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Gallucci M, Smith JD, Limbucci N, Giangaspero F, Rossi A. Pediatric Inflammatory Diseases. Part II: Acute Post-Infectious Immune Disorders. Neuroradiol J 2012; 25:702-14. [PMID: 24029184 DOI: 10.1177/197140091202500610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 10/15/2012] [Indexed: 11/16/2022] Open
Abstract
Acute post-infectious immune disorders include Acute Disseminated Encephalomyelitis (ADEM) and its variants such as Acute Hemorrhagic Encephalomyelitis (AHEM), acute necrotizing hemorrhagic leukoencephalitis (ANHLE) of Weston Hurst, multiphasic and recurrent ADEM. Acute Necrotizing Encephalopathy of Childhood (ANE or ANEC) represents a dramatic event, consequent to viral infections, especially Influenza-A, and is now considered different from ADEM. ADEM and variants are classically described as uniphasic syndrome occurring in association with an immunization or vaccination (postvaccine encephalomyelitis) or systemic viral infection (parainfectious encephalomyelitis). However, multiphasic forms are not rare. Pathologically, there is perivascular inflammation, edema, and demyelination within the CNS. Clinical features are focal or multifocal neurologic disorder following exposure to virus or receipt of vaccine. The onset of the CNS disorder is usually rapid and include encephalopathy ranging from lethargy to coma, seizures, and focal and multifocal signs reflecting cerebral and spinal cord involvement. The mortality rate is estimated at 10 to 30 percent, with complete recovery rates of 50 percent cited. Poor prognosis is correlated with severity and abruptness of onset of the clinical syndrome. Multifocal CNS lesions are generally evident on MRI that can be similar from those observed in MS.
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Smith JD, Nash GM, Weiser MR, Temple LK, Guillem JG, Paty PB. Multivisceral resections for rectal cancer. Br J Surg 2012; 99:1137-43. [PMID: 22696063 DOI: 10.1002/bjs.8820] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2012] [Indexed: 01/22/2023]
Abstract
BACKGROUND En bloc resection of adjacent pelvic organ(s) may be needed to achieve clear surgical margins in rectal cancer surgery. An institutional experience is reported with perioperative morbidity and oncological outcomes. METHODS Patients were identified retrospectively from a prospectively collected institutional database (1992-2010). Outcomes, and clinical and pathological factors were determined from medical records. Estimated overall survival, overall recurrence and local recurrence were compared using the log rank method and Cox regression analysis. RESULTS Among 1831 patients with rectal cancer, 124 (6·8 per cent) underwent en bloc resection of part or all of an adjacent organ (vagina/uterus/ovary 90, prostate/seminal vesicle 23, bladder/ureter 15, small bowel/appendix 7). Five-year overall survival and local recurrence rates were 53·3 and 18·8 per cent respectively. There was one postoperative death, from multiple organ failure in a patient with liver cirrhosis. Fifty-two patients underwent sphincter-preserving surgery and three (6 per cent) developed an anastomotic leak. On univariable analysis, the only factor associated with local recurrence was completeness of resection (local recurrence rate 15 per cent versus 69 per cent for R0 versus R1 resection; P < 0·001). On multivariable analysis, factors associated with overall survival were sphincter-preserving surgery, absence of metastatic disease and R0 resection. CONCLUSION Multiple organ resection for locally advanced primary rectal cancer had good oncological outcomes when clear resection margins were achieved.
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Smith JD, Greenlee JJ, Foster GH, Nicholson EM. Acetone precipitation of the scrapie agent results in successful recovery of PrP(Sc) but decreased infectivity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:4758-4762. [PMID: 22519670 DOI: 10.1021/jf300639h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Bioassay is considered the most sensitive method for evaluating prion inactivation procedures. Because prions are resistant to methods effective at inactivating conventional microorganisms, prion inactivation research has focused on relatively harsh alternatives, such as concentrated sodium hypochlorite or sodium hydroxide. Often, bioassay for residual infectivity in these studies requires dilution or biochemical alteration of the treated sample in order to maintain subject health and survival. Ideally, prions from treated samples could be sufficiently separated from the inactivating agent without alteration of the sample and with negligible loss of infectivity prior to inoculation into the bioassay host. The current study was designed to evaluate acetone precipitation of the disease-associated form of the prion protein (PrP(Sc)) from brain homogenate derived from mice with the RML (Rocky Mountain Laboratory) strain of scrapie. The ability to recover PrP(Sc) was evaluated by Western blot. Dilutions of acetone-precipitated RML-positive brain homogenate were compared to nonprecipitated RML homogenate, resulting in similar PrP(Sc) detection levels down to 0.025 mg equivalents of brain tissue. The impact of the method on infectivity was investigated by bioassay in intracranially inoculated tga20 mice. Additionally, contributions to infectivity from the pellet and supernatant fractions were investigated. Acetone precipitation resulted in a 1-log₁₀ reduction in infectivity. Infectivity could not be reconstituted by the acetone soluble fraction of the infectious sample or uninfected brain. This study demonstrates that PrP(Sc) can successfully be precipitated out of infected brain homogenate using acetone but that there is a reduction in infectivity attributable to the procedure that would need to be considered when evaluating bioassay results.
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Welsh J, Smith JD, Yates KR, Greenman J, Maraveyas A, Madden LA. Tissue factor expression determines tumour cell coagulation kinetics. Int J Lab Hematol 2012; 34:396-402. [PMID: 22348286 DOI: 10.1111/j.1751-553x.2012.01409.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Cancers are associated with varying degrees of an increased risk of venous thromboembotic events (VTE) occurring. This increased risk is tumour driven and associated with tumour expression of tissue factor (TF) and tumour-derived microparticles (MP). In this study, cancer cell lines from phenotypically distinct tumours were assessed for cell surface TF expression and prothrombin time (PT) taken as a measure of procoagulant potential. METHODS Breast (T47D, MCF-7), colorectal (Colo320 and LoVo), head and neck (USCC 11b, 12, 81b and SIHN-011A) and pancreatic tumour cell lines (ASPC-1 and CFPAC-1) were assessed for TF expression by flow cytometry and relative mean fluorescence determined. Procoagulant potential of the cells was then determined by PT assay. RESULTS Cell-supported coagulation was shown to be cell number dependent, defined by a logarithmic relationship that was consistent across all cell lines. Single cell PT was determined for each cell line from the slope of a logarithmically transformed data plot. A near linear relationship was observed between TF expression and single cell clotting time where a higher expression of TF results in a proportionally faster PT (P < 0.001). CONCLUSIONS This study shows that across a range of tumour sites a consistent relationship is seen between procoagulant potential and both cell number and TF cell surface expression.
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Smith JD, Ray DA. Expedited batch processing and analysis of transposon insertions. BMC Res Notes 2011; 4:482. [PMID: 22054356 PMCID: PMC3222620 DOI: 10.1186/1756-0500-4-482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 11/04/2011] [Indexed: 11/10/2022] Open
Abstract
Background With advances in sequencing technology, greater and greater amounts of eukaryotic genome data are becoming available. Often, large portions of these genomes consist of transposable elements, frequently accounting for 50% or more in vertebrates. Each transposable element family may have thousands or tens of thousands of individual copies within a given genome, and therefore it can take an exorbitant amount of time and effort to process data in a meaningful fashion. Findings In order to combat this problem, we developed a set of bioinformatics techniques and programs to streamline the analysis. This includes a unique Perl script which automates the process of taking BLAST, Repeatmasker and similar data to extract and manipulate the hit sequences from the genome. This script, called Process_hits uses an object-oriented methodology to compile all hit locations from a given file for processing, organize this data into useable categories, and output it in multiple formats. Conclusions The program proved capable of handling large amounts of transposon data in an efficient fashion. It is equipped with a number of useful sub-functions, each of which is contained within its own sub-module to allow for greater expandability and as a foundation for future program design.
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Carpenter AL, Smith JD, Heise GD, Repka CP, Schneider CM. Postural Steadiness in Cancer Survivors Based on Time Domain Measures of Center of Pressure. Med Sci Sports Exerc 2011. [DOI: 10.1249/01.mss.0000401468.87751.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Smith JD, Carpenter AL, Heise GD, Repka CP, Schneider CM. Center of Pressure Frequency Measures For Assessing Postural Steadiness in Cancer Survivors. Med Sci Sports Exerc 2011. [DOI: 10.1249/01.mss.0000401447.17353.d7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Smith JD, Banner NR, Hamour IM, Ozawa M, Goh A, Robinson D, Terasaki PI, Rose ML. De novo donor HLA-specific antibodies after heart transplantation are an independent predictor of poor patient survival. Am J Transplant 2011; 11:312-9. [PMID: 21219570 DOI: 10.1111/j.1600-6143.2010.03383.x] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Preformed donor HLA-specific antibodies are a known indicator for poor patient survival after cardiac transplantation. The role of de novo donor-specific antibodies (DSA) formed after cardiac transplantation is less clear. Here we have retrospectively analyzed 243 cardiac transplant recipients, measuring HLA antibody production every year after transplantation up to 13 years post-transplant. Production of de novo DSA was analyzed in patients who had been negative for DSA prior to their transplant. DSA including transient antibodies were associated with poor patient survival (p = 0.0018, HR = 3.198). However, de novo and persistent DSA was strongly associated with poor patient survival (p = 0.0001 HR = 4.351). Although complement fixing persistent DSA correlated with poor patient survival, this was not increased compared to noncomplement fixing persistent DSA. Multivariable analysis indicated de novo persistent DSA to be an independent predictor of poor patient survival along with HLA-DR mismatch and donor age. Only increasing donor age was found to be an independent risk factor for earlier development of CAV. In conclusion, patients who are transplanted in the absence of pre-existing DSA make de novo DSA after transplantation which are associated with poor survival. Early and regular monitoring of post-transplant DSA is required to identify patients at risk of allograft failure.
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Novick PA, Smith JD, Floumanhaft M, Ray DA, Boissinot S. The evolution and diversity of DNA transposons in the genome of the Lizard Anolis carolinensis. Genome Biol Evol 2010; 3:1-14. [PMID: 21127169 PMCID: PMC3014272 DOI: 10.1093/gbe/evq080] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2010] [Indexed: 01/19/2023] Open
Abstract
DNA transposons have considerably affected the size and structure of eukaryotic genomes and have been an important source of evolutionary novelties. In vertebrates, DNA transposons are discontinuously distributed due to the frequent extinction and recolonization of these genomes by active elements. We performed a detailed analysis of the DNA transposons in the genome of the lizard Anolis carolinensis, the first non-avian reptile to have its genome sequenced. Elements belonging to six of the previously recognized superfamilies of elements (hAT, Tc1/Mariner, Helitron, PIF/Harbinger, Polinton/Maverick, and Chapaev) were identified. However, only four (hAT, Tc1/Mariner, Helitron, and Chapaev) of these superfamilies have successfully amplified in the anole genome, producing 67 distinct families. The majority (57/67) are nonautonomous and demonstrate an extraordinary diversity of structure, resulting from frequent interelement recombination and incorporation of extraneous DNA sequences. The age distribution of transposon families differs among superfamilies and reveals different dynamics of amplification. Chapaev is the only superfamily to be extinct and is represented only by old copies. The hAT, Tc1/Mariner, and Helitron superfamilies show different pattern of amplification, yet they are predominantly represented by young families, whereas divergent families are exceedingly rare. Although it is likely that some elements, in particular long ones, are subjected to purifying selection and do not reach fixation, the majority of families are neutral and accumulate in the anole genome in large numbers. We propose that the scarcity of old copies in the anole genome results from the rapid decay of elements, caused by a high rate of DNA loss.
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Smith JD, Hamir AN, Greenlee JJ. Cartilaginous metaplasia in the sclera of Suffolk sheep. Vet Pathol 2010; 48:827-9. [PMID: 20861498 DOI: 10.1177/0300985810382669] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Scleral cartilaginous metaplasia was detected by routine histologic examination of globes from 5 Suffolk sheep from a scrapie pathogenesis study. The extent of the metaplasia varied among the sheep but was always posterior to the tapetal fundus. The matrix surrounding chondrocytes stained intensely with alcian blue and was immunopositive for type II collagen. Retrospective evaluation of additional eyes from Suffolk and Cheviot sheep used in various scrapie pathogenesis studies at the authors' facility revealed similar histologic changes in 40% and 12.7% of eyes examined, respectively. The clinical significance of this previously unreported finding is unknown.
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Pagan HJT, Smith JD, Hubley RM, Ray DA. PiggyBac-ing on a primate genome: novel elements, recent activity and horizontal transfer. Genome Biol Evol 2010; 2:293-303. [PMID: 20624734 PMCID: PMC2997546 DOI: 10.1093/gbe/evq021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
To better understand the extent of Class II transposable element activity in mammals, we investigated the mouse lemur, Microcebus murinus, whole genome shotgun (2X) draft assembly. Analysis of this strepsirrhine primate extended previous research that targeted anthropoid primates and found no activity within the last 37 Myr. We tested the hypothesis that members of the piggyBac Class II superfamily have been inactive in the strepsirrhine lineage of primates during the same period. Evidence against this hypothesis was discovered in the form of three nonautonomous piggyBac elements with activity periods within the past 40 Myr and possibly into the very recent past. In addition, a novel family of piggyBac transposons was identified, suggesting introduction via horizontal transfer. A second autonomous element was also found with high similarity to an element recently described from the little brown bat, Myotis lucifugus, further implicating horizontal transfer in the evolution of this genome. These findings indicate a more complex history of transposon activity in mammals rather than a uniform shutdown of Class II transposition, which had been suggested by analyses of more common model organisms.
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Abbasi RU, Abu-Zayyad T, Al-Seady M, Allen M, Amman JF, Anderson RJ, Archbold G, Belov K, Belz JW, Bergman DR, Blake SA, Brusova OA, Burt GW, Cannon C, Cao Z, Deng W, Fedorova Y, Finley CB, Gray RC, Hanlon WF, Hoffman CM, Holzscheiter MH, Ivanov D, Hughes G, Hüntemeyer P, Ivanov D, Jones BF, Jui CCH, Kim K, Kirn MA, Loh EC, Liu J, Lundquist JP, Maestas MM, Manago N, Marek LJ, Martens K, Matthews JAJ, Matthews JN, Moore SA, O'Neill A, Painter CA, Perera L, Reil K, Riehle R, Roberts M, Rodriguez D, Sasaki N, Schnetzer SR, Scott LM, Sinnis G, Smith JD, Sokolsky P, Song C, Springer RW, Stokes BT, Stratton S, Thomas SB, Thomas JR, Thomson GB, Tupa D, Zech A, Zhang X. Indications of proton-dominated cosmic-ray composition above 1.6 EeV. PHYSICAL REVIEW LETTERS 2010; 104:161101. [PMID: 20482038 DOI: 10.1103/physrevlett.104.161101] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 03/28/2010] [Indexed: 05/29/2023]
Abstract
We report studies of ultrahigh-energy cosmic-ray composition via analysis of depth of air shower maximum (X(max)), for air shower events collected by the High-Resolution Fly's Eye (HiRes) observatory. The HiRes data are consistent with a constant elongation rate d<X(max)>/d[log(E)] of 47.9+/-6.0(stat)+/-3.2(syst) g/cm2/decade for energies between 1.6 and 63 EeV, and are consistent with a predominantly protonic composition of cosmic rays when interpreted via the QGSJET01 and QGSJET-II high-energy hadronic interaction models. These measurements constrain models in which the galactic-to-extragalactic transition is the cause of the energy spectrum ankle at 4x10(18) eV.
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O'Boyle PJ, Smith JD, Danskine AJ, Lyster HS, Burke MM, Banner NR. De novo HLA sensitization and antibody mediated rejection following pregnancy in a heart transplant recipient. Am J Transplant 2010; 10:180-3. [PMID: 19951281 DOI: 10.1111/j.1600-6143.2009.02875.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here we report a case wherein both donor-specific and third-party, paternal, HLA class II specific antibodies developed following a spontaneous miscarriage resulting in antibody-mediated rejection in a patient who had undergone an orthotopic cardiac transplant six years earlier.
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Jimenez JL, Canagaratna MR, Donahue NM, Prevot ASH, Zhang Q, Kroll JH, DeCarlo PF, Allan JD, Coe H, Ng NL, Aiken AC, Docherty KS, Ulbrich IM, Grieshop AP, Robinson AL, Duplissy J, Smith JD, Wilson KR, Lanz VA, Hueglin C, Sun YL, Tian J, Laaksonen A, Raatikainen T, Rautiainen J, Vaattovaara P, Ehn M, Kulmala M, Tomlinson JM, Collins DR, Cubison MJ, Dunlea EJ, Huffman JA, Onasch TB, Alfarra MR, Williams PI, Bower K, Kondo Y, Schneider J, Drewnick F, Borrmann S, Weimer S, Demerjian K, Salcedo D, Cottrell L, Griffin R, Takami A, Miyoshi T, Hatakeyama S, Shimono A, Sun JY, Zhang YM, Dzepina K, Kimmel JR, Sueper D, Jayne JT, Herndon SC, Trimborn AM, Williams LR, Wood EC, Middlebrook AM, Kolb CE, Baltensperger U, Worsnop DR. Evolution of Organic Aerosols in the Atmosphere. Science 2009; 326:1525-9. [PMID: 20007897 DOI: 10.1126/science.1180353] [Citation(s) in RCA: 1053] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Smith JD, Brunner VM, Jigjidsuren S, Hamour IM, McCormack AM, Banner NR, Rose ML. Lack of effect of MICA antibodies on graft survival following heart transplantation. Am J Transplant 2009; 9:1912-9. [PMID: 19563343 DOI: 10.1111/j.1600-6143.2009.02722.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Little is known about the effect of MICA antibodies (Abs) on cardiac allograft function and survival. Pretransplant and posttransplant serum from 491 and 196 adult cardiac allograft recipients, respectively, has been investigated for MICA Abs, donor specificity and the effect of MICA Abs on graft survival, acute rejection episodes (AR) and cardiac allograft vasculopathy (CAV). Patients with HLA Abs (11.6%) were excluded from the analysis. A total of 11.8% of patients had MICA Abs, without HLA Abs, before their transplant. Actuarial graft survival demonstrated slightly better survival of patients with donor-specific MICA Abs at 1 and 5 years (88.9% and 83.3%) than patients negative for MICA Abs (72% and 63.7%, p = 0.051). After transplantation, 15.8% of patients produced MICA Abs, and in 17 patients these were produced de novo. There was no effect of pretransplant or posttransplant production of MICA Abs on numbers of AR episodes in year 1, or CAV assessed at years 3 and 5. Immunocytochemistry of cardiac biopsies from 11 patients did not demonstrate a presence of MICA. Sera from only 4/69 patients with MICA Abs fixed complement prior to transplantation and from 7/38 patients following transplantation. In conclusion, this study suggests that MICA Abs do not adversely affect the outcome of cardiac transplantation.
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Smith JD, West AA. A modular rehabilitation system with enhanced functionality and safety to support improved recovery from injury and quality of life. Proc Inst Mech Eng H 2008; 222:947-58. [DOI: 10.1243/09544119jeim368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The rehabilitation of the range of individuals covering medical patients to elite athletes is a costly and time-consuming process involving the knowledge of experienced physical therapists, medical practitioners, coaches, and dedicated training facilities. In order to improve the effectiveness and efficiency of the rehabilitation process, a modular variable-resistance rehabilitation device has been developed. The mechanical, electromechanical, and software systems identified during this research have been shown to provide a step change in exercise functionality, real-time patient monitoring, performance feedback, and safety. Using distributed network concepts, the physical therapist will be able to design and implement training regimes remotely, which can subsequently be downloaded to the localized resistance devices. The patient and/or athlete is able to complete the required exercises without personal supervision. The data from these sessions can be saved and accessed for assessment at a convenient time, thereby maximizing therapist productivity and optimizing the utilization of medical resources.
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Abbasi RU, Abu-Zayyad T, Allen M, Amman JF, Archbold G, Belov K, Belz JW, Ben Zvi SY, Bergman DR, Blake SA, Brusova OA, Burt GW, Cannon C, Cao Z, Connolly BC, Deng W, Fedorova Y, Finley CB, Gray RC, Hanlon WF, Hoffman CM, Holzscheiter MH, Hughes G, Hüntemeyer P, Jones BF, Jui CCH, Kim K, Kirn MA, Loh EC, Maestas MM, Manago N, Marek LJ, Martens K, Matthews JAJ, Matthews JN, Moore SA, O'Neill A, Painter CA, Perera L, Reil K, Riehle R, Roberts M, Rodriguez D, Sasaki N, Schnetzer SR, Scott LM, Sinnis G, Smith JD, Sokolsky P, Song C, Springer RW, Stokes BT, Thomas SB, Thomas JR, Thomson GB, Tupa D, Westerhoff S, Wiencke LR, Zhang X, Zech A. First observation of the Greisen-Zatsepin-Kuzmin suppression. PHYSICAL REVIEW LETTERS 2008; 100:101101. [PMID: 18352170 DOI: 10.1103/physrevlett.100.101101] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 01/07/2008] [Indexed: 05/26/2023]
Abstract
The High Resolution Fly's Eye (HiRes) experiment has observed the Greisen-Zatsepin-Kuzmin suppression (called the GZK cutoff) with a statistical significance of five standard deviations. HiRes' measurement of the flux of ultrahigh energy cosmic rays shows a sharp suppression at an energy of 6 x 10(19) eV, consistent with the expected cutoff energy. We observe the ankle of the cosmic-ray energy spectrum as well, at an energy of 4 x 10(18) eV. We describe the experiment, data collection, and analysis and estimate the systematic uncertainties. The results are presented and the calculation of the statistical significance of our observation is described.
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Ray DA, Feschotte C, Pagan HJT, Smith JD, Pritham EJ, Arensburger P, Atkinson PW, Craig NL. Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Res 2008; 18:717-28. [PMID: 18340040 DOI: 10.1101/gr.071886.107] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and Helitron elements, two distinct groups of DNA transposons, in the lineage of the vespertilionid bat Myotis lucifugus. Here, we describe seven additional families that have also been recently active in the bat lineage. Early vespertilionid genome evolution was dominated by the activity of Helitrons, mariner-like and Tc2-like elements. This was followed by the colonization of Tc1-like elements, and by a more recent explosion of hAT-like elements. Finally, and most recently, piggyBac-like elements have amplified within the Myotis genome and our results indicate that one of these families is probably still expanding in natural populations. Together, these data suggest that there has been tremendous recent activity of various DNA transposons in the bat lineage that far exceeds those previously reported for any mammalian lineage. The diverse and recent populations of DNA transposons in genus Myotis will provide an unprecedented opportunity to study the impact of this class of elements on mammalian genome evolution and to better understand what makes some species more susceptible to invasion by genomic parasites than others.
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Smith JD, Greenlee JJ, Hamir AN, West Greenlee MH. Retinal cell types are differentially affected in sheep with scrapie. J Comp Pathol 2007; 138:12-22. [PMID: 18061608 DOI: 10.1016/j.jcpa.2007.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 09/15/2007] [Indexed: 10/22/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs) are a group of fatal neurodegenerative diseases characterized microscopically by spongiform lesions (vacuolation) in the neuropil, neuronal loss, and gliosis. Accumulation of the abnormal form of the prion protein (PrP(Sc)) has been demonstrated in the retina of natural and non-natural TSE-affected hosts, with or without evidence of microscopically detectable retinal pathology. This study was conducted to investigate the effect of PrP(Sc) accumulation on retinal neurons in a natural host lacking overt microscopical evidence of retinal degeneration by comparing the distribution of retinal cell type-specific markers in control and scrapie-affected sheep. In retinas with PrP(Sc)-immunoreactivity, there was disruption of the normal immunoreactivity patterns of the alpha isoform of protein kinase C (PKCalpha) and vesicular glutamate transporter 1 (VGLUT1), markers of retinal bipolar cells. Altered immunoreactivity was also observed for microtubule-associated protein 2 (MAP2), a marker of a subset of retinal ganglion cells, and glutamine synthetase (GS), a marker of Müller glia. These results demonstrate alterations of immunoreactivity patterns for proteins associated with specific cell types in retinas with PrP(Sc) accumulation, despite an absence of microscopical evidence of retinal degeneration.
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Smith JD, Hamour IM, Banner NR, Rose ML. C4d fixing, luminex binding antibodies - a new tool for prediction of graft failure after heart transplantation. Am J Transplant 2007; 7:2809-15. [PMID: 17908268 DOI: 10.1111/j.1600-6143.2007.01991.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The standard method to detect pretransplant antibodies has been the complement dependent cytotoxicity (CDC) test of donor leukocytes. Solid phase assays to detect HLA antibodies in pretransplant serum reveal a greater number of sensitized patients, but their clinical impact is less certain. Here we have developed a method of detecting C4d fixing HLA antibodies on Luminex beads. Pretransplant serum from 565 cardiac transplant patients was retrospectively tested for the presence of HLA antibodies using CDC, HLA coated Luminex beads and C4d deposition on Luminex beads, and the results correlated with graft survival. Whereas 5/565 patients had CDC positive donor specific antibodies (DSA) before their transplant, this number was increased by 19 using Luminex beads. The 1-year survival of CDC -ve/Luminex +ve patients with DSA (n = 19) was 42% compared with 77% for CDC -ve/Luminex +ve without DSA (n = 39, p = 0.0039). Fixation of C4d (22/67 Luminex positive sera) had a negative effect on graft outcome; 1-year graft survival was, C4d +ve/DSA +ve (n = 11) 20%, C4d +ve/DSA -ve (n = 11) 91%, C4d -ve DSA +ve (n = 13) 54%, C4d -ve DSA -ve (n = 32) 75%, compared with 75% for antibody-negative patients (p = 0.0002). In conclusion, detection of Luminex +ve DSA in pretransplant serum provides a powerful negative predictor of graft survival, especially if they bind C4d.
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Leong HS, Mahesh BM, Day JR, Smith JD, McCormack AD, Ghimire G, Podor TJ, Rose ML. Vimentin autoantibodies induce platelet activation and formation of platelet-leukocyte conjugates via platelet-activating factor. J Leukoc Biol 2007; 83:263-71. [PMID: 17974709 DOI: 10.1189/jlb.0607339] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Anti-vimentin antibodies (AVA) are associated with autoimmunity and solid organ transplantation, conditions associated with vascular disease, but their contribution to disease pathogenesis is unknown. Here, we have examined interactions between AVA (mAb and serum from patients) and various leukocyte populations using whole blood and flow cytometry. Normal blood treated with patient sera containing high AVA-IgM titers or with a vimentin-specific monoclonal IgM led to activation of platelets and other leukocytes, as demonstrated by induced expression of P-selectin, fibrinogen, tissue factor, and formation of platelet:leukocyte (P:L) conjugates and a reduction in platelet counts. This activity was antigen (vimentin)-specific and was not mediated by irrelevant IgM antibodies. Flow cytometry demonstrated that AVA do not bind directly to resting platelets in whole blood, but they bind to approximately 10% of leukocytes. Supernatant, derived from AVA-treated leukocytes, induced platelet activation, as measured by the generation of platelet microparticles, when added to platelet-rich plasma. When AVA were added to whole blood in the presence of CV-6209, a platelet-activating factor (PAF) receptor inhibitor, platelet depletion was inhibited. This suggests that PAF is one of the mediators released from AVA-activated leukocytes that leads to P:L conjugation formation and platelet activation. In summary, AVA bind to leukocytes, resulting in release of a PAF and prothrombotic factor that exert a paracrine-activating effect on platelets. Overall, this proposed mechanism may explain the pathogenesis of thrombotic events in autoimmune diseases associated with AVA.
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Smith JD, Prideaux D, Wolfe CL, Wilkinson TJ, Sen Gupta T, DeWitt DE, Worley P, Hays RB, Cowie M. Developing the accredited postgraduate assessment program for Fellowship of the Australian College of Rural and Remote Medicine. Rural Remote Health 2007; 7:805. [PMID: 17953499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
INTRODUCTION Accreditation of the Australian College of Rural and Remote Medicine (ACRRM) as a standards and training provider, by the Australian Medical Council (AMC) in 2007, is the first time in the world that a peak professional organisation for rural and remote medical education has been formally recognised. As a consequence, the Australian Government provided rural and remote medicine with formal recognition under Medicare as a generalist discipline. This accreditation was based on the ability of ACRRM to meet the AMC's guidelines for its training and assessment program. METHODS The methodology was a six-step process that included: developing an assessment blueprint and a classification scheme; identifying an assessment model; choosing innovative summative and formative assessment methods that met the needs of rural and remote located medical practitioner candidates; 21 rural doctors and academics developing the assessment items as part of a week-long writing workshop; investigating the feasibility of purchasing assessment items; and 48 rural candidates piloting three of the assessment items to ensure they would meet the guidelines for national accreditation. RESULTS The project resulted in an innovative formative and summative assessment program that occurs throughout 4 years of vocational training, using innovative, reliable, valid and acceptable methods with educational impact. The piloting process occurred for 3 of the 6 assessment tools. Structured Assessment Using Multiple Patient Scenarios (StAMPS) is a new assessment method developed as part of this project. The StAMPS pilot found that it was reliable, with a generalisability coefficient of >0.76 and was a valid, acceptable and feasible assessment tool with desired educational impact. The multiple choice question (MCQ) examination pilot found that the applied clinical nature of the questions and their wide range of scenarios proved a very acceptable examination to the profession. The web based in-training assessment examination pilot revealed that it would serve well as a formative process until ACRRM can further develop their MCQ database. CONCLUSIONS The ACRRM assessment program breaks new ground for assessing rural and remote doctors in Australia, and provides new evidence regarding how a comprehensive and contemporary assessment system can work within a postgraduate medical setting.
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Messer BM, Cappa CD, Smith JD, Wilson KR, Gilles MK, Cohen RC, Saykally RJ. pH dependence of the electronic structure of glycine. J Phys Chem B 2007; 109:5375-82. [PMID: 16863204 DOI: 10.1021/jp0457592] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The carbon, nitrogen, and oxygen K-edge spectra were measured for aqueous solutions of glycine by total electron yield near-edge X-ray absorption fine structure (TEY NEXAFS) spectroscopy. The bulk solution pH was systematically varied while maintaining a constant amino acid concentration. Spectra were assigned through comparisons with both previous studies and ab initio computed spectra of isolated glycine molecules and hydrated glycine clusters. Nitrogen K-edge solution spectra recorded at low and moderate pH are nearly identical to those of solid glycine, whereas basic solution spectra strongly resemble those of the gas phase. The carbon 1s --> pi*(C=O) transition exhibits a 0.2 eV red shift at high pH due to the deprotonation of the amine terminus. This deprotonation also effects a 1.4 eV red shift in the nitrogen K-edge at high pH. Two sharp preedge features at 401.3 and 402.5 eV are also observed at high pH. These resonances, previously observed in the vapor-phase ISEELS spectrum of glycine, have been reassigned as transitions to sigma* bound states. The observation of these peaks indicates that the amine moiety is in an acceptor-only hydrogen bond configuration at high pH. At low pH, the oxygen 1s --> pi*(C=O) transition exhibits a 0.25-eV red shift due to the protonation of the carboxylic acid terminus. These spectral differences indicate that the variations in electronic structure observed in the NEXAFS spectra are determined by the internal charge state and hydration environment of the molecule in solution.
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Smith JD, Martin PE. Walking patterns change rapidly following asymmetrical lower extremity loading. Hum Mov Sci 2007; 26:412-25. [PMID: 17289193 DOI: 10.1016/j.humov.2006.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 12/04/2006] [Accepted: 12/08/2006] [Indexed: 10/23/2022]
Abstract
The purpose of this study was to determine the amount of time needed for individuals to become well accommodated to asymmetrical changes in lower extremity inertial properties. Participants walked at 1.57 m s(-1) during four separate data collection sessions over the period of eight days. On days 1 and 7, participants completed a 60 min treadmill protocol consisting of both overground (motion and ground reaction force recorded) and treadmill (vertical ground reaction force recorded) walking. On day 1, 1.95 kg was attached distally to one shank prior to the start of the 60 min treadmill protocol and was not removed until day 7. On day 7, the load was permanently removed prior to the 60 min treadmill protocol. On days 2 and 8 participants completed three overground walking trials and walked on the treadmill for approximately 5 min. Stance and swing time asymmetries appeared immediately and were complete following initial assessment after the load was attached. Net joint moments at the knee and hip were altered and continued to change beyond initial exposure to the load, but these changes were complete within 5 min. Overall, results suggest that changes in walking symmetry due to asymmetrical lower extremity loading are immediate and complete within 5 min of exposure to the load. We recommend that at least 5 min of walking or other normal activity be used to accommodate individuals to novel asymmetrical lower extremity loading.
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Smith JD, Melhem ME, Magge KT, Waggoner AS, Campbell PG. Improved growth factor directed vascularization into fibrin constructs through inclusion of additional extracellular molecules. Microvasc Res 2007; 73:84-94. [PMID: 17223139 PMCID: PMC3013344 DOI: 10.1016/j.mvr.2006.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 09/08/2006] [Accepted: 10/05/2006] [Indexed: 11/18/2022]
Abstract
Using the chick chorioallantoic membrane assay (CAM) and a novel histological technique, we investigated the ability of blood vessels to directly invade fibrin-based scaffolds. In our initial experiments utilizing vascular endothelial growth factor (VEGF(165)), we found no direct invasion. Instead, the fibrin was completely degraded and replaced with highly vascularized new tissue. Addition of fibroblast growth factor-2 (FGF-2), bone morphogenic protein-2 (BMP-2), or platelet-derived growth factor-BB (PDGF-BB) to the fibrin construct also did not result in construct vascularization. Because natural and regenerating tissues exhibit complex extracellular matrices (ECMs), we hypothesized that a more complex scaffold may improve blood vessel invasion. Addition of fibronectin, hyaluronic acid, and collagen type I within 20 mg/mL fibrin constructs resulted in no significant improvement. However, the same additive concentrations within 10 mg/mL fibrin constructs resulted in dramatic improvements, specifically with hyaluronic acid. Overall, we believe that these results indicate the importance of structural and functional cues of not only in the initial scaffold but also as the construct is degraded and remodeled. Furthermore, the CAM assay may represent a useful model for understanding ECM interactions as well as for screening and designing tissue-engineered scaffolds.
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