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2. New detectors for electron microscopy

Author

Clough, Robert N. and Kirkland, Angus I.

Subjects
502.8, Electron image analysis, Detectors, Electron Microscopy
Abstract

Detectors for Electron Microscopy have traditionally used a scintillator to generate photons from fast electrons, which are then detected by a sensor. However, in recent years direct detection has become an area of interest due to the potential improvements to detector performance. In this thesis various aspects of direct detection are presented. I will begin with simulations of direct detectors based on Joy’s model of straight trajectories between Rutherford scattering events, where signal is generated by inelastic scattering events. The effects of microscope operating voltage, detector thickness, a surface electrically dead layer and diode depth on detector performance are presented. A prototype detector was developed using the DUOS sensor, two thicknesses of the sensor were produced a 50μm thick detector and a 20μm thick detector. EBSD results are presented which show how the use of a reactive ion etch to reduce the dead layer thickness of a mechanically thinned sensor improve the detection efficiency of a sensor allowing EBSD work to be carried out at operating voltages as low as 5keV. The MTF and DQE of both thicknesses of DUOS sensor are measured at 80kV and 200kV, which show that there is little difference between the two thicknesses at 80kV, but at 200kV the thinner detector shows an improved MTF. The results are then and compared with the equivalent simulated detectors. I show how the high frame rate of a detector and rigid and non-rigid registration can be used to improve image quality, resolving the {331} lattice spacing which is not visible with a simple summation of frames. Detectors using gallium nitride rather than silicon as the base semiconductor are simulated. The MTF at the Nyquist frequency for a GaN detector is double that of a Si detector at an operating voltages of 80kV due to the smaller interaction volume of an electron in GaN. However, at higher voltages the improvement is much smaller as most electrons pass through the detector.

Published
2015

5. Uncertainty contributions to species specific isotope dilution analysis

Author

Clough, Robert

Subjects
543.65
Abstract

Mercury speciation in solid sample matrices has been investigated using high performance liquid chromatography (HPLC) coupled with multicollector sector field (MCSF) and quadrupole (Q) inductively coupled plasma mass spectrometry (ICP-MS) for species specific isotope dilution mass spectrometry (IDMS). 199Hg enriched methylmercurychloride has been synthesised and recovered in the solid form for use as a spike material. The stability of methylmercury during the IDMS procedure was investigated using 199Hg and 13C labelled methylmercury isotopomers and ¹H Nuclear Magnetic Resonance spectroscopy. IntermoIecuJar exchange of the methylmercury halide counter ion was observed, the halide counter ion order of preference was l>Br>Cl. No evidence was found for the decomposition, or formation, of methylmercury during equilibration with soil (NIST2710 SRM) or dogfish muscle (DORM-2 CRM), or during chromatographic separation. The extent of equilibration between the spike and the particulate bound mercury compounds was studied by temporal monitoring of the 200Hg:199Hg isotope amount ratio and determining the amount of Hg species in the liquid phase. For N1ST2710, complete equilibration was only achieved when concentrated HNO3 in combination with a microwave digestion was employed. For DORM-2, complete equilibration was achieved when using 1:1 H2O.CH3OH v\v and 0.01 % 2-mercaptoethanol as the solvent, even though only 47% of the analyte was extracted into the liquid phase. The mass fraction of methylmercurychloride has been determined in E)ORM-2 and BCR464 lobster hepatopancreas CRM by two different procedures, single IDMS and approximate matching double IDMS. Mercury cold vapour generation of the HPLC column eluent allowed isotope amount ratios measurements by MC-SF-ICP-MS. For each CRM the mass fraction of methylmercury determined by the two IDMS methods was not statistically different, within the limits of uncertainty, from the certified values. An uncertainty budget for both IDMS procedures has been formulated to allow the performance of each method to be compared For single IDMS the major uncertainty contribution was derived from the within replicate uncertainty, Uwithin The combined standard uncertainty of each replicate analysis was dominated by two components, the uncertainty associated with the natural isotonic abundance 200Hg: 199Hg isotope amount ratio and the uncertainty associated with the 199Hg enriched methylmercurychloride spike mass fraction. The between blend standard uncertainty, Ubetween, was the major contributor to the expanded uncertainty for approximate matching double IDMS. The combined standard uncertainty for each individual replicate was dominated by the contribution from the standard uncertainty associated with the measured 200Hg:199Hg isotope amount ratios in the spiked sample and the mass bias calibration blend.

Published
2003

12. Estimating uncertainties in oceanographic trace element measurements

Author

Worsfold, Paul, Achterberg, Eric, Birchill, Antony, Clough, Robert, Leito, Ivo, Lohan, Maeve, Milne, Angela, Ussher, Simin, Worsfold, Paul, Achterberg, Eric, Birchill, Antony, Clough, Robert, Leito, Ivo, Lohan, Maeve, Milne, Angela, and Ussher, Simin

Abstract

A realistic estimation of uncertainty is an essential requirement for all analytical measurements. It is common practice, however, for the uncertainty estimate of a chemical measurement to be based on the instrumental precision associated with the analysis of a single or multiple samples, which can lead to underestimation. Within the context of chemical oceanography such an underestimation of uncertainty could lead to an over interpretation of the result(s) and hence impact on, e.g., studies of biogeochemical cycles, and the outputs from oceanographic models. Getting high quality observational data with a firm uncertainty assessment is therefore essential for proper model validation. This paper describes and compares two recommended approaches that can give a more holistic assessment of the uncertainty associated with such measurements, referred to here as the “bottom up” or modeling approach and the “top down” or empirical approach. “Best practice” recommendations for the implementation of these strategies are provided. The “bottom up” approach combines the standard uncertainties associated with each stage of the entire measurement procedure. The “top down” approach combines the uncertainties associated with day to day reproducibility and possible bias in the complete data set and is easy to use. For analytical methods that are routinely used, laboratories will have access to the information required to calculate the uncertainty from archived quality assurance data. The determination of trace elements in seawater is a significant analytical challenge and iron is used as an example for the implementation of both approaches using real oceanographic data. Relative expanded uncertainties of 10 – 20% were estimated for both approaches compared with a typical short term precision (rsd) of ≤5%

Published
2019

13. Estimating Uncertainties in Oceanographic Trace Element Measurements

Author

Worsfold, Paul J., Achterberg, Eric P., Birchill, Antony J., Clough, Robert, Leito, Ivo, Lohan, Maeve C., Milne, Angela, Ussher, Simon J., Worsfold, Paul J., Achterberg, Eric P., Birchill, Antony J., Clough, Robert, Leito, Ivo, Lohan, Maeve C., Milne, Angela, and Ussher, Simon J.

Abstract

A realistic estimation of uncertainty is an essential requirement for all analytical measurements. It is common practice, however, for the uncertainty estimate of a chemical measurement to be based on the instrumental precision associated with the analysis of a single or multiple samples, which can lead to underestimation. Within the context of chemical oceanography such an underestimation of uncertainty could lead to an over interpretation of the result(s) and hence impact on, e.g., studies of biogeochemical cycles, and the outputs from oceanographic models. Getting high quality observational data with a firm uncertainty assessment is therefore essential for proper model validation. This paper describes and compares two recommended approaches that can give a more holistic assessment of the uncertainty associated with such measurements, referred to here as the “bottom up” or modeling approach and the “top down” or empirical approach. “Best practice” recommendations for the implementation of these strategies are provided. The “bottom up” approach combines the standard uncertainties associated with each stage of the entire measurement procedure. The “top down” approach combines the uncertainties associated with day to day reproducibility and possible bias in the complete data set and is easy to use. For analytical methods that are routinely used, laboratories will have access to the information required to calculate the uncertainty from archived quality assurance data. The determination of trace elements in seawater is a significant analytical challenge and iron is used as an example for the implementation of both approaches using real oceanographic data. Relative expanded uncertainties of 10 – 20% were estimated for both approaches compared with a typical short term precision (rsd) of≤5%.

Published
2019
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14. Intensity of Glycemic Control Affects Long-Term Survival After Coronary Artery Bypass Graft Surgery

Author

Robich, Michael P., primary, Iribarne, Alexander, additional, Leavitt, Bruce J., additional, Malenka, David J., additional, Quinn, Reed D., additional, Olmstead, Elaine M., additional, Ross, Cathy S., additional, Sawyer, Douglas B., additional, Klemperer, John D., additional, Clough, Robert A., additional, Kramer, Robert S., additional, Baribeau, Yvon R., additional, Sardella, Gerald L., additional, and DiScipio, Anthony W., additional

Published
2019
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16. Lowest hematocrit on bypass and adverse outcomes associated with coronary artery bypass grafting

Author

DeFoe, Gordon R, Ross, Cathy S, Olmstead, Elaine M, Surgenor, Stephen D, Fillinger, Mary P, Groom, Robert C, Forest, Richard J, Pieroni, John W, Warren, Craig S, Bogosian, Mary E, Krumholz, Charles F, Clark, Cantwell, Clough, Robert A, Weldner, Paul W, Lahey, Stephen J, Leavitt, Bruce J, Marrin, Charles A.S, Charlesworth, David C, Marshall, Peter, and O’Connor, Gerald T

Published
2001
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17. M6P/IGF2R loss of heterozygosity in head and neck cancer associated with poor patient prognosis

Author

Jang Hong-Seok, Oka Yoshihiko, Killian J Keith, Brizel David M, Jamieson Timothy A, Fu Xiaolong, Clough Robert W, Vollmer Robin T, Anscher Mitchell S, and Jirtle Randy L

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background The mannose 6-phosphate/insulin-like growth factor 2 receptor (M6P/IGF2R) encodes for a multifunctional receptor involved in lysosomal enzyme trafficking, fetal organogenesis, cytotoxic T cell-induced apoptosis and tumor suppression. The purpose of this investigation was to determine if the M6P/IGF2R tumor suppressor gene is mutated in human head and neck cancer, and if allelic loss is associated with poor patient prognosis. Methods M6P/IGF2R loss of heterozygosity in locally advanced squamous cell carcinoma of the head and neck was assessed with six different gene-specific nucleotide polymorphisms. The patients studied were enrolled in a phase 3 trial of twice daily radiotherapy with or without concurrent chemotherapy; median follow-up for surviving patients is 76 months. Results M6P/IGF2R was polymorphic in 64% (56/87) of patients, and 54% (30/56) of the tumors in these informative patients had loss of heterozygosity. M6P/IGF2R loss of heterozygosity was associated with a significantly reduced 5 year relapse-free survival (23% vs. 69%, p = 0.02), locoregional control (34% vs. 75%, p = 0.03) and cause specific survival (29% vs. 75%, p = 0.02) in the patients treated with radiotherapy alone. Concomitant chemotherapy resulted in a better outcome when compared to radiotherapy alone only in those patients whose tumors had M6P/IGF2R loss of heterozygosity. Conclusions This study provides the first evidence that M6P/IGF2R loss of heterozygosity predicts for poor therapeutic outcome in patients treated with radiotherapy alone. Our findings also indicate that head and neck cancer patients with M6P/IGF2R allelic loss benefit most from concurrent chemotherapy.

Published
2003
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20. Comparative effectiveness of coronary artery bypass grafting versus percutaneous coronary intervention in a real-world Surgical Treatment for Ischemic Heart Failure trial population

Author

Iribarne, Alexander, primary, DiScipio, Anthony W., additional, Leavitt, Bruce J., additional, Baribeau, Yvon R., additional, McCullough, Jock N., additional, Weldner, Paul W., additional, Huang, Yi-Ling, additional, Robich, Michael P., additional, Clough, Robert A., additional, Sardella, Gerald L., additional, Olmstead, Elaine M., additional, and Malenka, David J., additional

Published
2018
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22. New detectors for electron microscopy

Author

Clough, R, Clough, Robert N., and Kirkland, A

Subjects
Electron image analysis
Abstract

Detectors for Electron Microscopy have traditionally used a scintillator to generate photons from fast electrons, which are then detected by a sensor. However, in recent years direct detection has become an area of interest due to the potential improvements to detector performance. In this thesis various aspects of direct detection are presented. I will begin with simulations of direct detectors based on Joy’s model of straight trajectories between Rutherford scattering events, where signal is generated by inelastic scattering events. The effects of microscope operating voltage, detector thickness, a surface electrically dead layer and diode depth on detector performance are presented. A prototype detector was developed using the DUOS sensor, two thicknesses of the sensor were produced a 50μm thick detector and a 20μm thick detector. EBSD results are presented which show how the use of a reactive ion etch to reduce the dead layer thickness of a mechanically thinned sensor improve the detection efficiency of a sensor allowing EBSD work to be carried out at operating voltages as low as 5keV. The MTF and DQE of both thicknesses of DUOS sensor are measured at 80kV and 200kV, which show that there is little difference between the two thicknesses at 80kV, but at 200kV the thinner detector shows an improved MTF. The results are then and compared with the equivalent simulated detectors. I show how the high frame rate of a detector and rigid and non-rigid registration can be used to improve image quality, resolving the {331} lattice spacing which is not visible with a simple summation of frames. Detectors using gallium nitride rather than silicon as the base semiconductor are simulated. The MTF at the Nyquist frequency for a GaN detector is double that of a Si detector at an operating voltages of 80kV due to the smaller interaction volume of an electron in GaN. However, at higher voltages the improvement is much smaller as most electrons pass through the detector.

Published
2016

27. IMPACT OF TIMING TO CORONARY ARTERY BYPASS GRAFTING FOR PATIENTS WITH SIGNIFICANT LEFT MAIN STENOSIS

Author

Fallon, John M., primary, DeSimone, Joseph P., additional, Leavitt, Bruce J., additional, Clough, Robert A., additional, Olmstead, Elaine M., additional, Sisto, Donato, additional, Kramer, Robert S., additional, Westbrook, Benjamin M., additional, Boss, Richard A., additional, Frumiento, Carmine, additional, Ross, Cathy S., additional, Malenka, David J., additional, and DiScipio, Anthony W., additional

Published
2015
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30. Limited Blood Transfusion Does Not Impact Survival in Octogenarians Undergoing Cardiac Operations

Author

Yun, James J., primary, Helm, Robert E., additional, Kramer, Robert S., additional, Leavitt, Bruce J., additional, Surgenor, Stephen D., additional, DiScipio, Anthony W., additional, Dacey, Lawrence J., additional, Baribeau, Yvon R., additional, Russo, Louis, additional, Sardella, Gerald L., additional, Charlesworth, David C., additional, Clough, Robert A., additional, DeSimone, Joseph P., additional, Ross, Cathy S., additional, Malenka, David J., additional, and Likosky, Donald S., additional

Published
2012
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31. Prospective Trial of Synchronous Bevacizumab, Erlotinib, and Concurrent Chemoradiation in Locally Advanced Head and Neck Cancer

Author

Yoo, David S., primary, Kirkpatrick, John P., additional, Craciunescu, Oana, additional, Broadwater, Gloria, additional, Peterson, Bercedis L., additional, Carroll, Madeline D., additional, Clough, Robert, additional, MacFall, James R., additional, Hoang, Jenny, additional, Scher, Richard L., additional, Esclamado, Ramon M., additional, Dunphy, Frank R., additional, Ready, Neal E., additional, and Brizel, David M., additional

Published
2012
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32. Abstract P158: Long-Term Outcomes of Endoscopic Vein Harvesting After Coronary Artery Bypass Grafting

Author

Dacey, Lawrence, primary, Braxton, John, additional, Kramer, Robert, additional, Schmoker, Joseph, additional, Charlesworth, David, additional, Helm, Robert, additional, Frumiento, Carmine, additional, Sardella, Gerald, additional, Clough, Robert, additional, Jones, Stephan, additional, Malenka, David, additional, Olmstead, Elaine, additional, Ross, Cathy, additional, O'Connor, Gerald, additional, and Likosky, Donald, additional

Published
2011
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33. Response to Letter Regarding Article, “Long-Term Outcomes of Endoscopic Vein Harvesting After Coronary Artery Bypass Grafting”

Author

Dacey, Lawrence J., primary, Malenka, David J., additional, Olmstead, Elaine M., additional, Ross, Cathy S., additional, O'Connor, Gerald T., additional, Likosky, Donald S., additional, Braxton, John H., additional, Kramer, Robert S., additional, Schmoker, Joseph D., additional, Charlesworth, David C., additional, Helm, Robert E., additional, Jones, Stephan R., additional, Frumiento, Carmine, additional, Sardella, Gerald L., additional, and Clough, Robert A., additional

Published
2011
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34. Long-Term Outcomes of Endoscopic Vein Harvesting After Coronary Artery Bypass Grafting

Author

Dacey, Lawrence J., primary, Braxton, John H., additional, Kramer, Robert S., additional, Schmoker, Joseph D., additional, Charlesworth, David C., additional, Helm, Robert E., additional, Frumiento, Carmine, additional, Sardella, Gerald L., additional, Clough, Robert A., additional, Jones, Stephan R., additional, Malenka, David J., additional, Olmstead, Elaine M., additional, Ross, Cathy S., additional, O'Connor, Gerald T., additional, and Likosky, Donald S., additional

Published
2011
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35. Perioperative 1- to 2-Unit Red Blood Cell Transfusion Is Associated with Decreased Short-Term, but Not Long-Term Survival

Author

Surgenor, Stephen D., primary, Marrin, Charles A. S., additional, Leavitt, Bruce J., additional, Morton, Jeremy R., additional, Kramer, Robert S., additional, Olmstead, Elaine M., additional, Ross, Cathy S., additional, Charlesworth, David C., additional, Clough, Robert A., additional, Hernandez, Felix, additional, Selke, Frank W., additional, Likosky, Donald S., additional, Helm, Robert E., additional, and O'Connor, Gerald T., additional

Published
2010
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36. Long-Term Survival of the Very Elderly Undergoing Aortic Valve Surgery

Author

Likosky, Donald S., primary, Sorensen, Meredith J., additional, Dacey, Lawrence J., additional, Baribeau, Yvon R., additional, Leavitt, Bruce J., additional, DiScipio, Anthony W., additional, Hernandez, Felix, additional, Cochran, Richard P., additional, Quinn, Reed, additional, Helm, Robert E., additional, Charlesworth, David C., additional, Clough, Robert A., additional, Malenka, David J., additional, Sisto, Donato A., additional, Sardella, Gerald, additional, Olmstead, Elaine M., additional, Ross, Cathy S., additional, and O'Connor, Gerald T., additional

Published
2009
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37. Outcomes of Patients Undergoing Concomitant Aortic and Mitral Valve Surgery in Northern New England

Author

Leavitt, Bruce J., primary, Baribeau, Yvon R., additional, DiScipio, Anthony W., additional, Ross, Cathy S., additional, Quinn, Reed D., additional, Olmstead, Elaine M., additional, Sisto, Donato, additional, Likosky, Donald S., additional, Cochran, Richard P., additional, Clough, Robert A., additional, Boss, Richard A., additional, Kramer, Robert S., additional, and O'Connor, Gerald T., additional

Published
2009
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38. The Association of Perioperative Red Blood Cell Transfusions and Decreased Long-Term Survival After Cardiac Surgery

Author

Surgenor, Stephen D., primary, Kramer, Robert S., additional, Olmstead, Elaine M., additional, Ross, Cathy S., additional, Sellke, Frank W., additional, Likosky, Donald S., additional, Marrin, Charles A. S., additional, Helm, Robert E., additional, Leavitt, Bruce J., additional, Morton, Jeremy R., additional, Charlesworth, David C., additional, Clough, Robert A., additional, Hernandez, Felix, additional, Frumiento, Carmine, additional, Benak, Arnold, additional, DioData, Christian, additional, and O’Connor, Gerald T., additional

Published
2009
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39. Abstract 2272: Three Year Survival of Drug-Eluting Stents versus Coronary Artery Surgery in Multivessel Coronary Disease

Author

Malenka, David J, primary, Langner, Craig W, additional, Robb, John F, additional, Dacey, Lawrence J, additional, Kellett, Mirle A, additional, Quinn, Reed D, additional, Silver, M. Theodore, additional, Lee, Peter N Ver, additional, Clough, Robert A, additional, Hearne, Micheal J, additional, Westbrook, Benjamin M, additional, Watkins, Matthew W, additional, Leavitt, Bruce J, additional, and O’Connor, Gerald T, additional

Published
2008
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40. Abstract 4788: Long-Term Survival of the Very Elderly Undergoing Aortic Valve Surgery

Author

Likosky, Donald S, primary, Dacey, Lawrence J, additional, Baribeau, Yvon R, additional, Leavitt, Bruce J, additional, DiScipio, Anthony W, additional, Hernandez, Felix, additional, Cochran, Richard P, additional, Quinn, Reed D, additional, Helm, Robert E, additional, Charlesworth, David C, additional, Clough, Robert A, additional, Malenka, David J, additional, Olmstead, Elaine M, additional, Ross, Cathy S, additional, and O’Connor, Gerald T, additional

Published
2008
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41. Abstract 4283: Outcomes of Patients Undergoing Concomitant Aortic and Mitral Valve Surgery in Northern New England

Author

Leavitt, Bruce J, primary, Baribeau, Yvon R, additional, DiScipio, Anthony W, additional, Quinn, Reed D, additional, Cochran, Richard P, additional, Sisto, Donato, additional, Boss, Richard A, additional, Clough, Robert A, additional, Olmstead, Elaine M, additional, Ross, Cathy S, additional, and O’Connor, Gerald T, additional

Published
2008
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42. Long-Term Survival of the Very Elderly Undergoing Coronary Artery Bypass Grafting

Author

Likosky, Donald S., primary, Dacey, Lawrence J., additional, Baribeau, Yvon R., additional, Leavitt, Bruce J., additional, Clough, Robert, additional, Cochran, Richard P., additional, Quinn, Reed, additional, Sisto, Donato A., additional, Charlesworth, David C., additional, Malenka, David J., additional, MacKenzie, Todd A., additional, Olmstead, Elaine M., additional, Ross, Cathy S., additional, and O’Connor, Gerald T., additional

Published
2008
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43. Long-Term Survival After Surgery Versus Percutaneous Intervention in Octogenarians With Multivessel Coronary Disease

Author

Dacey, Lawrence J., primary, Likosky, Donald S., additional, Ryan, Thomas J., additional, Robb, John F., additional, Quinn, Reed D., additional, DeVries, James T., additional, Hearne, Michael J., additional, Leavitt, Bruce J., additional, Dunton, Robert F., additional, Clough, Robert A., additional, Sisto, Donato, additional, Ross, Cathy S., additional, Olmstead, Elaine M., additional, O’Connor, Gerald T., additional, and Malenka, David J., additional

Published
2007
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46. Perioperative Increases in Serum Creatinine Are Predictive of Increased 90-Day Mortality After Coronary Artery Bypass Graft Surgery

Author

Brown, Jeremiah R., primary, Cochran, Richard P., additional, Dacey, Lawrence J., additional, Ross, Cathy S., additional, Kunzelman, Karyn S., additional, Dunton, Robert F., additional, Braxton, John H., additional, Charlesworth, David C., additional, Clough, Robert A., additional, Helm, Robert E., additional, Leavitt, Bruce J., additional, MacKenzie, Todd A., additional, and O’Connor, Gerald T., additional

Published
2006
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49. Multivariable prediction of in-hospital mortality associated with aortic and mitral valve surgery in Northern New England

Author

Nowicki, Edward R, primary, Birkmeyer, Nancy J.O, additional, Weintraub, Ronald W, additional, Leavitt, Bruce J, additional, Sanders, John H, additional, Dacey, Lawrence J, additional, Clough, Robert A, additional, Quinn, Reed D, additional, Charlesworth, David C, additional, Sisto, Donato A, additional, Uhlig, Paul N, additional, Olmstead, Elaine M, additional, and O'Connor, Gerald T, additional

Published
2004
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