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152. Nisar L-band Digital Electronics Subsystem

Author

Chuang, Chung-Lun, Shaffer, Scott, Niamsuwan, Noppasin, Li, Samuel, Liao, Eric, Lim, Chester, Duong, Vu, Volain, Barry, Vines, Ken, Yang, Muh-Wang, and Wheeler, Kevin

Subjects
Computer Programming And Software
Abstract

The NASA-ISRO Synthetic Aperture Radar (NISAR) L-band SAR instrument employs multiple digital channels to optimize resolution while keeping a large swath on a single pass. High-speed digitization with fine synchronization and digital beam forming are necessary in order to facilitate this new technique called SweepSAR. An architecture employing multiple FPGA based digital signal processors has been conceived to facilitate digital calibration on an individual channel basis as well as digital signal processing to optimize the receive signal. On-board processing and data compression has been implemented to reduce the volume of data in order to satisfy the operational requirements of near global coverage for the desired science targets. A novel command and timing architecture was developed to manage this complex system to meet the challenging project requirements. The NISAR L-band Digital Electronics Subsystem is the combination of the hardware, firmware and software components architected and implemented to operate this radar and return the desired quantity and quality of data for the science community.

Published
2016

154. Alzheimer’s disease associated AKAP 9 I2558M mutation alters posttranslational modification and interactome of tau and cellular functions in CRISPR‐edited human neuronal cells

Author

Hersh, Samuel Walter, primary, You, Yang, additional, Aslebagh, Roshanak, additional, Shaffer, Scott A, additional, Ikezu, Seiko, additional, Mez, Jesse, additional, Lunetta, Kathryn L, additional, Logue, Mark W., additional, Farrer, Lindsay A., additional, and Ikezu, Tsuneya, additional

Published
2021
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172. Additional file 4 of Hidden Markov models identify major movement modes in accelerometer and magnetometer data from four albatross species

Author

Conners, Melinda G., Michelot, Théo, Heywood, Eleanor I., Orben, Rachael A., Phillips, Richard A., Vyssotski, Alexei L., Shaffer, Scott A., and Thorne, Lesley H.

Subjects
Statistics::Methodology
Abstract

Additional file 4: Supplemental Table S3. HMM-converged parameters for the Weibull distribution of each feature and state.

Published
2021
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173. Successful Long-Distance Breeding Range Expansion of a Top Marine Predator

Author

Henry, Robert William, Shaffer, Scott A., Antolos, Michelle, Félix-lizárraga, María, Foley, David G., Hazen, Elliott L., Tremblay, Yann, Costa, Daniel P., Tershy, Bernie R., Croll, Donald A., Henry, Robert William, Shaffer, Scott A., Antolos, Michelle, Félix-lizárraga, María, Foley, David G., Hazen, Elliott L., Tremblay, Yann, Costa, Daniel P., Tershy, Bernie R., and Croll, Donald A.

Abstract

Little is known about the effects of large-scale breeding range expansions on the ecology of top marine predators. We examined the effects of a recent range expansion on the breeding and foraging ecology of Laysan albatrosses (Phoebastria immutabilis). Laysan albatrosses expanded from historical breeding colonies in the Central Pacific Ocean to the Eastern Pacific Ocean around central Baja California, Mexico, leading to a 4,000-km shift from colonies located adjacent to the productive transition zone in the Central Pacific to colonies embedded within the eastern boundary current upwelling system of the Eastern Pacific California Current. We use electronic tagging and remote sensing data to examine the consequences of this range expansion on at-sea distribution, habitat use, foraging habitat characteristics, and foraging behavior at sea by comparing birds from historic and nascent colonies. We found the expansion resulted in distinct at-sea segregation and differential access to novel oceanographic habitats. Birds from the new Eastern Pacific colony on Guadalupe Island, Mexico have reduced ranges, foraging trip lengths and durations, and spend more time on the water compared to birds breeding in the Central Pacific on Tern Island, United States. Impacts of the range expansion to the post-breeding season were less pronounced where birds maintained some at-sea segregation but utilized similar habitat and environmental variables. These differences have likely benefited the Eastern Pacific colony which has significantly greater reproductive output and population growth rates. Laysan albatrosses have the plasticity to adapt to distinctly different oceanographic habitats and also provide insight on the potential consequences of range shifts to marine organisms.

Published
2021
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174. Global political responsibility for the conservation of albatrosses and large petrels

Author

Beal, Martin, Dias, Maria P., Phillips, Richard A., Oppel, Steffen, Hazin, Carolina, Pearmain, Elizabeth J., Adams, Josh, Anderson, David J., Antolos, Michelle, Arata, Javier A., Arcos, José Manuel, Arnould, John P. Y., Awkerman, Jill, Bell, Elizabeth, Bell, Mike, Carey, Mark, Carle, Ryan, Clay, Thomas A., Cleeland, Jaimie, Colodro, Valentina, Conners, Melinda, Cruz-flores, Marta, Cuthbert, Richard, Delord, Karine, Deppe, Lorna, Dilley, Ben J., Dinis, Herculano, Elliott, Graeme, De Felipe, Fernanda, Felis, Jonathan, Forero, Manuela G., Freeman, Amanda, Fukuda, Akira, González-solís, Jacob, Granadeiro, José Pedro, Hedd, April, Hodum, Peter, Igual, José Manuel, Jaeger, Audrey, Landers, Todd J., Le Corre, Mathieu, Makhado, Azwianewi, Metzger, Benjamin, Militão, Teresa, Montevecchi, William A., Morera-pujol, Virginia, Navarro-herrero, Leia, Nel, Deon, Nicholls, David, Oro, Daniel, Ouni, Ridha, Ozaki, Kiyoaki, Quintana, Flavio, Ramos, Raül, Reid, Tim, Reyes-gonzález, José Manuel, Robertson, Christopher, Robertson, Graham, Romdhane, Mohamed Salah, Ryan, Peter G., Sagar, Paul, Sato, Fumio, Schoombie, Stefan, Scofield, R. Paul, Shaffer, Scott A., Shah, Nirmal Jivan, Stevens, Kim L., Surman, Christopher, Suryan, Robert M., Takahashi, Akinori, Tatayah, Vikash, Taylor, Graeme, Thompson, David R., Torres, Leigh, Walker, Kath, Wanless, Ross, Waugh, Susan M., Weimerskirch, Henri, Yamamoto, Takashi, Zajkova, Zuzana, Zango, Laura, Catry, Paulo, Beal, Martin, Dias, Maria P., Phillips, Richard A., Oppel, Steffen, Hazin, Carolina, Pearmain, Elizabeth J., Adams, Josh, Anderson, David J., Antolos, Michelle, Arata, Javier A., Arcos, José Manuel, Arnould, John P. Y., Awkerman, Jill, Bell, Elizabeth, Bell, Mike, Carey, Mark, Carle, Ryan, Clay, Thomas A., Cleeland, Jaimie, Colodro, Valentina, Conners, Melinda, Cruz-flores, Marta, Cuthbert, Richard, Delord, Karine, Deppe, Lorna, Dilley, Ben J., Dinis, Herculano, Elliott, Graeme, De Felipe, Fernanda, Felis, Jonathan, Forero, Manuela G., Freeman, Amanda, Fukuda, Akira, González-solís, Jacob, Granadeiro, José Pedro, Hedd, April, Hodum, Peter, Igual, José Manuel, Jaeger, Audrey, Landers, Todd J., Le Corre, Mathieu, Makhado, Azwianewi, Metzger, Benjamin, Militão, Teresa, Montevecchi, William A., Morera-pujol, Virginia, Navarro-herrero, Leia, Nel, Deon, Nicholls, David, Oro, Daniel, Ouni, Ridha, Ozaki, Kiyoaki, Quintana, Flavio, Ramos, Raül, Reid, Tim, Reyes-gonzález, José Manuel, Robertson, Christopher, Robertson, Graham, Romdhane, Mohamed Salah, Ryan, Peter G., Sagar, Paul, Sato, Fumio, Schoombie, Stefan, Scofield, R. Paul, Shaffer, Scott A., Shah, Nirmal Jivan, Stevens, Kim L., Surman, Christopher, Suryan, Robert M., Takahashi, Akinori, Tatayah, Vikash, Taylor, Graeme, Thompson, David R., Torres, Leigh, Walker, Kath, Wanless, Ross, Waugh, Susan M., Weimerskirch, Henri, Yamamoto, Takashi, Zajkova, Zuzana, Zango, Laura, and Catry, Paulo

Abstract

Migratory marine species cross political borders and enter the high seas, where the lack of an effective global management framework for biodiversity leaves them vulnerable to threats. Here, we combine 10,108 tracks from 5775 individual birds at 87 sites with data on breeding population sizes to estimate the relative year-round importance of national jurisdictions and high seas areas for 39 species of albatrosses and large petrels. Populations from every country made extensive use of the high seas, indicating the stake each country has in the management of biodiversity in international waters. We quantified the links among national populations of these threatened seabirds and the regional fisheries management organizations (RFMOs) which regulate fishing in the high seas. This work makes explicit the relative responsibilities that each country and RFMO has for the management of shared biodiversity, providing invaluable information for the conservation and management of migratory species in the marine realm.

Published
2021
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175. Global political responsibility for the conservation of albatrosses and large petrels

Author

European Commission, National Science Foundation (US), Universidad de Barcelona, Ministerio de Educación y Ciencia (España), Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Beal, Martin, Dias, Maria P., Phillips, Richard A., Oppel, Steffen, Hazin, Carolina, Pearmain, Elizabeth J., Adams, Josh, Anderson, David J., Antolos, Michelle, Arata, Javier A., Arcos, José Manuel, Arnould, John P. Y., Awkerman, Jill, Bell, Elizabeth, Bell, Mike, Carey, Mark, Carle, Ryan, Clay, Thomas A., Cleeland, Jaimie, Colodro, Valentina, Conners, Melinda, Cruz-Flores, Marta, Cuthbert, Richard, Delord, Karine, Deppe, Lorna, Dilley, Ben J., Dinis, Herculano, Elliott, Graeme, De Felipe, Fernanda, Felis, Jonathan, Forero, Manuela G., Freeman, Amanda, Fukuda, Akira, González-Solís, Jacob, Granadeiro, José Pedro, Hedd, April, Hodum, Peter, Igual, José Manuel, Jaeger, Audrey, Landers, Todd J., Le Corre, Matthieu, Makhado, Azwianewi, Metzger, Benjamin, Militão, Teresa, Montevecchi, William A., Morera-Pujol, Virginia, Navarro-Herrero, Leia, Nel, Deon, Nicholls, David, Oro, Daniel, Ouni, Ridha, Ozaki, Kiyoaki, Quintana, Flavio, Ramos, Raül, Reid, Tim, Reyes-González, José M., Robertson, Christopher, Robertson, Graham, Romdhane, Mohamed Salah, Ryan, Peter G., Sagar, Paul, Sato, Fumio, Schoombie, Stefan, Scofield, R. Paul, Shaffer, Scott A., Shah, Nirmal Jivan, Stevens, Kim L., Surman, Christopher, Suryan, Robert M., Takahashi, Akinori, Tatayah, Vikash, Taylor, Graeme, Thompson, David R., Torres, Leigh, Walker, Kath, Wanless, Ross M., Waugh, Susan M., Weimerskirch, Henri, Yamamoto, Takashi, Zajková, Zuzana, Zango, Laura, Catry, Paulo, European Commission, National Science Foundation (US), Universidad de Barcelona, Ministerio de Educación y Ciencia (España), Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Beal, Martin, Dias, Maria P., Phillips, Richard A., Oppel, Steffen, Hazin, Carolina, Pearmain, Elizabeth J., Adams, Josh, Anderson, David J., Antolos, Michelle, Arata, Javier A., Arcos, José Manuel, Arnould, John P. Y., Awkerman, Jill, Bell, Elizabeth, Bell, Mike, Carey, Mark, Carle, Ryan, Clay, Thomas A., Cleeland, Jaimie, Colodro, Valentina, Conners, Melinda, Cruz-Flores, Marta, Cuthbert, Richard, Delord, Karine, Deppe, Lorna, Dilley, Ben J., Dinis, Herculano, Elliott, Graeme, De Felipe, Fernanda, Felis, Jonathan, Forero, Manuela G., Freeman, Amanda, Fukuda, Akira, González-Solís, Jacob, Granadeiro, José Pedro, Hedd, April, Hodum, Peter, Igual, José Manuel, Jaeger, Audrey, Landers, Todd J., Le Corre, Matthieu, Makhado, Azwianewi, Metzger, Benjamin, Militão, Teresa, Montevecchi, William A., Morera-Pujol, Virginia, Navarro-Herrero, Leia, Nel, Deon, Nicholls, David, Oro, Daniel, Ouni, Ridha, Ozaki, Kiyoaki, Quintana, Flavio, Ramos, Raül, Reid, Tim, Reyes-González, José M., Robertson, Christopher, Robertson, Graham, Romdhane, Mohamed Salah, Ryan, Peter G., Sagar, Paul, Sato, Fumio, Schoombie, Stefan, Scofield, R. Paul, Shaffer, Scott A., Shah, Nirmal Jivan, Stevens, Kim L., Surman, Christopher, Suryan, Robert M., Takahashi, Akinori, Tatayah, Vikash, Taylor, Graeme, Thompson, David R., Torres, Leigh, Walker, Kath, Wanless, Ross M., Waugh, Susan M., Weimerskirch, Henri, Yamamoto, Takashi, Zajková, Zuzana, Zango, Laura, and Catry, Paulo

Abstract

Migratory marine species cross political borders and enter the high seas, where the lack of an effective global management framework for biodiversity leaves them vulnerable to threats. Here, we combine 10,108 tracks from 5775 individual birds at 87 sites with data on breeding population sizes to estimate the relative year-round importance of national jurisdictions and high seas areas for 39 species of albatrosses and large petrels. Populations from every country made extensive use of the high seas, indicating the stake each country has in the management of biodiversity in international waters. We quantified the links among national populations of these threatened seabirds and the regional fisheries management organizations (RFMOs) which regulate fishing in the high seas. This work makes explicit the relative responsibilities that each country and RFMO has for the management of shared biodiversity, providing invaluable information for the conservation and management of migratory species in the marine realm.

Published
2021

176. Hidden Markov models identify major movement modes in accelerometer and magnetometer data from four albatross species

Author

Conners, Melinda G; https://orcid.org/0000-0003-0572-0026, Michelot, Théo, Heywood, Eleanor I, Orben, Rachael A, Phillips, Richard A, Vyssotski, Alexei L, Shaffer, Scott A, Thorne, Lesley H, Conners, Melinda G; https://orcid.org/0000-0003-0572-0026, Michelot, Théo, Heywood, Eleanor I, Orben, Rachael A, Phillips, Richard A, Vyssotski, Alexei L, Shaffer, Scott A, and Thorne, Lesley H

Abstract

Background Inertial measurement units (IMUs) with high-resolution sensors such as accelerometers are now used extensively to study fine-scale behavior in a wide range of marine and terrestrial animals. Robust and practical methods are required for the computationally-demanding analysis of the resulting large datasets, particularly for automating classification routines that construct behavioral time series and time-activity budgets. Magnetometers are used increasingly to study behavior, but it is not clear how these sensors contribute to the accuracy of behavioral classification methods. Development of effective classification methodology is key to understanding energetic and life-history implications of foraging and other behaviors. Methods We deployed accelerometers and magnetometers on four species of free-ranging albatrosses and evaluated the ability of unsupervised hidden Markov models (HMMs) to identify three major modalities in their behavior: ‘flapping flight’, ‘soaring flight’, and ‘on-water’. The relative contribution of each sensor to classification accuracy was measured by comparing HMM-inferred states with expert classifications identified from stereotypic patterns observed in sensor data. Results HMMs provided a flexible and easily interpretable means of classifying behavior from sensor data. Model accuracy was high overall (92%), but varied across behavioral states (87.6, 93.1 and 91.7% for ‘flapping flight’, ‘soaring flight’ and ‘on-water’, respectively). Models built on accelerometer data alone were as accurate as those that also included magnetometer data; however, the latter were useful for investigating slow and periodic behaviors such as dynamic soaring at a fine scale. Conclusions The use of IMUs in behavioral studies produces large data sets, necessitating the development of computationally-efficient methods to automate behavioral classification in order to synthesize and interpret underlying patterns. HMMs provide an accessible and robust fra

Published
2021

180. Median and ulnar neuropathies in US Army dental personnel at Fort Sam, Houston, Texas

Author

Shaffer, Scott W., Alexander, Kaitland, Huffman, Daniel, Kambe, Charles, Miller, Ronald, Moore, Josef H., and Greathouse, David G.

Subjects
Military personnel -- Medical examination -- Social aspects, Neuromuscular diseases -- Diagnosis, United States. Army -- Social aspects
Abstract

Median mononeuropathy at or distal to the wrist, or carpal tunnel syndrome, and other musculoskeletal dysfunction of the upper extremities is a well-documented problem in dental personnel, including dentists and [...]

Published
2014

181. Surface acoustic wave nebulization of peptides as a microfluidic interface for mass spectrometry

Author

Heron, Scott R., Wilson, Rab, Shaffer, Scott A., Goodlett, David R., and Cooper, Jonathan M.

Subjects
Mass spectrometry -- Methods, Mass spectrometry -- Equipment and supplies, Peptides -- Chemical properties, Peptides -- Acoustic properties, Microfluidics -- Research, Acoustic surface waves -- Usage, Chemistry
Abstract

We describe the fabrication of a surface acoustic wave (SAW) device on a LiNb[O.sub.3] piezoelectric transducer for the transfer of nonvolatile analytes to the gas phase at atmospheric pressure (a process referred to as nebulization or atomization). We subsequently show how such a device can be used in the field of mass spectrometry (MS) detection, demonstrating that SAW nebulization (SAWN) can be performed either in a discontinuous or pulsed mode, similar to that for matrix assisted laser desorption ionization (MALDI) or in a continuous mode like electrospray ionization (ESI). We present data showing the transfer of peptides to the gas phase, where ions are detected by MS. These peptide ions were subsequently fragmented by collision-induced dissociation, from which the sequence was assigned. Unlike MALDI mass spectra, which are typically contaminated with matrix ions at low m/z, the SAWN generated spectra had no such interference. In continuous mode, the SAWN plume was sampled on a microsecond time scale by a linear ion trap mass spectrometer and produced multiply charged peptide precursor ions with a charge state distribution shifted to higher m/z compared to an identical sample analyzed by ESI. The SAWN technology also provides the opportunity to re-examine a sample from a flat surface, repeatedly. The process can be performed without the need for capillaries, which can clog, reservoirs, which dilute the sample, and electrodes, which when in direct contact with sample, cause unwanted electrochemical oxidation. In both continuous and pulsed sampling modes, the quality of precursor ion scans and tandem mass spectra of peptides was consistent across the plume's lifetime. 10.1021/ac100372c

Published
2010

182. Phosphorylation within the cysteine-rich region of dystrophin enhances its association with β-dystroglycan and identifies a potential novel therapeutic target for skeletal muscle wasting

Author

Swiderski, Kristy, Shaffer, Scott A., Gallis, Byron, Odom, Guy L., Arnett, Andrea L., Scott Edgar, J., Baum, Dale M., Chee, Annabel, Naim, Timur, Gregorevic, Paul, Murphy, Kate T., Moody, James, Goodlett, David R., Lynch, Gordon S., and Chamberlain, Jeffrey S.

Published
2014
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184. Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean

Author

Panchaud, Alexandre, Scherl, Alexander, Shaffer, Scott A., von Haller, Priska D., Kulasekara, Hemantha D., Miller, Samuel I., and Goodlett, David R.

Subjects
Proteomics -- Methods, Mass spectrometry -- Methods, Liquid chromatography -- Methods, Chemistry
Abstract

Data-dependent precursor ion selection is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, this bottom-up method presents major drawbacks in terms of detectable dynamic range. Here, we demonstrate the superior performance of a data-independent method we term precursor acquisition independent from ion count (PAcIFIC). Our results show that almost the entire, predicted, soluble bacterial proteome can be thoroughly analyzed by PAcIFIC without the need for any sample fractionation other than the C18-based liquid chromatograph used to introduce the peptide mixture into the mass spectrometer. Importantly, we also show that PAcIFIC provides unique performance for analysis of human plasma in terms of the number of proteins identified (746 at FDR [less than or equal to] 0.5%) and achieved dynamic range (8 orders of magnitude at FDR [less than or equal to] 0.5%), without any fractionation other than immuno-depletion of the seven most abundant proteins.

Published
2009

185. Cassini RADAR sequence planning and instrument performance

Author

West, Richard D., Anderson, Yanhua, Boehmer, Rudy, Borgarelli, Leonardo, Callahan, Philip, Elachi, Charles, Gim, Yonggyu, Hamilton, Gary, Hensley, Scott, Janssen, Michael A., Johnson, William T.K., Kelleher, Kathleen, Lorenz, Ralph, Ostro, Steve, Roth, Ladislav, Shaffer, Scott, Stiles, Bryan, Wall, Steve, Wye, Lauren C., and Zebker, Howard A.

Subjects
Artificial satellites in remote sensing -- Methods, Synthetic aperture radar -- Design and construction, Synthetic aperture radar -- Usage, Saturn (Planet) -- Discovery and exploration, Titan (Satellite) -- Discovery and exploration, Planets -- Atmosphere, Planets -- Discovery and exploration, Business, Earth sciences, Electronics and electrical industries
Abstract

The Cassini RADAR is a multimode instrument used to map the surface of Titan, the atmosphere of Saturn, the Saturn ring system, and to explore the properties of the icy satellites. Four different active mode bandwidths and a passive radiometer mode provide a wide range of flexibility in taking measurements. The scatterometer mode is used for real aperture imaging of Titan, high-altitude (around 20 000 km) synthetic aperture imaging of Titan and Iapetus, and long range (up to 700 000 km) detection of disk integrated albedos for satellites in the Saturn system. Two SAR modes are used for high-and medium-resolution (300--1000 m) imaging of Titan's surface during close flybys. A high-bandwidth altimeter mode is used for topographic profiling in selected areas with a range resolution of about 35 m. The passive radiometer mode is used to map emission from Titan, from Saturn's atmosphere, from the rings, and from the icy satellites. Repeated scans with differing polarizations using both active and passive data provide data that can usefully constrain models of surface composition and structure. The radar and radiometer receivers show very good stability, and calibration observations have provided an absolute calibration good to about 1.3 dB. Relative uncertainties within a pass and between passes can be even smaller. Data are currently being processed and delivered to the planetary data system at quarterly intervals one year after being acquired. Index Terms--Cassini, RADAR, radiometer, synthetic aperture radar (SAR).

Published
2009

187. Dysbiosis exacerbates colitis by promoting ubiquitination and accumulation of the innate immune adaptor STING in myeloid cells

Author

Shmuel-Galia, Liraz, primary, Humphries, Fiachra, additional, Lei, Xuqiu, additional, Ceglia, Simona, additional, Wilson, Ruth, additional, Jiang, Zhaozhao, additional, Ketelut-Carneiro, Natalia, additional, Foley, Sage E., additional, Pechhold, Susanne, additional, Houghton, JeanMarie, additional, Muneeruddin, Khaja, additional, Shaffer, Scott A., additional, McCormick, Beth A., additional, Reboldi, Andrea, additional, Ward, Doyle, additional, Marshak-Rothstein, Ann, additional, and Fitzgerald, Katherine A., additional

Published
2021
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189. Chemical-genetic interaction mapping links carbon metabolism and cell wall structure to tuberculosis drug efficacy

Author

Koh, Eun-Ik, primary, Oluoch, Peter O., additional, Ruecker, Nadine, additional, Proulx, Megan K., additional, Soni, Vijay, additional, Murphy, Kenan C., additional, Papavinasasundaram, Kadamba G., additional, Reames, Charlotte J., additional, Trujillo, Carolina, additional, Zaveri, Anisha, additional, Zimmerman, Matthew D., additional, Aslebagh, Roshanak, additional, Baker, Richard E., additional, Shaffer, Scott A., additional, Guinn, Kristine M., additional, Fitzgerald, Michael, additional, Dartois, Véronique A., additional, Ehrt, Sabine, additional, Hung, Deborah T., additional, Ioerger, Thomas R., additional, Rubin, Eric, additional, Rhee, Kyu Y., additional, Schnappinger, Dirk, additional, and Sassetti, Christopher M., additional

Published
2021
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190. Characterization of protein cross-links via mass spectrometry and an open-modification search strategy

Author

Singh, Pragya, Shaffer, Scott A., Scherl, Alexander, Holman, Carol, Pfuetzner, Richard A., Freeman, Theodore J. Larson, Miller, Samuel I., Hernandez, Patricia, Appel, Ron D., and Goodlett, David R.

Subjects
Mass spectrometry -- Methods, Protein-protein interactions -- Research, Proteins -- Crosslinking, Proteins -- Research, Chemistry
Abstract

Protein--protein interactions are key to function and regulation of many biological pathways. To facilitate characterization of protein--protein interactions using mass spectrometry, a new data acquisition/analysis pipeline was designed. The goal for this pipeline was to provide a generic strategy for identifying cross-linked peptides from single LC/MS/MS data sets, without using specialized cross-linkers or custom-written software. To achieve this, each peptide in the pair of cross-linked peptides was considered to be 'post-translationally' modified with an unknown mass at an unknown amino acid. This allowed use of an open-modification search engine, Popitam, to interpret the tandem mass spectra of cross-linked peptides. False positives were reduced and database selectivity increased by acquiring precursors and fragments at high mass accuracy. Additionally, a high-charge-state-driven data acquisition scheme was utilized to enrich data sets for cross-linked peptides. This open-modification search based pipeline was shown to be useful for characterizing both chemical as well as native cross-links in proteins. The pipeline was validated by characterizing the known interactions in the chemically cross-linked CYP2E1--b5 complex. Utility of this method in identifying native cross-links was demonstrated by mapping disulfide bridges in RcsF, an outer membrane lipoprotein involved in Rcs phosphorelay.

Published
2008

191. Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides

Author

Scherl, Alexander, Shaffer, Scott A., Taylor, Gregory K., Kulasekara, Hemantha D., Miller, Samuel I., and Goodlett, David R.

Subjects
Peptides -- Properties, Cell fractionation -- Methods, Cell fractionation -- Genetic aspects, Proteomics -- Research, Genomes -- Properties, Chemistry
Abstract

Gas-phase fractionation (GPF) is an efficient and straightforward method to increase proteome coverage. In this report, optimal m/z ranges were calculated based on genomic complexity and experimental data. Then, theoretical precursor ion densities were calculated in silico from various organisms' genomes and found to corroborate the empirical selection of m/z ranges based on ion density mapping. According to both calculations, the choice of m/z range for most efficient GPF coverage in the lower m/z range should be very narrow and increase as m/z value increases. Next, a systematic LC-MS/MS analysis was performed to confirm this observation. The behavior of data-dependent precursor ion selection and the origin of the observed variability was investigated under three different scan modes of an LTQ-Orbitrap hybrid mass spectrometer. Finally, GPF combined with data-dependent analysis was compared to a targeted, pseudo-multiple reaction monitoring analysis of proteotypic peptides that should be, based on empirical observation of LC-ESI-MS/MS data, detectable. The result of the latter experiment supported our conclusion that data-dependent analysis using rational gas-phase fractionation was sufficient for comprehensive proteomic analysis of the proteotypic peptides in an unfractionated cell lysate.

Published
2008

194. 34181_Appendix – Supplemental material for Identification of Risk Factors Prospectively Associated With Musculoskeletal Injury in a Warrior Athlete Population

Author

Deydre S. Teyhen, Shaffer, Scott W., Goffar, Stephen L., Kiesel, Kyle, Butler, Robert J., Rhon, Daniel I., and Plisky, Phillip J.

Subjects
111708 Health and Community Services, FOS: Clinical medicine, 110604 Sports Medicine, FOS: Health sciences, humanities, 110314 Orthopaedics
Abstract

Supplemental material, 34181_Appendix for Identification of Risk Factors Prospectively Associated With Musculoskeletal Injury in a Warrior Athlete Population by Deydre S. Teyhen, Scott W. Shaffer, Stephen L. Goffar, Kyle Kiesel, Robert J. Butler, Daniel I. Rhon and Phillip J. Plisky in Sports Health: A Multidisciplinary Approach

Published
2020
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196. Diurnal timing of nonmigratory movement by birds: the importance of foraging spatial scales

Author

Universidad de Alicante. Departamento de Ciencias Ambientales y Recursos Naturales, Universidad de Alicante. Departamento de Didáctica General y Didácticas Específicas, Mallon, Julie M., Tucker, Marlee A., Beard, Annalea, Bierregaard Jr., Richard O., Bildstein, Keith L., Böhning‐Gaese, Katrin, Brzorad, John N., Buechley, Evan R., Bustamante, Javier, Carrapato, Carlos, Castillo‐Guerrero, José Alfredo, Clingham, Elizabeth, Desholm, Mark, DeSorbo, Christopher R., Domenech, Robert, Douglas, Hayley, Duriez, Olivier, Enggist, Peter, Farwig, Nina, Fiedler, Wolfgang, Gagliardo, Anna, García Ripollés, Clara, Gil Gallús, José Antonio, Gilmour, Morgan E., Harel, Roi, Harrison, Autumn‐Lynn, Henry, Leeann, Katzner, Todd E., Kays, Roland, Kleyheeg, Erik, Limiñana, Rubén, López-López, Pascual, Lucia, Giuseppe, Maccarone, Alan, Mallia, Egidio, Mellone, Ugo, Mojica, Elizabeth K., Nathan, Ran, Newman, Scott H., Oppel, Steffen, Orchan, Yotam, Prosser, Diann J., Riley, Hannah, Rösner, Sascha, Schabo, Dana G., Schulz, Holger, Shaffer, Scott, Shreading, Adam, Silva, João Paulo, Sim, Jolene, Skov, Henrik, Spiegel, Orr, Stuber, Matthew J., Takekawa, John Y., Urios, Vicente, Vidal‐Mateo, Javier, Warner, Kevin, Watts, Bryan D., Weber, Nicola, Weber, Sam, Wikelski, Martin, Žydelis, Ramunas, Mueller, Thomas, Fagan, William F., Universidad de Alicante. Departamento de Ciencias Ambientales y Recursos Naturales, Universidad de Alicante. Departamento de Didáctica General y Didácticas Específicas, Mallon, Julie M., Tucker, Marlee A., Beard, Annalea, Bierregaard Jr., Richard O., Bildstein, Keith L., Böhning‐Gaese, Katrin, Brzorad, John N., Buechley, Evan R., Bustamante, Javier, Carrapato, Carlos, Castillo‐Guerrero, José Alfredo, Clingham, Elizabeth, Desholm, Mark, DeSorbo, Christopher R., Domenech, Robert, Douglas, Hayley, Duriez, Olivier, Enggist, Peter, Farwig, Nina, Fiedler, Wolfgang, Gagliardo, Anna, García Ripollés, Clara, Gil Gallús, José Antonio, Gilmour, Morgan E., Harel, Roi, Harrison, Autumn‐Lynn, Henry, Leeann, Katzner, Todd E., Kays, Roland, Kleyheeg, Erik, Limiñana, Rubén, López-López, Pascual, Lucia, Giuseppe, Maccarone, Alan, Mallia, Egidio, Mellone, Ugo, Mojica, Elizabeth K., Nathan, Ran, Newman, Scott H., Oppel, Steffen, Orchan, Yotam, Prosser, Diann J., Riley, Hannah, Rösner, Sascha, Schabo, Dana G., Schulz, Holger, Shaffer, Scott, Shreading, Adam, Silva, João Paulo, Sim, Jolene, Skov, Henrik, Spiegel, Orr, Stuber, Matthew J., Takekawa, John Y., Urios, Vicente, Vidal‐Mateo, Javier, Warner, Kevin, Watts, Bryan D., Weber, Nicola, Weber, Sam, Wikelski, Martin, Žydelis, Ramunas, Mueller, Thomas, and Fagan, William F.

Abstract

Timing of activity can reveal an organism's efforts to optimize foraging either by minimizing energy loss through passive movement or by maximizing energetic gain through foraging. Here, we assess whether signals of either of these strategies are detectable in the timing of activity of daily, local movements by birds. We compare the similarities of timing of movement activity among species using six temporal variables: start of activity relative to sunrise, end of activity relative to sunset, relative speed at midday, number of movement bouts, bout duration and proportion of active daytime hours. We test for the influence of flight mode and foraging habitat on the timing of movement activity across avian guilds. We used 64 570 days of GPS movement data collected between 2002 and 2019 for local (non‐migratory) movements of 991 birds from 49 species, representing 14 orders. Dissimilarity among daily activity patterns was best explained by flight mode. Terrestrial soaring birds began activity later and stopped activity earlier than pelagic soaring or flapping birds. Broad‐scale foraging habitat explained less of the clustering patterns because of divergent timing of active periods of pelagic surface and diving foragers. Among pelagic birds, surface foragers were active throughout all 24 hrs of the day while diving foragers matched their active hours more closely to daylight hours. Pelagic surface foragers also had the greatest daily foraging distances, which was consistent with their daytime activity patterns. This study demonstrates that flight mode and foraging habitat influence temporal patterns of daily movement activity of birds.

Published
2020

198. Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry

Author

Gao, Qiuxia, Xue, Song, Doneanu, Catalin E., Shaffer, Scott A., Goodlett, David R., and Nelson, Sidney D.

Subjects
Mass spectrometry -- Usage, Peptides -- Structure, Peptides -- Chemical properties, Science -- Computer programs, Science -- Usage, Scientific software, Chemistry
Abstract

To facilitate structural analysis of proteins and protein-protein interactions, we developed Pro-CrossLink, a suite of software tools consisting of three programs (Figure 1), DetectShift, IdentifyXLink, and AssignXLink. DetectShift was developed to detect ions of cross-linked peptide pairs in a mixture of [sup.18]O-labeled peptides obtained from protein proteolytic digests. The selected candidate ions of crosslinked peptide pairs subsequently undergo tandem mass spectrometric (MS/MS) analysis for sequence determination. Based on the masses of candidate ions as well as y- and b-type ions in the tandem mass spectra, IdenfifyXLink assigns the candidate ions to cross-linked peptide pairs. For an identified cross-linked peptide pair, AssignXLink generates an extensive fragment ion list, including a-, b-, c-type, x-, y-, z-type, internal, and immonium ions with associated common losses of [H.sub.2]0, N[H.sub.3], CO, and C[O.sub.2], and facilitates a precise location of the cross-linked residues. Pro-CrossLink is automated, highly configurable by the user, and applicable to many studies that map low-resolution protein structures and molecular interfaces in protein complexes.

Published
2006

199. Across borders: External factors and prior behaviour influence North Pacific albatross associations with fishing vessels

Author

Orben, Rachael A., primary, Adams, Josh, additional, Hester, Michelle, additional, Shaffer, Scott A., additional, Suryan, Robert M., additional, Deguchi, Tomohiro, additional, Ozaki, Kiyoaki, additional, Sato, Fumio, additional, Young, Lindsay C., additional, Clatterbuck, Corey, additional, Conners, Melinda G., additional, Kroodsma, David A., additional, and Torres, Leigh G., additional

Published
2021
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200. Global political responsibility for the conservation of albatrosses and large petrels

Author

Beal, Martin, primary, Dias, Maria P., additional, Phillips, Richard A., additional, Oppel, Steffen, additional, Hazin, Carolina, additional, Pearmain, Elizabeth J., additional, Adams, Josh, additional, Anderson, David J., additional, Antolos, Michelle, additional, Arata, Javier A., additional, Arcos, José Manuel, additional, Arnould, John P. Y., additional, Awkerman, Jill, additional, Bell, Elizabeth, additional, Bell, Mike, additional, Carey, Mark, additional, Carle, Ryan, additional, Clay, Thomas A., additional, Cleeland, Jaimie, additional, Colodro, Valentina, additional, Conners, Melinda, additional, Cruz-Flores, Marta, additional, Cuthbert, Richard, additional, Delord, Karine, additional, Deppe, Lorna, additional, Dilley, Ben J., additional, Dinis, Herculano, additional, Elliott, Graeme, additional, De Felipe, Fernanda, additional, Felis, Jonathan, additional, Forero, Manuela G., additional, Freeman, Amanda, additional, Fukuda, Akira, additional, González-Solís, Jacob, additional, Granadeiro, José Pedro, additional, Hedd, April, additional, Hodum, Peter, additional, Igual, José Manuel, additional, Jaeger, Audrey, additional, Landers, Todd J., additional, Le Corre, Matthieu, additional, Makhado, Azwianewi, additional, Metzger, Benjamin, additional, Militão, Teresa, additional, Montevecchi, William A., additional, Morera-Pujol, Virginia, additional, Navarro-Herrero, Leia, additional, Nel, Deon, additional, Nicholls, David, additional, Oro, Daniel, additional, Ouni, Ridha, additional, Ozaki, Kiyoaki, additional, Quintana, Flavio, additional, Ramos, Raül, additional, Reid, Tim, additional, Reyes-González, José Manuel, additional, Robertson, Christopher, additional, Robertson, Graham, additional, Romdhane, Mohamed Salah, additional, Ryan, Peter G., additional, Sagar, Paul, additional, Sato, Fumio, additional, Schoombie, Stefan, additional, Scofield, R. Paul, additional, Shaffer, Scott A., additional, Shah, Nirmal Jivan, additional, Stevens, Kim L., additional, Surman, Christopher, additional, Suryan, Robert M., additional, Takahashi, Akinori, additional, Tatayah, Vikash, additional, Taylor, Graeme, additional, Thompson, David R., additional, Torres, Leigh, additional, Walker, Kath, additional, Wanless, Ross, additional, Waugh, Susan M., additional, Weimerskirch, Henri, additional, Yamamoto, Takashi, additional, Zajkova, Zuzana, additional, Zango, Laura, additional, and Catry, Paulo, additional

Published
2021
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