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72 results on '"Payne, S. H."'

1. Towards a first-principles theory of surface thermodynamics and kinetics

Author

Stampfl, C., Kreuzer, H. J., Payne, S. H., Pfnuer, H., and Scheffler, M.

Subjects
Condensed Matter - Materials Science
Abstract

Understanding of the complex behavior of particles at surfaces requires detailed knowledge of both macroscopic and microscopic processes that take place; also certain processes depend critically on temperature and gas pressure. To link these processes we combine state-of-the-art microscopic, and macroscopic phenomenological, theories. We apply our theory to the O/Ru(0001) system and calculate thermal desorption spectra, heat of adsorption, and the surface phase diagram. The agreement with experiment provides validity for our approach which thus identifies the way for a predictive simulation of surface thermodynamics and kinetics., Comment: 4 pages including 3 figures. Related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.html

Published
1999
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2. ABRF Proteome Informatics Research Group (iPRG) 2016 Study : Inferring Proteoforms from Bottom-up Proteomics Data

Author

Lee, J. -Y, Choi, H., Colangelo, C. M., Davis, D., Hoopmann, M. R., Käll, Lukas, Lam, H., Payne, S. H., Perez-Riverol, Y., The, Matthew, Wilson, R., Weintraub, S. T., Palmblad, M., Lee, J. -Y, Choi, H., Colangelo, C. M., Davis, D., Hoopmann, M. R., Käll, Lukas, Lam, H., Payne, S. H., Perez-Riverol, Y., The, Matthew, Wilson, R., Weintraub, S. T., and Palmblad, M.

Abstract

This report presents the results from the 2016 Association of Biomolecular Resource Facilities Proteome Informatics Research Group (iPRG) study on proteoform inference and false discovery rate (FDR) estimation from bottom-up proteomics data. For this study, 3 replicate Q Exactive Orbitrap liquid chromatography-tandom mass spectrometry datasets were generated from each of 4 Escherichia coli samples spiked with different equimolar mixtures of small recombinant proteins selected to mimic pairs of homologous proteins. Participants were given raw data and a sequence file and asked to identify the proteins and provide estimates on the FDR at the proteoform level. As part of this study, we tested a new submission system with a format validator running on a virtual private server (VPS) and allowed methods to be provided as executable R Markdown or IPython Notebooks. The task was perceived as difficult, and only eight unique submissions were received, although those who participated did well with no one method performing best on all samples. However, none of the submissions included a complete Markdown or Notebook, even though examples were provided. Future iPRG studies need to be more successful in promoting and encouraging participation. The VPS and submission validator easily scale to much larger numbers of participants in these types of studies. The unique "ground-truth" dataset for proteoform identification generated for this study is now available to the research community, as are the server-side scripts for validating and managing submissions., QC 20190415

Published
2018
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3. Theory of dissociative and nondissociative adsorption and desorption.

Author

Kreuzer, H. J. and Payne, S. H.

Subjects
*GAS absorption & adsorption, *DISSOCIATION (Chemistry), *GEOMETRIC surfaces
Abstract

Formulates a general theory of the kinetics of adsorption, desorption and dissociation of gases at surfaces. Establishment of dissociation equilibrium; Derivation of kinetic equations for adsorption, desorption and dissociation; Employment of a lattice gas model for homonuclear molecules with both atoms and molecules present on the surface.

Published
1999
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5. Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

Author

Webb-Robertson, B.-J. M., primary, Matzke, M. M., additional, Datta, S., additional, Payne, S. H., additional, Kang, J., additional, Bramer, L. M., additional, Nicora, C. D., additional, Shukla, A. K., additional, Metz, T. O., additional, Rodland, K. D., additional, Smith, R. D., additional, Tardiff, M. F., additional, McDermott, J. E., additional, Pounds, J. G., additional, and Waters, K. M., additional

Published
2014
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28. Neutron scattering as a probe of particle-like excitations in superfluid4He: A model calculation

Author

Griffin, A. and Payne, S. H.

Abstract

In the microscopic theory of Bose-condensed liquids, the condensate wave function leads to a coupling of the density fluctuations and the single-particle excitations. A simple parametrized model of this based on coupling weakly damped zero-sound modes with strongly damped free-particle-like excitations ~Q2/2m* explains why the phonon-roton resonance inS(Q, ?) for superfluid4He exists above and belowT? but only plays the role of an elementary excitation belowT?. It is pointed out that this model also predicts thatS(Q, ?) should exhibit a weak, low-frequency peak centered atQ2/2m*, with weight roughly proportional to the condensate fractionn0. As a stimulus to further experimental searches for this branch, some model calculations are given forS(Q, ?) forQ~1 Å-1.

Published
1986
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39. Proteogenomic and metabolomic characterization of human glioblastoma

Author

Cristina E. Tognon, Larisa Polonskaya, Tara Skelly, Shuang Cai, Francesmary Modugno, Larissa Rossell, Nancy Roche, Chen Huang, Jessika Baral, Fulvio D'Angelo, Wen-Wei Liang, Chia-Feng Tsai, Sneha P. Couvillion, Karin D. Rodland, Jun Zhu, Liang-Bo Wang, Paul D. Piehowski, Antonio Colaprico, Anupriya Agarwal, Matthew A. Wyczalkowski, Umut Ozbek, Francesca Petralia, Alexis Demopoulos, William W. Maggio, Lin Chen, Katherine A. Hoadley, Richard D. Smith, Sandra Cottingham, John McGee, Marcin J. Domagalski, Houxiang Zhu, Emek Demir, Rebecca I. Montgomery, Jamie Moon, Rashna Madan, George D. Wilson, Luciano Garofano, Ewa P. Malc, Chelsea J. Newton, Steven A. Carr, Chandan Kumar-Sinha, Donghui Tan, Christopher R. Kinsinger, Oxana Paklina, Weiqing Wan, Stephanie De Young, Sandra Cerda, Shankha Satpathy, Wojciech Kaspera, Linda Hannick, Gad Getz, Runyu Hong, Shuangjia Lu, Ziad Hanhan, Daniel C. Rohrer, Annette Marrero-Oliveras, Wojciech Szopa, Yuxing Liao, Amanda G. Paulovich, Jiayi Ji, Denis A. Golbin, Tara Hiltke, Weiva Sieh, Piotr A. Mieczkowski, Matthew E. Monroe, Gilbert S. Omenn, Jill S. Barnholtz-Sloan, Azra Krek, Bing Zhang, Brittany Henderson, Peter B. McGarvey, Ratna R. Thangudu, Maciej Wiznerowicz, Saravana M. Dhanasekaran, Alex Webster, Kai Li, Karna Robinson, Nan Ji, Karl K. Weitz, Simina M. Boca, Xiaoyu Song, Anna Calinawan, Adam C. Resnick, Brian J. Druker, Dana R. Valley, David J. Clark, Tao Liu, Eric J. Jaehnig, Alicia Francis, Michele Ceccarelli, Rui Zhao, Dmitry Rykunov, Boris Reva, Elizabeth R. Duffy, Antonio Iavarone, Dave Tabor, Joshua F. McMichael, Daniel Cui Zhou, Maureen Dyer, Kimberly Elburn, Scott D. Jewell, Negin Vatanian, Shirley Tsang, Seungyeul Yoo, Alexander R. Pico, Grace Zhao, Kent J. Bloodsworth, Chet Birger, Jena Lilly, Eunkyung An, Jeffrey R. Whiteaker, Albert H. Kim, Yige Wu, Karen A. Ketchum, Felipe D. Leprevost, Alcida Karz, Uma Borate, Nathan Edwards, Uma Velvulou, Melissa Borucki, Vasileios Stathias, Sanford P. Markey, Corbin D. Jones, Ronald J. Moore, MacIntosh Cornwell, Karsten Krug, Michael J. Birrer, James Suh, Tomasz Czernicki, Jason E. McDermott, Emily S. Boja, Pei Wang, Nina Martinez, Wenke Liu, Yan Shi, Lili Blumenberg, Emily Kawaler, Jeffrey W. Tyner, Feng Chen, Jakub Stawicki, Ki Sung Um, Arul M. Chinnaiyan, Robert Zelt, Jacob J. Day, Zhen Zhang, Caleb M. Lindgren, Li Ding, Nikolay Gabrovski, Hongwei Liu, Jonathan T. Lei, Alla Karpova, Ramani B. Kothadia, Sailaja Mareedu, Mitual Amin, Hannah Boekweg, Jennifer E. Kyle, Sara R. Savage, Brian R. Rood, Yuriy Zakhartsev, Matthew L. Anderson, Alyssa Charamut, Wagma Caravan, Shakti Ramkissoon, Junmei Wang, Song Cao, Samuel H. Payne, Rosalie K. Chu, Rajiv Dhir, David W. Andrews, Galen Hostetter, Liqun Qi, Zhiao Shi, Milan G. Chheda, Robert Edwards, Hui Zhang, Weiping Ma, Jennifer M. Eschbacher, Stacey Gabriel, Jan Lubinski, Lijun Yao, Erika M. Zink, Kelly L. Stratton, William Bocik, Mathangi Thiagarajan, Shilpi Singh, Michael A. Gillette, Lisa M. Bramer, Thomas L. Bauer, Michael Vernon, Henry Rodriguez, Dimitris G. Placantonakis, Eric E. Schadt, Alexey I. Nesvizhskii, Vladislav A. Petyuk, Ana I. Robles, Yvonne Shutack, Anna Malovannaya, Stephen E. Stein, Xi Chen, Lyndon Kim, Yize Li, Shannon Richey, Stephan C. Schürer, Barbara Hindenach, Matthew J. Ellis, Yongchao Dou, David Fenyö, Amy M. Perou, Olga Potapova, Shrabanti Chowdhury, Andrew K. Godwin, Marcin Cieślik, Michael C. Wendl, Marina A. Gritsenko, Pietro Pugliese, Elie Traer, Simona Migliozzi, D. R. Mani, Houston Culpepper, Gregory J. Riggins, Xiaolu Yang, Mehdi Mesri, David Chesla, Lindsey K. Olsen, Lori J. Sokoll, Suhas Vasaikar, Liwei Zhang, Meghan C. Burke, Kelly V. Ruggles, Qing Kay Li, Daniel W. Chan, Bo Wen, Nicollette Maunganidze, Darlene Tansil, Joseph H. Rothstein, Barbara Pruetz, Pushpa Hariharan, Wang, L. -B., Karpova, A., Gritsenko, M. A., Kyle, J. E., Cao, S., Li, Y., Rykunov, D., Colaprico, A., Rothstein, J. H., Hong, R., Stathias, V., Cornwell, M., Petralia, F., Wu, Y., Reva, B., Krug, K., Pugliese, P., Kawaler, E., Olsen, L. K., Liang, W. -W., Song, X., Dou, Y., Wendl, M. C., Caravan, W., Liu, W., Cui Zhou, D., Ji, J., Tsai, C. -F., Petyuk, V. A., Moon, J., Ma, W., Chu, R. K., Weitz, K. K., Moore, R. J., Monroe, M. E., Zhao, R., Yang, X., Yoo, S., Krek, A., Demopoulos, A., Zhu, H., Wyczalkowski, M. A., Mcmichael, J. F., Henderson, B. L., Lindgren, C. M., Boekweg, H., Lu, S., Baral, J., Yao, L., Stratton, K. G., Bramer, L. M., Zink, E., Couvillion, S. P., Bloodsworth, K. J., Satpathy, S., Sieh, W., Boca, S. M., Schurer, S., Chen, F., Wiznerowicz, M., Ketchum, K. A., Boja, E. S., Kinsinger, C. R., Robles, A. I., Hiltke, T., Thiagarajan, M., Nesvizhskii, A. I., Zhang, B., Mani, D. R., Ceccarelli, M., Chen, X. S., Cottingham, S. L., Li, Q. K., Kim, A. H., Fenyo, D., Ruggles, K. V., Rodriguez, H., Mesri, M., Payne, S. H., Resnick, A. C., Wang, P., Smith, R. D., Iavarone, A., Chheda, M. G., Barnholtz-Sloan, J. S., Rodland, K. D., Liu, T., Ding, L., Agarwal, A., Amin, M., An, E., Anderson, M. L., Andrews, D. W., Bauer, T., Birger, C., Birrer, M. J., Blumenberg, L., Bocik, W. E., Borate, U., Borucki, M., Burke, M. C., Cai, S., Calinawan, A. P., Carr, S. A., Cerda, S., Chan, D. W., Charamut, A., Chen, L. S., Chesla, D., Chinnaiyan, A. M., Chowdhury, S., Cieslik, M. P., Clark, D. J., Culpepper, H., Czernicki, T., D'Angelo, F., Day, J., De Young, S., Demir, E., Dhanasekaran, S. M., Dhir, R., Domagalski, M. J., Druker, B., Duffy, E., Dyer, M., Edwards, N. J., Edwards, R., Elburn, K., Ellis, M. J., Eschbacher, J., Francis, A., Gabriel, S., Gabrovski, N., Garofano, L., Getz, G., Gillette, M. A., Godwin, A. K., Golbin, D., Hanhan, Z., Hannick, L. I., Hariharan, P., Hindenach, B., Hoadley, K. A., Hostetter, G., Huang, C., Jaehnig, E., Jewell, S. D., Ji, N., Jones, C. D., Karz, A., Kaspera, W., Kim, L., Kothadia, R. B., Kumar-Sinha, C., Lei, J., Leprevost, F. D., Li, K., Liao, Y., Lilly, J., Liu, H., Lubinski, J., Madan, R., Maggio, W., Malc, E., Malovannaya, A., Mareedu, S., Markey, S. P., Marrero-Oliveras, A., Martinez, N., Maunganidze, N., Mcdermott, J. E., Mcgarvey, P. B., Mcgee, J., Mieczkowski, P., Migliozzi, S., Modugno, F., Montgomery, R., Newton, C. J., Omenn, G. S., Ozbek, U., Paklina, O. V., Paulovich, A. G., Perou, A. M., Pico, A. R., Piehowski, P. D., Placantonakis, D. G., Polonskaya, L., Potapova, O., Pruetz, B., Qi, L., Ramkissoon, S., Resnick, A., Richey, S., Riggins, G., Robinson, K., Roche, N., Rohrer, D. C., Rood, B. R., Rossell, L., Savage, S. R., Schadt, E. E., Shi, Y., Shi, Z., Shutack, Y., Singh, S., Skelly, T., Sokoll, L. J., Stawicki, J., Stein, S. E., Suh, J., Szopa, W., Tabor, D., Tan, D., Tansil, D., Thangudu, R. R., Tognon, C., Traer, E., Tsang, S., Tyner, J., Um, K. S., Valley, D. R., Vasaikar, S., Vatanian, N., Velvulou, U., Vernon, M., Wan, W., Wang, J., Webster, A., Wen, B., Whiteaker, J. R., Wilson, G. D., Zakhartsev, Y., Zelt, R., Zhang, H., Zhang, L., Zhang, Z., Zhao, G., and Zhu, J.

Subjects
Proteomics, 0301 basic medicine, Cancer Research, CPTAC, Histone H2B acetylation, Protein Tyrosine Phosphatase, Non-Receptor Type 11, Computational biology, Biology, Article, 03 medical and health sciences, lipidome, 0302 clinical medicine, Metabolomics, proteogenomic, Humans, Phosphorylation, EP300, proteomic, Proteogenomics, acetylome, single nuclei RNA-seq, Brain Neoplasms, Phospholipase C gamma, glioblastoma, Computational Biology, Lipidome, 030104 developmental biology, Histone, Oncology, Acetylation, 030220 oncology & carcinogenesis, Mutation, biology.protein, metabolome, signaling
Abstract

Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs provides insights to GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors. Immune subtypes with distinct immune cell types are discovered using bulk omics methodologies, validated by snRNA-seq, and correlated with specific expression and histone acetylation patterns. Histone H2B acetylation in classical-like and immune-low GBM is driven largely by BRDs, CREBBP, and EP300. Integrated metabolomic and proteomic data identify specific lipid distributions across subtypes and distinct global metabolic changes in IDH-mutated tumors. This work highlights biological relationships that could contribute to stratification of GBM patients for more effective treatment. Wang et al. perform integrated proteogenomic analysis of adult glioblastoma (GBM), including metabolomics, lipidomics, and single nuclei RNA-Seq, revealing insights into the immune landscape of GBM, cell-specific nature of EMT signatures, histone acetylation in classical GBM, and the existence of signaling hubs which could provide therapeutic vulnerabilities.

Published
2021

40. Nerve repair and grafting in the upper extremity.

Author

Payne SH Jr

Subjects
Humans, Nerve Regeneration, Peripheral Nerves transplantation, Peripheral Nervous System anatomy & histology, Suture Techniques, Wallerian Degeneration, Peripheral Nervous System injuries
Abstract

Knowledge of peripheral nerve anatomy, coupled with available clinical tools for examination, provides the foundation for initial evaluation. Use of this information may be related to the specific injury and a reconstructive plan formulated to maximize the potential for recovery. Realistic expectations can be presented to the patient based on information from summarized clinical experience. The field of nerve repair continues to change rapidly, and clinicians must utilize all resources available for planning, evaluation, and management. As the cellular behaviors of nerve regeneration are delineated, new avenues of research will open.

Published
2001

41. Vascular anatomy of the brachioradialis rotational musculocutaneous flap.

Author

Leversedge FJ, Casey PJ, Payne SH, and Seiler JG 3rd

Subjects
Aged, Aged, 80 and over, Brachial Artery anatomy & histology, Contracture surgery, Dissection, Elbow Joint, Female, Humans, Male, Radial Artery anatomy & histology, Rotation, Forearm blood supply, Muscle, Skeletal blood supply, Surgical Flaps blood supply
Abstract

The purpose of this 2-part vascular injection study was to (1) determine the sources of blood supply to the brachioradialis muscle and the distance around which the brachioradialis muscle flap may be rotated for local soft tissue reconstruction and (2) determine the fasciocutaneous vascular perfusion territory associated with the vascular pedicle of the brachioradialis muscle flap. Lead oxide injections were administered in 16 fresh frozen human upper extremity amputation specimens to determine the contribution of the isolated radial recurrent artery (RRA) and subsequent 3- and 6-cm segments of radial artery (RA) to a rotational brachioradialis muscle flap. The RRA perfused an average of 41% (range, 20% to 60%) of the brachioradialis muscle length. Selective injection of the RRA and the proximal 3-cm segment of the RA perfused 80% (range, 59% to 100%) of the muscle length, corresponding to more than 90% of muscle volume. Flap rotation consistently provided adequate tissue coverage to the antecubital fossa, the lateral elbow, and the proximal one-third volar forearm. Based on these findings, the fasciocutaneous perfusion territory of the isolated vascular pedicle was quantified by selective India ink injection studies in 10 fresh frozen cadaveric specimens. Consistent fasciocutaneous perfusion occurred directly over the muscle belly. No specimen, however, was perfused greater than approximately 1 cm distal to the musculocutaneous junction. This 2-part study defines the vascular anatomy and local utility of the brachioradialis rotational musculocutaneous flap.

Published
2001
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42. Stretching a macromolecule in an atomic force microscope: statistical mechanical analysis.

Author

Kreuzer HJ, Payne SH, and Livadaru L

Subjects
Molecular Conformation, Polyethylene Glycols chemistry, Polymers chemistry, Statistics as Topic, Thermodynamics, Biomechanical Phenomena, Microscopy, Atomic Force methods, Models, Chemical
Abstract

We formulate the proper statistical mechanics to describe the stretching of a macromolecule under a force provided by the cantilever of an Atomic Force Microscope. In the limit of a soft cantilever, the generalized ensemble of the coupled molecule-cantilever system reduces to the Gibbs ensemble for an isolated molecule subject to a constant force in which the extension is fluctuating. For a stiff cantilever, one obtains the Helmholtz ensemble for an isolated molecule held at a fixed extension with the force fluctuating. Numerical examples and predictions for experiments with cantilevers of differing stiffness are given for short and long chains of poly (ethylene glycol), based on parameter-free ab initio calculations.

Published
2001
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43. Treatment of peripheral nerve injuries: surgeons' perspective.

Author

Seiler JG 3rd and Payne SH

Subjects
Animals, Female, Humans, Laser Therapy, Male, Muscle, Skeletal innervation, Orthopedic Procedures, Prognosis, Rabbits, Rats, Treatment Outcome, Ulnar Nerve Compression Syndromes diagnosis, Peripheral Nerve Injuries, Peripheral Nerves surgery, Ulnar Nerve Compression Syndromes surgery
Published
1999
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44. Neurotization of the rat soleus muscle: a quantitative analysis of reinnervation.

Author

Payne SH Jr and Brushart TM

Subjects
Acetylcholinesterase, Animals, Axons pathology, Female, Hindlimb, Motor Endplate pathology, Muscle Denervation, Nerve Regeneration, Peripheral Nerves pathology, Rats, Rats, Sprague-Dawley, Silver Staining, Tibial Nerve surgery, Muscle, Skeletal innervation, Nerve Transfer
Abstract

Neurotization--reinnervation of muscle by direct nerve implantation--has been the subject of several reports. The underlying neurobiology, however, has not been adequately studied. The use of a combined silver-acetylcholinesterase stain was used in this study to identify reinnervated motor endplates and to quantify motor endplates reinnervated by the neurotization process. This study examined the effect of distance between nerve implantation and native motor endplate zone on the formation of ectopic motor endplates and on the total number of motor endplates reinnervated. Experiments were performed on the rat soleus muscle. The transected tibial nerve was implanted directly into the motor endplate zone (near, n = 10) or distally, far from the motor endplate zone (far, n = 10). After a reinnervation interval, frozen sections were processed to demonstrate both axons and motor endplates. In the near group, a mean of 566 motor endplates were reinnervated in the native motor endplate zone and a mean of only 13 in distant locations. In the far group, a mean of 362 motor endplates were reinnervated in the native zone, while a mean of 477 were reinnervated in distant locations. Significantly more ectopic motor endplates were generated by far implantation, and native motor endplates were increased by near implantation. The total number of motor endplates was independent of implant location. These experiments demonstrate that the distance between implanted nerve and the native motor endplate zone influences the morphology of reinnervation.

Published
1997
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50. Construction of custom denture teeth.

Author

Payne SH

Subjects
Acrylic Resins, Dental Impression Technique, Denture, Complete, Immediate, Denture, Partial, Removable, Humans, Pigmentation, Technology, Dental, Denture, Complete, Esthetics, Dental, Tooth, Artificial
Published
1975

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