can be identified by routine serological ELISA in specimens from the early antibody-negative phase of HCV infection. A test for HCV core antigen may be a useful test for identifying window phase blood donations from antibody negative donors infected with HCV.
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148
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Tobler LH, Lee SR, Stramer SL, Peterson J, Kochesky R, Watanabe K, Quan S, Polito A, Busch MP. Performance of second- and third-generation RIBAs for confirmation of third-generation HCV EIA-reactive blood donations. Retrovirus Epidemiology Donor Study. Transfusion 2000; 40:917-23. [PMID: 10960517 DOI: 10.1046/j.1537-2995.2000.40080917.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Licensure of an enhanced HCV screening assay (HCV 3.0 EIA) without concurrent licensure of a complementary supplemental assay (i.e., RIBA HCV 3.0 strip immunoblot assay [RIBA-3]) decoupled screening and supplemental testing. In March 1998, the FDA Center for Biologics Evaluation and Research (CBER) recommended the use of RIBA-3 on RIBA HCV 2.0 strip immunoblot assay (RIBA-2)-indeterminate units screened with HCV EIA 3.0. STUDY DESIGN AND METHODS The sensitivity of RIBA-2 and RIBA-3 was compared in tests on HCV 3.0 EIA-repeatably reactive (RR) units identified immediately after the implementation of HCV 3.0 EIA screening. Two protocols were evaluated: parallel testing of HCV 3.0 EIA-RR units by RIBA-2 and RIBA-3 and reflex testing of HCV 3.0 EIA-RR and RIBA-3-confirmed-positive units by RIBA-2. All specimens with discordant RIBA-2 and RIBA-3 results and a representative sampling with concordant RIBA results were tested by PCR. RESULTS In the parallel testing protocol, 99,777 donations were screened, with 245 HCV 3.0 EIA-RR specimens included in the study. Of 166 RIBA-2-positive samples, 165 tested positive in RIBA-3 (1 sample reacted to the control superoxide dismutase antigen in RIBA-3). Thirty-two (74%) of 43 RIBA-2-indeterminate specimens and 4 (11%) of 36 RIBA-2-negative specimens tested positive in RIBA-3. HCV RNA was identified in 5 (16%) of 32 RIBA-2-indeterminate/RIBA-3-positive donations, as well as in 26 (70%) of 37 concordant RIBA-2/RIBA-3-positive donations. In the reflex testing protocol, 292,459 donations were screened, with 709 HCV 3.0 EIA-RR specimens included in the study. RIBA-3 testing yielded 517 (73%) positive specimens, of which 50 (9.7%) tested indeterminate and 15 (2.9%) tested negative in RIBA-2. Among the RIBA-discordant specimens, 10 (20%) RIBA-2-indeterminate specimens and 1 (7%) RIBA-2-negative specimens tested positive in PCR; in comparison, 60 (77%) of 78 concordant RIBA-2/RIBA-3-positive units tested positive in PCR. CONCLUSIONS RIBA-3 is significantly more sensitive than RIBA-2 in testing of HCV 3.0 EIA-screened donations. During the review process of this manuscript, the FDA licensed the RIBA-3 test.
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Yoo SJ, Meyer J, Achim C, Peterson J, Hendrich MP, Münck E. Mössbauer, EPR, and MCD studies of the C9S and C42S variants of Clostridium pasteurianum rubredoxin and MDC studies of the wild-type protein. J Biol Inorg Chem 2000; 5:475-87. [PMID: 10968619 DOI: 10.1007/s007750050008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rubredoxins contain a mononuclear iron tetrahedrally coordinated by four cysteinyl sulfurs. We have studied the wild-type protein from Clostridium pasteurianum and two mutated forms, C9S and C42S, in the oxidized and reduced states, with Mössbauer, integer-spin EPR, and magnetic circular dichroism (MCD) spectroscopies. The Mössbauer spectra of the ferric C42S and C9S mutant forms yielded zero-field splittings, D = 1.2 cm(-1), that are about 40% smaller than the D-value of the wild-type protein. The 57Fe hyperfine coupling constants were found to be ca. 8% larger than those of the wild-type proteins. The present study also revealed that the ferric wild-type protein has delta=0.24+/-0.01 mm/s at 4.2 K rather than delta = 0.32 mm/s as reported in the literature. The Mössbauer spectra of both dithionite-reduced mutant proteins revealed the presence of two ferrous forms, A and B. These forms have isomer shifts delta = 0.79 mm/s at 4.2 K, consistent with tetrahedral Fe2+(Cys)3(O-R) coordination. The zero-field splittings of the two forms differ substantially; we found D = -7+/-1 cm(-1), E/D = 0.09 for form A and D = +6.2+/-1.3 cm(-1), E/D = 0.15 for form B. Form A exhibits a well-defined integer-spin EPR signal; from studies at X- and Q-band we obtained g(z) = 2.08+/-0.01, which is the first measured g-value for any ferrous rubredoxin. It is known from X-ray crystallographic studies that ferric C42S rubredoxin is coordinated by a serine oxygen. We achieved 75% reduction of C42S rubredoxin by irradiating an oxidized sample at 77 K with synchrotron X-rays; the radiolytic reduction produced exclusively form A, suggesting that this form represents a serine-bound Fe2+ site. Studies in different buffers in the pH 6-9 range showed that the A:B ratios, but not the spectral parameters of A and B, are buffer dependent, but no systematic variation of the ratio of the two forms with pH was observed. The presence of glycerol (30-50 % v/v) was found to favor the B form. Previous absorption and circular dichroism studies of reduced wild-type rubredoxin have suggested d-d bands at 7400, 6000, and 3700 cm(-1). Our low-temperature MCD measurements place the two high-energy transitions at ca. 5900 and 6300 cm(-1); a third d-d transition, if present, must occur with energy lower than 3300 cm(-1). The mutant proteins have d-d transitions at slightly lower energy, namely 5730, 6100 cm(-1) in form A and 5350, 6380 cm(-1) in form B.
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Peterson J, Green G, Iida K, Caldwell B, Kerrison P, Bernich S, Aoyagi K, Lee SR. Detection of hepatitis C core antigen in the antibody negative 'window' phase of hepatitis C infection. Vox Sang 2000. [PMID: 10765142 DOI: 10.1046/j.1423-0410.2000.7820080.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND OBJECTIVES Despite improvements in assays for anti-HCV, there remains a significant delay before the appearance of antibodies following infection, during which, circulating viral RNA is present. We have evaluated a prototype assay for the serological detection of hepatitis C virus (HCV) core antigen with specimens derived from the early phase of HCV infection. MATERIALS AND METHODS Serial specimens from 24 individuals undergoing HCV seroconversion were tested for the presence of anti-HCV, HCV RNA and HCV core antigen. RESULTS HCV antigen was detected at the same time as HCV RNA in 83% (20/24) cases. The mean time to the first detection of HCV antigen was approximately 1 day later than HCV RNA. Overall, 87% of HCV-RNA-positive specimens contained detectable HCV core antigen. CONCLUSION These results indicate that HCV core antigen can be identified by routine serological ELISA in specimens from the early antibody-negative phase of HCV infection. A test for HCV core antigen may be a useful test for identifying window phase blood donations from antibody negative donors infected with HCV.
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