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476 results on '"Hink, P."'

1. A generalized software framework for consolidation of radiotherapy planning and delivery data from diverse data sources

Author

Abdulkadir, Yasin, Hink, Justin, Boyle, Peter, Luximon, Dishane, Pijanowski, Justin, Ritter, Timothy, Curran, Bruce, Leu, Min, Nickols, Nicholas, Lee, Steve P., Palta, Jatinder R., Kelly, Maria, Kapoor, Rishabh, Thompson, Reid, Low, Daniel A., Lamb, James M., and Neylon, Jack

Subjects
Physics - Medical Physics
Abstract

Aggregating large-scale radiotherapy planning and delivery data is crucial for advancing radiation oncology research and improving clinical practice, yet challenges persist due to the diversity of treatment planning systems (TPS), record and verify (R&V) systems, and complex data formats lacking standardized retrieval methods. We developed a robust software framework that automates the collection and integration of multi-institutional radiotherapy data from diverse TPS and R&V systems. By utilizing the unidirectional references of DICOM objects, our framework reconstructs complete patient datasets starting from Radiotherapy Treatment Records (RTRECORDs), managing tasks such as data queries, transfers, verification, and logging. It effectively maps DICOM linkages between RTRECORDs, RTPLANs, RTDOSEs, RTSTRUCTs, planning images, registrations, and associated diagnostic images, incorporating custom modules for data conversion and comprehensive error handling. Implemented across multiple institutions using various systems$-$ including ARIA, Eclipse, MOSAIQ, RayStation, MIM, Pinnacle$-$ the framework successfully collected data from two clinics over an 11-year period, aggregating data from 6,022 patients and 13,871 treatment plans with a success rate of 99.76% and an average processing time of approximately 18 minutes per patient. Ongoing efforts are extending data collection to clinics lacking DICOM Query/Retrieve capabilities, demonstrating the framework's adaptability to various clinical environments. This efficient automation of comprehensive data collection overcomes significant technical barriers, facilitating the creation of large-scale datasets that can accelerate advancements in radiation oncology., Comment: 11 pages, 5 figures

Published
2024

4. De novo design of high-affinity binders of bioactive helical peptides.

Author

Vázquez Torres, Susana, Leung, Philip, Venkatesh, Preetham, Lutz, Isaac, Hink, Fabian, Huynh, Huu-Hien, Becker, Jessica, Yeh, Andy, Juergens, David, Bennett, Nathaniel, Hoofnagle, Andrew, Huang, Eric, MacCoss, Michael, Expòsit, Marc, Lee, Gyu, Bera, Asim, Kang, Alex, De La Cruz, Joshmyn, Levine, Paul, Li, Xinting, Lamb, Mila, Gerben, Stacey, Murray, Analisa, Heine, Piper, Korkmaz, Elif, Nivala, Jeff, Stewart, Lance, Watson, Joseph, Rogers, Joseph, and Baker, David

Subjects
Biosensing Techniques, Computer-Aided Design, Deep Learning, Diffusion, Glucagon, Luminescent Measurements, Mass Spectrometry, Parathyroid Hormone, Peptides, Protein Structure, Secondary, Proteins, Substrate Specificity, Models, Molecular
Abstract

Many peptide hormones form an α-helix on binding their receptors1-4, and sensitive methods for their detection could contribute to better clinical management of disease5. De novo protein design can now generate binders with high affinity and specificity to structured proteins6,7. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion8 to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.

Published
2024

5. Engineered phage with antibacterial CRISPR–Cas selectively reduce E. coli burden in mice

Author

Gencay, Yilmaz Emre, Jasinskytė, Džiuginta, Robert, Camille, Semsey, Szabolcs, Martínez, Virginia, Petersen, Anders Østergaard, Brunner, Katja, de Santiago Torio, Ana, Salazar, Alex, Turcu, Iszabela Cristiana, Eriksen, Melissa Kviesgaard, Koval, Lev, Takos, Adam, Pascal, Ricardo, Schou, Thea Staffeldt, Bayer, Lone, Bryde, Tina, Johansen, Katja Chandelle, Bak, Emilie Glad, Smrekar, Frenk, Doyle, Timothy B., Satlin, Michael J., Gram, Aurelie, Carvalho, Joana, Jessen, Lene, Hallström, Björn, Hink, Jonas, Damholt, Birgitte, Troy, Alice, Grove, Mette, Clube, Jasper, Grøndahl, Christian, Haaber, Jakob Krause, van der Helm, Eric, Zdravkovic, Milan, and Sommer, Morten Otto Alexander

Published
2024
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8. Stress‐dependent macromolecular crowding in the mitochondrial matrix

Author

Bulthuis, Elianne P, Dieteren, Cindy E J, Bergmans, Jesper, Berkhout, Job, Wagenaars, Jori A, van de Westerlo, Els M A, Podhumljak, Emina, Hink, Mark A, Hesp, Laura F B, Rosa, Hannah S, Malik, Afshan N, Lindert, Mariska Kea‐te, Willems, Peter H G M, Gardeniers, Han J G E, den Otter, Wouter K, Adjobo‐Hermans, Merel J W, and Koopman, Werner J H

Published
2023
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9. Inferring fusion nuclear burnwidths with low gain photomultiplier impulse response functions.

Author

Meaney, K. D., Jeet, J., Carrera, J., Mariscal, E., Schlossberg, D., Moore, A., Eckart, M., Milnes, J., Hink, P., Hillyard, P., Holdener, D., Herrmann, H., Geppert-Kleinrath, H., and Kim, Y.

Subjects
IMPULSE response, NUCLEAR fusion, PHOTOMULTIPLIERS, IMPLOSIONS, INERTIAL confinement fusion, PHYSICS
Abstract

When an inertial confinement fusion implosion is compressed, it maintains thermonuclear density and temperatures for a very short time scale, about 100 ps. The Gamma Reaction History diagnostic measures the time evolution of the fusion burn, but its temporal resolution is limited by the use of a photomultiplier tube (PMT) to amplify the photon signal. Multichannel plate-based PMTs have a fast (∼120 ps) full-width at half-max impulse response function (IRF), but the time scale is similar to the incoming physics signal. An analysis routine is used to remove the effect of the PMT IRF and infer the incident fusion burnwidth. With the National Ignition Facility achieving ignition and creating much brighter signals, the PMTs are run at gains three orders of magnitude lower than nominal operation. Calibration at these settings shows the PMT IRFs get ∼15% wider. Taking the gain-dependent IRF can affect the inferred nuclear burnwidths by up to ∼15%. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Observations of the Li, Be, and B isotopes and constraints on cosmic-ray propagation

Author

de Nolfo, G. A., Moskalenko, I. V., Binns, W. R., Christian, E. R., Cummings, A. C., Davis, A. J., George, J. S., Hink, P. L., Israel, M. H., Leske, R. A., Lijowski, M., Mewaldt, R. A., Stone, E. C., Strong, A. W., von Rosenvinge, T. T., Wiedenbeck, M. E., and Yanasak, N. E.

Subjects
Astrophysics
Abstract

The abundance of Li, Be, and B isotopes in galactic cosmic rays (GCR) between E=50-200 MeV/nucleon has been observed by the Cosmic Ray Isotope Spectrometer (CRIS) on NASA's ACE mission since 1997 with high statistical accuracy. Precise observations of Li, Be, B can be used to constrain GCR propagation models. \iffalse Precise observations of Li, Be, and B in addition to well-measured production cross-sections are used to further constrain GCR propagation models. \fi We find that a diffusive reacceleration model with parameters that best match CRIS results (e.g. B/C, Li/C, etc) are also consistent with other GCR observations. A $\sim$15--20% overproduction of Li and Be in the model predictions is attributed to uncertainties in the production cross-section data. The latter becomes a significant limitation to the study of rare GCR species that are generated predominantly via spallation., Comment: 9 pages of TeX format with three figures. Accepted for publication to Advances in Space Research (Elsevier)

Published
2006
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22. In-flight Performance of the High Energy X-ray Timing Experiment on the Rossi X-ray Timing Explorer

Author

Rothschild, R. E., Blanco, P. R., Gruber, D. E., Heindl, W. A., MacDonald, D. R., Marsden, D. C., Pelling, M. R., Wayne, L. R., and Hink, P. L.

Subjects
Astrophysics
Abstract

The High Energy X-ray Timing Experiment (HEXTE) is one of three scientific instruments aboard the Rossi X-ray Timing Explorer (RXTE), which was launched on December 30, 1995. RXTE performs timing and spectral studies of bright x-ray sources to determine the physical parameters of these systems. The HEXTE consists of two independent clusters of detectors, each cluster containing four NaI(Tl)/CsI(Na) phoswich scintillation counters sharing a common 1 degree FWHM field of view. The field of view of each cluster is switched on- and off-source to provide near real-time background measurements. The net open area of the eight detectors is 1600 cm2, and each detector covers the energy range 15-250 keV with an average energy resolution of 15.4% at 60 keV. The in-flight performance of the HEXTE is described, the light curve and spectrum of the Crab Nebula/Pulsar is given, and the 15-240 keV spectrum of the weak source, active galaxy MCG 8-11-11 is presented to demonstrate the weak source spectral capabilities of HEXTE., Comment: 30 pages, 14 figures, 4 tables, accepted by Ap. J., to be published in vol 496, March 20, 1998

Published
1997
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33. Radioactive Clocks and Cosmic-Ray Transport in the Galaxy

Author

Mewaldt, R. A., Yanasak, N. E., Wiedenbeck, M. E., Davis, A. J., Binns, W. R., Christian, E. R., Cummings, A. C., Hink, P. L., Leske, R. A., Niebur, S. M., Stone, E. C., Von Rosenvinge, T. T., Diehl, Roland, editor, Parizot, Etienne, editor, Kallenbach, Reinald, editor, and Von Steiger, Rudolf, editor

Published
2001
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36. The Cosmic-Ray Isotope Spectrometer for the Advanced Composition Explorer

Author

Stone, E. C., Cohen, C. M. S., Cook, W. R., Cummings, A. C., Gauld, B., Kecman, B., Leske, R. A., Mewaldt, R. A., Thayer, M. R., Dougherty, B. L., Grumm, R. L., Milliken, B. D., Radocinski, R. G., Wiedenbeck, M. E., Christian, E. R., Shuman, S., Trexel, H., Von Rosenvinge, T. T., Binns, W. R., Crary, D. J., Dowkontt, P., Epstein, J., Hink, P. L., Klarmann, J., Lijowski, M., Olevitch, M. A., Russell, C. T., editor, Mewaldt, R. A., editor, and Von Rosenvinge, T. T., editor

Published
1998
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42. Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization.

Author

Fishbein, Skye R.S., DeVeaux, Anna L., Khanna, Sakshi, Ferreiro, Aura L., Liao, James, Agee, Wesley, Ning, Jie, Mahmud, Bejan, Wallace, Miranda J., Hink, Tiffany, Reske, Kimberly A., Cass, Candice, Guruge, Janaki, Leekha, Sidh, Rengarajan, Sunaina, Dubberke, Erik R., and Dantas, Gautam

Abstract

Gastrointestinal colonization by Clostridioides difficile is common in healthcare settings and ranges in presentation from asymptomatic carriage to lethal C. difficile infection (CDI). We used a systems biology approach to investigate why patients colonized with C. difficile have a range of clinical outcomes. Microbiota humanization of germ-free mice with fecal samples from toxigenic C. difficile carriers revealed a spectrum of virulence among clinically prevalent clade 1 lineages and identified candidate taxa, including Blautia , as markers of stable colonization. Using gnotobiotic mice engrafted with defined human microbiota, we validated strain-specific CDI severity across clade 1 strains isolated from patients. Mice engrafted with a community broadly representative of colonized patients were protected from severe disease across all strains without suppression of C. difficile colonization. These results underline the capacity of gut community structure to attenuate a diversity of pathogenic strains without inhibiting colonization, providing insight into determinants of stable C. difficile carriage. [Display omitted] • Carriage of toxigenic Clostridioides difficile is common in healthcare settings • The microbiota and pathogen strain are key mediators of colonization outcomes • Microbiome engraftment screen recapitulates the spectrum of C. difficile disease • Defined microbiome enables colonization and suppresses strain-specific virulence Fishbein, DeVeaux, and Khanna et al. investigate determinants of Clostridioides difficile carriage versus infection. Using C. difficile -colonized patient cohorts and microbiota-humanized mouse models, they show that clinically prevalent clade 1 strains have a range of virulence that can be suppressed by the microbiota without inhibiting colonization. [ABSTRACT FROM AUTHOR]

Published
2025
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43. The X-Ray Timing Explorer

Author

Bradt, H. V., Levine, A. M., Morgan, E. H., Remillard, R. A., Swank, J. H., Dingus, B. L., Holt, S. S., Jahoda, K. M., Rothschild, R. E., Gruber, D. E., Hink, P. L., Pelling, R. M., Jernigan, J. G., and Kondo, Y., editor

Published
1990
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44. Orbital Compartment Syndrome in Severe Burns: Predictive Factors, Timing, and Complications of Intervention

Author

Echalier, E. Lacey, Larochelle, Ryan D., Patnaik, Jennifer L., Echalier, Benjamin R., Wagner, Anne, Hink, Eric M., Subramanian, Prem S., and Liao, Sophie D.

Abstract

Severe burn patients, particularly those with higher total body surface area, renal failure, inhalation injury, increased lactate, high fluid resuscitation, eyelid burns, and nonorbital compartment syndromes, should be monitored closely for orbital compartment syndrome.

Published
2023
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