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151. A Phenomenological Understanding of the Intersection-ality of Ageism and Racism Among Older Adults: Individual-Level Experiences

Author

Andrew T Steward, Carson M De Fries, Annie Zean Dunbar, Miguel Trujillo, Yating Zhu, Nicole Nicotera, and Leslie Hasche

Subjects
Clinical Psychology, Social Psychology, Geriatrics and Gerontology, Gerontology
Abstract

Objectives Ageism is a prevalent, insidious social justice issue that has harmful effects on the health of older adults. Preliminary literature explores the intersectionality of ageism with sexism, ableism, and ageism experienced among LGBTQ+ older adults. Yet, the intersectionality of ageism with racism remains largely absent from the literature. Therefore, this study explores the lived experience of the intersectionality of ageism and racism among older adults. Methods This qualitative study applied a phenomenological approach. Twenty participants 60+ years of age (M = 69, standard deviation = 8.84) in the U.S. Mountain West identifying as Black, Latino(a), Asian–American/Pacific Islander, Indigenous, or White engaged in a 1-hr interview between February and July 2021. A 3-cycle coding process applied constant comparison methods. Five coders independently coded interviews, engaging in critical discussion to resolve disagreements. An audit trail, member checking, and peer debriefing enhanced credibility. Results This study focuses on individual-level experiences exemplified by 3 umbrella themes and 7 subthemes. The subthemes are (a) compounding oppression, (b) intersection of disparities, (c) White privilege, (d) racism and ageism: being tokenized or ignored, (e) ageism and racism: unspoken bias, (f) racism versus ageism: overt or covert? and (g) racism versus ageism: differentiated or ubiquitous? Discussion The findings indicate how ageism may be racialized through stereotypes related to mental (in)capability. Practitioners can apply the findings to enhance support for older adults by designing interventions aimed at reducing racialized ageist stereotypes and increasing collaboration through education across anti-ageism/anti-racism initiatives. Future research should focus on the impacts of the intersectionality of ageism and racism on specific health outcomes in addition to structural-level interventions.

Published
2023

153. First measurement of low intensity fast neutron background from rock at the Boulby Underground Laboratory

Author

Tziaferi, E., Carson, M. J., Kudryavtsev, V. A., Lerner, R., Lightfoot, P. K., Paling, S. M., Robinson, M., and Spooner, N. J. C.

Subjects
High Energy Physics - Experiment, Physics - Instrumentation and Detectors
Abstract

A technique to measure low intensity fast neutron flux has been developed. The design, calibrations, procedure for data analysis and interpretation of the results are discussed in detail. The technique has been applied to measure the neutron background from rock at the Boulby Underground Laboratory, a site used for dark matter and other experiments, requiring shielding from cosmic ray muons. The experiment was performed using a liquid scintillation detector. A 6.1 litre volume stainless steel cell was filled with an in-house made liquid scintillator loaded with Gd to enhance neutron capture. A two-pulse signature (proton recoils followed by gammas from neutron capture) was used to identify the neutron events from much larger gamma background from PMTs. Suppression of gammas from the rock was achieved by surrounding the detector with high-purity lead and copper. Calibrations of the detector were performed with various gamma and neutron sources. Special care was taken to eliminate PMT afterpulses and correlated background events from the delayed coincidences of two pulses in the Bi-Po decay chain. A four month run revealed a neutron-induced event rate of 1.84 +- 0.65 (stat.) events/day. Monte Carlo simulations based on the GEANT4 toolkit were carried out to estimate the efficiency of the detector and the energy spectra of the expected proton recoils. From comparison of the measured rate with Monte Carlo simulations the flux of fast neutrons from rock was estimated as (1.72 +- 0.61 (stat.) +- 0.38 (syst.))*10^(-6) cm^(-2) s^(-1) above 0.5 MeV., Comment: 37 pages, 24 figures, to be published in Astroparticle Physics

Published
2006
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154. The ZEPLIN-III dark matter detector: instrument design, manufacture and commissioning

Author

Akimov, D. Yu., Alner, G. J., Araujo, H. M., Bewick, A., Bungau, C., Burenkov, A. A., Carson, M. J., Chepel, V., Cline, D., Davidge, D., Davies, J. C., Daw, E., Dawson, J., Durkin, T., Edwards, B., Gamble, T., Chag, C., Hollingworth, R. J., Howard, A. S., Jones, W. G., Joshi, M., Kirkpatrick, J., Kovalenko, A., Kudryavtsev, V. A., Kuznetsov, I. S., Lawson, T., Lebedenko, V. N., Lewin, J. D., Lightfoot, P., Lindote, A., Liubarsky, I., Lopes, M. I., Luscher, R., McMillan, J. E., Morgan, B., Muna, D., Murphy, A. S., Neves, F., Nicklin, G. G., Paling, S. M., da Cunha, J. Pinto, Plank, S. J. S., Preece, R., Quenby, J. J., Robinson, M., Silva, C., Solovov, V. N., Smith, N. J. T., Smith, P. F., Spooner, N. J. C., Stekhanov, V., Sumner, T. J., Thorne, C., Tovey, D. R., Tziaferi, E., Walker, R. J., Wang, H., White, J., and Wolfs, F.

Subjects
Astrophysics
Abstract

We present details of the technical design and manufacture of the ZEPLIN-III dark matter experiment. ZEPLIN-III is a two-phase xenon detector which measures both the scintillation light and the ionisation charge generated in the liquid by interacting particles and radiation. The instrument design is driven by both the physics requirements and by the technology requirements surrounding the use of liquid xenon. These include considerations of key performance parameters, such as the efficiency of scintillation light collection, restrictions placed on the use of materials to control the inherent radioactivity levels, attainment of high vacuum levels and chemical contamination control. The successful solution has involved a number of novel design and manufacturing features which will be of specific use to future generations of direct dark matter search experiments as they struggle with similar and progressively more demanding requirements., Comment: 25 pages, 19 figures. Submitted to Astropart. Phys. Some figures down sampled to reduce size

Published
2006
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155. The ZEPLIN-III dark matter detector: performance study using an end-to-end simulation tool

Author

Araujo, H. M., Akimov, D. Yu., Alner, G. J., Bewick, A., Bungau, C., Camanzi, B., Carson, M. J., Chepel, V., Chagani, H., Davidge, D., Davies, J. C., Daw, E., Dawson, J., Durkin, T., Edwards, B., Gamble, T., Ghag, C., Hollingworth, R., Howard, A. S., Jones, W. G., Joshi, M., Kirkpatrick, J., Kovalenko, A., Kudryavtsev, V. A., Lebedenko, V. N., Lawson, T., Lewin, J. D., Lightfoot, P., Lindote, A., Liubarsky, I., Lopes, M. I., Luscher, R., Majewski, P., Mavrokoridis, K., McMillan, J., Morgan, B., Muna, D., Murphy, A. S., Neves, F., Nicklin, G., Paling, S., da Cunha, J. Pinto, Preece, R., Quenby, J. J., Robinson, M., Silva, C., Solovov, V. N., Smith, N. J. T., Smith, P. F., Spooner, N. J. C., Stekhanov, V., Sumner, T. J., Tovey, D. R., Thorne, C., Tziaferi, E., and Walker, R. J.

Subjects
Astrophysics
Abstract

We present results from a GEANT4-based Monte Carlo tool for end-to-end simulations of the ZEPLIN-III dark matter experiment. ZEPLIN-III is a two-phase detector which measures both the scintillation light and the ionisation charge generated in liquid xenon by interacting particles and radiation. The software models the instrument response to radioactive backgrounds and calibration sources, including the generation, ray-tracing and detection of the primary and secondary scintillations in liquid and gaseous xenon, and subsequent processing by data acquisition electronics. A flexible user interface allows easy modification of detector parameters at run time. Realistic datasets can be produced to help with data analysis, an example of which is the position reconstruction algorithm developed from simulated data. We present a range of simulation results confirming the original design sensitivity of a few times $10^{-8}$ pb to the WIMP-nucleon cross-section., Comment: Submitted to Astroparticle Physics

Published
2006
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158. Simulations of neutron background in a time projection chamber relevant to dark matter searches

Author

Carson, M. J., Davies, J. C., Daw, E., Hollingworth, R. J., Kirkpatrick, J. A., Kudryavtsev, V. A., Lawson, T. B., Lightfoot, P. K., McMillan, J. E., Morgan, B., Paling, S. M., Robinson, M., Spooner, N. J. C, Tovey, D. R., and Tziaferi, E.

Subjects
High Energy Physics - Experiment
Abstract

Presented here are results of simulations of neutron background performed for a time projection chamber acting as a particle dark matter detector in an underground laboratory. The investigated background includes neutrons from rock and detector components, generated via spontaneous fission and (alpha, n) reactions, as well as those due to cosmic-ray muons. Neutrons were propagated to the sensitive volume of the detector and the nuclear recoil spectra were calculated. Methods of neutron background suppression were also examined and limitations to the sensitivity of a gaseous dark matter detector are discussed. Results indicate that neutrons should not limit sensitivity to WIMP-nucleon interactions down to a level of (1 - 3) x 10^{-8} pb in a 10 kg detector., Comment: 27 pages (total, including 3 tables and 11 figures). Accepted for publication in Nuclear Instruments and Methods in Physics Research - Section A

Published
2005
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159. Reduction of Coincident Photomultiplier Noise Relevant to Astroparticle Physics Experiment

Author

Robinson, M., Lightfoot, P. K., Carson, M. J., Kudryavtsev, V. A., and Spooner, N. J. C.

Subjects
Physics - Instrumentation and Detectors
Abstract

In low background and low threshold particle astrophysics experiments using observation of Cherenkov or scintillation light it is common to use pairs or arrays of photomultipliers operated in coincidence. In such circumstances, for instance in dark matter and neutrino experiments, unexpected PMT noise events have been observed, probably arising from generation of light from one PMT being detected by one or more other PMTs. We describe here experimental investigation of such coincident noise events and development of new techniques to remove them using novel pulse shape discrimination procedures. When applied to data from a low background NaI detector with facing PMTs the new procedures are found to improve noise rejection by a factor of 20 over conventional techniques, with significantly reduced loss of signal events., Comment: Submitted to NIM A

Published
2005
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160. Neutron background in large-scale xenon detectors for dark matter searches

Author

Carson, M. J., Davies, J. C., Daw, E., Hollingworth, R. J., Kudryavtsev, V. A., Lawson, T. B., Lightfoot, P. K., McMillan, J. E., Morgan, B., Paling, S. M., Robinson, M., Spooner, N. J. C., and Tovey, D. R.

Subjects
High Energy Physics - Experiment
Abstract

Simulations of the neutron background for future large-scale particle dark matter detectors are presented. Neutrons were generated in rock and detector elements via spontaneous fission and (alpha,n) reactions, and by cosmic-ray muons. The simulation techniques and results are discussed in the context of the expected sensitivity of a generic liquid xenon dark matter detector. Methods of neutron background suppression are investigated. A sensitivity of $10^{-9}-10^{-10}$ pb to WIMP-nucleon interactions can be achieved by a tonne-scale detector., Comment: 35 pages, 13 figures, 2 tables, accepted for publication in Astroparticle Physics

Published
2004
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161. Classification of Trauma-Associated Invasive Fungal Infections to Support Wound Treatment Decisions

Author

Ganesan, Anuradha, Shaikh, Faraz, Bradley, William, Blyth, Dana M., Bennett, Denise, Petfield, Joseph L., Carson, M. Leigh, Wells, Justin M., and Tribble, David R.

Subjects
United States. Army. Landstuhl Regional Medical Center -- Analysis, Diseases -- Maryland -- Afghanistan -- Analysis -- Health aspects, Fungi -- Analysis -- Health aspects, American soldiers -- Analysis -- Health aspects, Antifungal agents -- Analysis -- Health aspects, Medical research -- Analysis -- Health aspects, Disease susceptibility, Mycoses, Necrosis, Infection, Health
Abstract

Cutaneous invasive fungal infections (IFI) occur in deep tissue wounds contaminated by environmental debris; such wounds are caused by agricultural accidents, tornadoes, and blast trauma (1-7). Among severely injured trauma [...]

Published
2019
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162. MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database

Author

Md Shamimuzzaman, Jack M. Gardiner, Amy T. Walsh, Deborah A. Triant, Justin J. Le Tourneau, Aditi Tayal, Deepak R. Unni, Hung N. Nguyen, John L. Portwood, Ethalinda K. S. Cannon, Carson M. Andorf, and Christine G. Elsik

Subjects
data mining, genome database, InterMine, maize, Zea mays, Plant culture, SB1-1110
Abstract

MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org). It enables researchers to create and export customized annotation datasets that can be merged with their own research data for use in downstream analyses. MaizeMine uses the InterMine data warehousing system to integrate genomic sequences and gene annotations from the Zea mays B73 RefGen_v3 and B73 RefGen_v4 genome assemblies, Gene Ontology annotations, single nucleotide polymorphisms, protein annotations, homologs, pathways, and precomputed gene expression levels based on RNA-seq data from the Z. mays B73 Gene Expression Atlas. MaizeMine also provides database cross references between genes of alternative gene sets from Gramene and NCBI RefSeq. MaizeMine includes several search tools, including a keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating custom queries. The Genomic Regions search tool executes queries based on lists of genome coordinates, and supports both the B73 RefGen_v3 and B73 RefGen_v4 assemblies. The List tool allows you to upload identifiers to create custom lists, perform set operations such as unions and intersections, and execute template queries with lists. When used with gene identifiers, the List tool automatically provides gene set enrichment for Gene Ontology (GO) and pathways, with a choice of statistical parameters and background gene sets. With the ability to save query outputs as lists that can be input to new queries, MaizeMine provides limitless possibilities for data integration and meta-analysis.

Published
2020
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163. The NAIAD experiment for WIMP searches at Boulby mine and recent results

Author

Ahmed, B., Alner, G. J., Araujo, H., Barton, J. C., Bewick, A., Carson, M. J., Davidge, D., Dawson, J. V., Gamble, T., Hart, S. P., Hollingworth, R., Howard, A. S., Jones, W. G., Joshi, M. K., Kudryavtsev, V. A., Lawson, T. B., Lebedenko, V., Lehner, M. J., Lewin, J. D., Lightfoot, P. K., Liubarsky, I., Luscher, R., McMillan, J. E., Morgan, B., Nicklin, G., Paling, S. M., Preece, R. M., Quenby, J. J., Roberts, J. W., Robinson, M., Smith, N. J. T., Smith, P. F., Spooner, N. J. C., Sumner, T. J., and Tovey, D. R.

Subjects
High Energy Physics - Experiment
Abstract

The NAIAD experiment (NaI Advanced Detector) for WIMP dark matter searches at Boulby mine (UK) is described. The detector consists of an array of encapsulated and unencapsulated NaI(Tl) crystals with high light yield. Six crystals are collecting data at present. Data accumulated by four of them (10.6 kg x year exposure) have been used to set upper limits on the WIMP-nucleon spin-independent and WIMP-proton spin-dependent cross-sections. Pulse shape analysis has been applied to discriminate between nuclear recoils, as may be caused by WIMP interactions, and electron recoils due to gamma background. Various calibrations of crystals are presented., Comment: 22 pages, 9 figures, to be published in Astroparticle Physics

Published
2003
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164. The IceCube Neutrino Observatory Part I: Point Source Searches

Author

Collaboration, IceCube, Aartsen, MG, Abbasi, R, Abdou, Y, Ackermann, M, Adams, J, Aguilar, JA, Ahlers, M, Altmann, D, Auffenberg, J, Bai, X, Baker, M, Barwick, SW, Baum, V, Bay, R, Beatty, JJ, Bechet, S, Tjus, J Becker, Becker, K-H, Bell, M, Benabderrahmane, ML, BenZvi, S, Berghaus, P, Berley, D, Bernardini, E, Bernhard, A, Bertrand, D, Besson, DZ, Binder, G, Bindig, D, Bissok, M, Blaufuss, E, Blumenthal, J, Boersma, DJ, Bohaichuk, S, Bohm, C, Bose, D, Böser, S, Botner, O, Brayeur, L, Bretz, H-P, Brown, AM, Bruijn, R, Brunner, J, Carson, M, Casey, J, Casier, M, Chirkin, D, Christov, A, Christy, B, Clark, K, Clevermann, F, Coenders, S, Cohen, S, Cowen, DF, Silva, AH Cruz, Danninger, M, Daughhetee, J, Davis, JC, Clercq, C De, Ridder, S De, Desiati, P, Vries, KD de, With, M de, DeYoung, T, Díaz-Vélez, JC, Dunkman, M, Eagan, R, Eberhardt, B, Eisch, J, Ellsworth, RW, Euler, S, Evenson, PA, Fadiran, O, Fazely, AR, Fedynitch, A, Feintzeig, J, Feusels, T, Filimonov, K, Finley, C, Fischer-Wasels, T, Flis, S, Franckowiak, A, Frantzen, K, Fuchs, T, Gaisser, TK, Gallagher, J, Gerhardt, L, Gladstone, L, Glüsenkamp, T, Goldschmidt, A, Golup, G, Gonzalez, JG, Goodman, JA, Góra, D, Grandmont, DT, Grant, D, Groß, A, Ha, C, and Ismail, A Haj

Subjects
astro-ph.HE
Abstract

Papers on point source searches submitted to the 33nd International CosmicRay Conference (Rio de Janeiro 2013) by the IceCube Collaboration.

Published
2013

165. The IceCube Neutrino Observatory Part III: Cosmic Rays

Author

Collaboration, IceCube, Aartsen, MG, Abbasi, R, Abdou, Y, Ackermann, M, Adams, J, Aguilar, JA, Ahlers, M, Altmann, D, Auffenberg, J, Bai, X, Baker, M, Barwick, SW, Baum, V, Bay, R, Beatty, JJ, Bechet, S, Tjus, J Becker, Becker, K-H, Bell, M, Benabderrahmane, ML, BenZvi, S, Berghaus, P, Berley, D, Bernardini, E, Bernhard, A, Bertrand, D, Besson, DZ, Binder, G, Bindig, D, Bissok, M, Blaufuss, E, Blumenthal, J, Boersma, DJ, Bohaichuk, S, Bohm, C, Bose, D, Böser, S, Botner, O, Brayeur, L, Bretz, H-P, Brown, AM, Bruijn, R, Brunner, J, Carson, M, Casey, J, Casier, M, Chirkin, D, Christov, A, Christy, B, Clark, K, Clevermann, F, Coenders, S, Cohen, S, Cowen, DF, Silva, AH Cruz, Danninger, M, Daughhetee, J, Davis, JC, Clercq, C De, Ridder, S De, Desiati, P, Vries, KD de, With, M de, DeYoung, T, Díaz-Vélez, JC, Dunkman, M, Eagan, R, Eberhardt, B, Eisch, J, Ellsworth, RW, Euler, S, Evenson, PA, Fadiran, O, Fazely, AR, Fedynitch, A, Feintzeig, J, Feusels, T, Filimonov, K, Finley, C, Fischer-Wasels, T, Flis, S, Franckowiak, A, Frantzen, K, Fuchs, T, Gaisser, TK, Gallagher, J, Gerhardt, L, Gladstone, L, Glüsenkamp, T, Goldschmidt, A, Golup, G, Gonzalez, JG, Goodman, JA, Góra, D, Grandmont, DT, Grant, D, Groß, A, Ha, C, and Ismail, A Haj

Subjects
astro-ph.HE
Abstract

Papers on cosmic rays submitted to the 33nd International Cosmic RayConference (Rio de Janeiro 2013) by the IceCube Collaboration.

Published
2013

166. The IceCube Neutrino Observatory Part IV: Searches for Dark Matter and Exotic Particles

Author

Collaboration, IceCube, Aartsen, MG, Abbasi, R, Abdou, Y, Ackermann, M, Adams, J, Aguilar, JA, Ahlers, M, Altmann, D, Auffenberg, J, Bai, X, Baker, M, Barwick, SW, Baum, V, Bay, R, Beatty, JJ, Bechet, S, Tjus, J Becker, Becker, K-H, Bell, M, Benabderrahmane, ML, BenZvi, S, Berghaus, P, Berley, D, Bernardini, E, Bernhard, A, Bertrand, D, Besson, DZ, Binder, G, Bindig, D, Bissok, M, Blaufuss, E, Blumenthal, J, Boersma, DJ, Bohaichuk, S, Bohm, C, Bose, D, Böser, S, Botner, O, Brayeur, L, Bretz, H-P, Brown, AM, Bruijn, R, Brunner, J, Carson, M, Casey, J, Casier, M, Chirkin, D, Christov, A, Christy, B, Clark, K, Clevermann, F, Coenders, S, Cohen, S, Cowen, DF, Silva, AH Cruz, Danninger, M, Daughhetee, J, Davis, JC, Clercq, C De, Ridder, S De, Desiati, P, Vries, KD de, With, M de, DeYoung, T, Díaz-Vélez, JC, Dunkman, M, Eagan, R, Eberhardt, B, Eisch, J, Ellsworth, RW, Euler, S, Evenson, PA, Fadiran, O, Fazely, AR, Fedynitch, A, Feintzeig, J, Feusels, T, Filimonov, K, Finley, C, Fischer-Wasels, T, Flis, S, Franckowiak, A, Frantzen, K, Fuchs, T, Gaisser, TK, Gallagher, J, Gerhardt, L, Gladstone, L, Glüsenkamp, T, Goldschmidt, A, Golup, G, Gonzalez, JG, Goodman, JA, Góra, D, Grandmont, DT, Grant, D, Groß, A, Ha, C, and Ismail, A Haj

Subjects
astro-ph.HE
Abstract

Papers on searches for Dark Matter and exotic particles submitted to the 33ndInternational Cosmic Ray Conference (Rio de Janeiro 2013) by the IceCubeCollaboration.

Published
2013

167. The IceCube Neutrino Observatory Part VI: Ice Properties, Reconstruction and Future Developments

Author

Collaboration, IceCube, Aartsen, MG, Abbasi, R, Abdou, Y, Ackermann, M, Adams, J, Aguilar, JA, Ahlers, M, Altmann, D, Auffenberg, J, Bai, X, Baker, M, Barwick, SW, Baum, V, Bay, R, Beatty, JJ, Bechet, S, Tjus, J Becker, Becker, K-H, Bell, M, Benabderrahmane, ML, BenZvi, S, Berghaus, P, Berley, D, Bernardini, E, Bernhard, A, Bertrand, D, Besson, DZ, Binder, G, Bindig, D, Bissok, M, Blaufuss, E, Blumenthal, J, Boersma, DJ, Bohaichuk, S, Bohm, C, Bose, D, Böser, S, Botner, O, Brayeur, L, Bretz, H-P, Brown, AM, Bruijn, R, Brunner, J, Carson, M, Casey, J, Casier, M, Chirkin, D, Christov, A, Christy, B, Clark, K, Clevermann, F, Coenders, S, Cohen, S, Cowen, DF, Silva, AH Cruz, Danninger, M, Daughhetee, J, Davis, JC, Clercq, C De, Ridder, S De, Desiati, P, Vries, KD de, With, M de, DeYoung, T, Díaz-Vélez, JC, Dunkman, M, Eagan, R, Eberhardt, B, Eisch, J, Ellsworth, RW, Euler, S, Evenson, PA, Fadiran, O, Fazely, AR, Fedynitch, A, Feintzeig, J, Feusels, T, Filimonov, K, Finley, C, Fischer-Wasels, T, Flis, S, Franckowiak, A, Frantzen, K, Fuchs, T, Gaisser, TK, Gallagher, J, Gerhardt, L, Gladstone, L, Glüsenkamp, T, Goldschmidt, A, Golup, G, Gonzalez, JG, Goodman, JA, Góra, D, Grandmont, DT, Grant, D, Groß, A, Ha, C, and Ismail, A Haj

Subjects
astro-ph.HE
Abstract

Papers on ice properties, reconstruction and future developments submitted tothe 33nd International Cosmic Ray Conference (Rio de Janeiro 2013) by theIceCube Collaboration.

Published
2013

168. The IceCube Neutrino Observatory Part II: Atmospheric and Diffuse UHE Neutrino Searches of All Flavors

Author

Collaboration, IceCube, Aartsen, MG, Abbasi, R, Abdou, Y, Ackermann, M, Adams, J, Aguilar, JA, Ahlers, M, Altmann, D, Auffenberg, J, Bai, X, Baker, M, Barwick, SW, Baum, V, Bay, R, Beatty, JJ, Bechet, S, Tjus, J Becker, Becker, K-H, Bell, M, Benabderrahmane, ML, BenZvi, S, Berghaus, P, Berley, D, Bernardini, E, Bernhard, A, Bertrand, D, Besson, DZ, Binder, G, Bindig, D, Bissok, M, Blaufuss, E, Blumenthal, J, Boersma, DJ, Bohaichuk, S, Bohm, C, Bose, D, Böser, S, Botner, O, Brayeur, L, Bretz, H-P, Brown, AM, Bruijn, R, Brunner, J, Carson, M, Casey, J, Casier, M, Chirkin, D, Christov, A, Christy, B, Clark, K, Clevermann, F, Coenders, S, Cohen, S, Cowen, DF, Silva, AH Cruz, Danninger, M, Daughhetee, J, Davis, JC, Clercq, C De, Ridder, S De, Desiati, P, Vries, KD de, With, M de, DeYoung, T, Díaz-Vélez, JC, Dunkman, M, Eagan, R, Eberhardt, B, Eisch, J, Ellsworth, RW, Euler, S, Evenson, PA, Fadiran, O, Fazely, AR, Fedynitch, A, Feintzeig, J, Feusels, T, Filimonov, K, Finley, C, Fischer-Wasels, T, Flis, S, Franckowiak, A, Frantzen, K, Fuchs, T, Gaisser, TK, Gallagher, J, Gerhardt, L, Gladstone, L, Glüsenkamp, T, Goldschmidt, A, Golup, G, Gonzalez, JG, Goodman, JA, Góra, D, Grandmont, DT, Grant, D, Groß, A, Ha, C, and Ismail, A Haj

Subjects
astro-ph.HE
Abstract

Papers on atmospheric and diffuse UHE neutrino searches of all flavorssubmitted to the 33nd International Cosmic Ray Conference (Rio de Janeiro 2013)by the IceCube Collaboration.

Published
2013

169. The IceCube Neutrino Observatory Part V: Neutrino Oscillations and Supernova Searches

Author

Collaboration, IceCube, Aartsen, MG, Abbasi, R, Abdou, Y, Ackermann, M, Adams, J, Aguilar, JA, Ahlers, M, Altmann, D, Auffenberg, J, Bai, X, Baker, M, Barwick, SW, Baum, V, Bay, R, Beatty, JJ, Bechet, S, Tjus, J Becker, Becker, K-H, Bell, M, Benabderrahmane, ML, BenZvi, S, Berghaus, P, Berley, D, Bernardini, E, Bernhard, A, Bertrand, D, Besson, DZ, Binder, G, Bindig, D, Bissok, M, Blaufuss, E, Blumenthal, J, Boersma, DJ, Bohaichuk, S, Bohm, C, Bose, D, Böser, S, Botner, O, Brayeur, L, Bretz, H-P, Brown, AM, Bruijn, R, Brunner, J, Carson, M, Casey, J, Casier, M, Chirkin, D, Christov, A, Christy, B, Clark, K, Clevermann, F, Coenders, S, Cohen, S, Cowen, DF, Silva, AH Cruz, Danninger, M, Daughhetee, J, Davis, JC, Clercq, C De, Ridder, S De, Desiati, P, Vries, KD de, With, M de, DeYoung, T, Díaz-Vélez, JC, Dunkman, M, Eagan, R, Eberhardt, B, Eisch, J, Ellsworth, RW, Euler, S, Evenson, PA, Fadiran, O, Fazely, AR, Fedynitch, A, Feintzeig, J, Feusels, T, Filimonov, K, Finley, C, Fischer-Wasels, T, Flis, S, Franckowiak, A, Frantzen, K, Fuchs, T, Gaisser, TK, Gallagher, J, Gerhardt, L, Gladstone, L, Glüsenkamp, T, Goldschmidt, A, Golup, G, Gonzalez, JG, Goodman, JA, Góra, D, Grandmont, DT, Grant, D, Groß, A, Ha, C, and Ismail, A Haj

Subjects
astro-ph.HE
Abstract

Papers on neutrino oscillation and supernova searches submitted to the 33ndInternational Cosmic Ray Conference (Rio de Janeiro 2013) by the IceCubeCollaboration.

Published
2013

171. Study and suppression of anomalous fast events in inorganic scintillators for dark matter searches

Author

Kudryavtsev, V. A., Spooner, N. J. C., Lightfoot, P. K., Roberts, J. W., Lehner, M. J., Gamble, T., Carson, M. J., Lawson, T. B., Luscher, R., McMillan, J. E., Morgan, B., Paling, S. M., Robinson, M., Tovey, D. R., Smith, N. J. T., Smith, P. F., Alner, G. J., Hart, S. P., Lewin, J. D., Preece, R. M., Sumner, T. J., Jones, W. G., Quenby, J. J., Ahmed, B., Bewick, A., Davidge, D., Dawson, J. V., Howard, A. S., Ivaniouchenkov, I., Joshi, M. K., Lebedenko, V., Liubarsky, I., Barton, J. C., Gerbier, G., Mallet, J., Mosca, L., and Tao, C.

Subjects
High Energy Physics - Experiment, Astrophysics
Abstract

The status of dark matter searches with inorganic scintillator detectors at Boulby mine is reviewed and the results of tests with a CsI(Tl) crystal are presented. The objectives of the latter experiment were to study anomalous fast events previously observed and to identify ways to remove this background. Clear indications were found that these events were due to surface contamination of crystals by alphas, probably from radon decay. A new array of unencapsulated NaI(Tl) crystals immersed either in liquid paraffin or pure nitrogen atmosphere is under construction at Boulby. Such an approach allows complete control of the surface of the crystals and the ability to remove any surface contamination. First data from the unencapsulated NaI(Tl) do not show the presence of anomalous fast events., Comment: 14 pages, 6 figures

Published
2001
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172. Impact of viral disease hypophagia on pig jejunal function and integrity.

Author

Emma T Helm, Shelby M Curry, Carson M De Mille, Wesley P Schweer, Eric R Burrough, and Nicholas K Gabler

Subjects
Medicine, Science
Abstract

Pathogen challenges are often accompanied by reductions in feed intake, making it difficult to differentiate impacts of reduced feed intake from impacts of pathogen on various response parameters. Therefore, the objective of this study was to determine the impact of Porcine Reproductive and Respiratory Syndrome virus (PRRSV) and feed intake on parameters of jejunal function and integrity in growing pigs. Twenty-four pigs (11.34 ± 1.54 kg BW) were randomly selected and allotted to 1 of 3 treatments (n = 8 pigs/treatment): 1) PRRSV naïve, ad libitum fed (Ad), 2) PRRSV-inoculated, ad libitum fed (PRRS+), and 3) PRRSV naïve, pair-fed to the PRRS+ pigs' daily feed intake (PF). At 17 days post inoculation, all pigs were euthanized and the jejunum was collected for analysis. At days post inoculation 17, PRRS+ and PF pigs had decreased (P < 0.05) transepithelial resistance compared with Ad pigs; whereas fluorescein isothiocyanate-dextran 4 kDa permeability was not different among treatments. Active glucose transport was increased (P < 0.05) in PRRS+ and PF pigs compared with Ad pigs. Brush border carbohydrase activity was reduced in PRRS+ pigs compared with PF pigs for lactase (55%; P = 0.015), sucrase (37%; P = 0.002), and maltase (30%; P = 0.015). For all three carbohydrases, Ad pigs had activities intermediate that of PRRS+ and PF pigs. The mRNA abundance of the tight junction proteins claudin 2, claudin 3, claudin 4, occludin, and zonula occludens-1 were reduced in PRRS+ pigs compared with Ad pigs; however, neither the total protein abundance nor the cellular compartmentalization of these tight junction proteins differed among treatments. Taken together, this study demonstrates that the changes that occur to intestinal epithelium structure, function, and integrity during a systemic PRRSV challenge can be partially explained by reductions in feed intake. Further, long term adaptation to PRRSV challenge and caloric restriction does reduce intestinal transepithelial resistance but does not appear to reduce the integrity of tight junction protein complexes.

Published
2020
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173. Short-timescale Variability in the Broadband Emission of the Blazars Mkn421 and Mkn501

Author

Carson, M. J., McKernan, B., Yaqoob, T., and Fegan, D. J.

Subjects
Astrophysics
Abstract

We analyse ASCA x-ray data and Whipple \gamma-ray data from the blazars Mkn421 and Mkn501 for short-timescale variability. We find no evidence for statistically significant (>3\sigma) variability in these data, in either source, on timescales of less than \sim 10 minutes., Comment: Submitted to ICRC, 4 pages, 4 figures

Published
1999

174. VHE gamma-ray observations of Markarian 501

Author

Whipple Collaboration, Breslin, A. C., Bond, I. H., Bradbury, S. M., Buckley, J. H., Burdett, A. M., Carson, M. J., Carter-Lewis, D. A., Catanese, M., Cawley, M. F., Dunlea, S., D'Vali, M., Fegan, D. J., Fegan, S. J., Finley, J. P., Gaidos, J. A., Hall, T. A., Hillas, A. M., Horan, D., Kildea, J., Knapp, J., Krennrich, F., LeBohec, S., Lessard, R. W., Masterson, C., McKernan, B., Quinn, J., Rose, H. J., Samuelson, F. W., Sembroski, G. H., Vassiliev, V. V., and Weekes, T. C.

Subjects
Astrophysics
Abstract

Markarian 501, a nearby (z=0.033) X-ray selected BL Lacertae object, is a well established source of Very High Energy (VHE, E>=300 GeV) gamma rays. Dramatic variability in its gamma-ray emission on time-scales from years to as short as two hours has been detected. Multiwavelength observations have also revealed evidence that the VHE gamma-ray and hard X-ray fluxes may be correlated. Here we present results of observations made with the Whipple Collaboration's 10 m Atmospheric Cerenkov Imaging Telescope during 1999 and discuss them in the context of observations made on Markarian 501 during the period from 1996-1998., Comment: 4 pages, 2 figures, to be published in the proceedings of 26th International Cosmic Ray Conference (Salt Lake City, 1999)

Published
1999

175. Search for relativistic magnetic monopoles with the AMANDA-II neutrino telescope

Author

The IceCube Collaboration, Abbasi, R, Abdou, Y, Abu-Zayyad, T, Adams, J, Aguilar, JA, Ahlers, M, Andeen, K, Auffenberg, J, Bai, X, Baker, M, Barwick, SW, Bay, R, Bazo Alba, JL, Beattie, K, Beatty, JJ, Bechet, S, Becker, JK, Becker, K-H, Benabderrahmane, ML, BenZvi, S, Berdermann, J, Berghaus, P, Berley, D, Bernardini, E, Bertrand, D, Besson, DZ, Bissok, M, Blaufuss, E, Boersma, DJ, Bohm, C, Böser, S, Botner, O, Bradley, L, Braun, J, Buitink, S, Carson, M, Chirkin, D, Christy, B, Clem, J, Clevermann, F, Cohen, S, Colnard, C, Cowen, DF, D’Agostino, MV, Danninger, M, Davis, JC, De Clercq, C, Demirörs, L, Depaepe, O, Descamps, F, Desiati, P, de Vries-Uiterweerd, G, DeYoung, T, Díaz-Vélez, JC, Dierckxsens, M, Dreyer, J, Dumm, JP, Duvoort, MR, Ehrlich, R, Eisch, J, Ellsworth, RW, Engdegård, O, Euler, S, Evenson, PA, Fadiran, O, Fazely, AR, Feusels, T, Filimonov, K, Finley, C, Foerster, MM, Fox, BD, Franckowiak, A, Franke, R, Gaisser, TK, Gallagher, J, Geisler, M, Gerhardt, L, Gladstone, L, Glüsenkamp, T, Goldschmidt, A, Goodman, JA, Grant, D, Griesel, T, Groß, A, Grullon, S, Gurtner, M, Ha, C, Hallgren, A, Halzen, F, Han, K, Hanson, K, Helbing, K, Herquet, P, Hickford, S, Hill, GC, Hoffman, KD, Homeier, A, Hoshina, K, and Hubert, D

Subjects
Nuclear and Plasma Physics, Particle and High Energy Physics, Astronomical Sciences, Physical Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Quantum Physics, Nuclear & Particles Physics, Astronomical sciences, Atomic, molecular and optical physics, Particle and high energy physics
Abstract

We present the search for Cherenkov signatures from relativistic magnetic monopoles in data taken with the AMANDA-II detector, a neutrino telescope deployed in the Antarctic ice cap at the Geographic South Pole. The non-observation of a monopole signal in data collected during the year 2000 improves present experimental limits on the flux of relativistic magnetic monopoles: Our flux limit varies between 3.8 × 10-17 cm-2 s-1 sr-1 (for monopoles moving at the vacuum speed of light) and 8.8 × 10-16 cm-2 s-1 sr-1 (for monopoles moving at a speed β=v/c=0.76, just above the Cherenkov threshold in ice). These limits apply to monopoles that are energetic enough to penetrate the Earth and enter the detector from below the horizon. The limit obtained for monopoles reaching the detector from above the horizon is less stringent by roughly an order of magnitude, due to the much larger background from down-going atmospheric muons. This looser limit is however valid for a larger class of magnetic monopoles, since the monopoles are not required to pass through the Earth. © 2010 The Author(s).

Published
2010

176. Search for relativistic magnetic monopoles with the AMANDA-II neutrino telescope: The IceCube Collaboration

Author

Abbasi, R, Abdou, Y, Abu-Zayyad, T, Adams, J, Aguilar, JA, Ahlers, M, Andeen, K, Auffenberg, J, Bai, X, Baker, M, Barwick, SW, Bay, R, Bazo Alba, JL, Beattie, K, Beatty, JJ, Bechet, S, Becker, JK, Becker, KH, Benabderrahmane, ML, BenZvi, S, Berdermann, J, Berghaus, P, Berley, D, Bernardini, E, Bertrand, D, Besson, DZ, Bissok, M, Blaufuss, E, Boersma, DJ, Bohm, C, Böser, S, Botner, O, Bradley, L, Braun, J, Buitink, S, Carson, M, Chirkin, D, Christy, B, Clem, J, Clevermann, F, Cohen, S, Colnard, C, Cowen, DF, D'Agostino, MV, Danninger, M, Davis, JC, de Clercq, C, Demirörs, L, Depaepe, O, Descamps, F, Desiati, P, de Vries-Uiterweerd, G, DeYoung, T, Díaz-Vélez, JC, Dierckxsens, M, Dreyer, J, Dumm, JP, Duvoort, MR, Ehrlich, R, Eisch, J, Ellsworth, RW, Engdegård, O, Euler, S, Evenson, PA, Fadiran, O, Fazely, AR, Feusels, T, Filimonov, K, Finley, C, Foerster, MM, Fox, BD, Franckowiak, A, Franke, R, Gaisser, TK, Gallagher, J, Geisler, M, Gerhardt, L, Gladstone, L, Glüsenkamp, T, Goldschmidt, A, Goodman, JA, Grant, D, Griesel, T, Groß, A, Grullon, S, Gurtner, M, Ha, C, Hallgren, A, Halzen, F, Han, K, Hanson, K, Helbing, K, Herquet, P, Hickford, S, Hill, GC, Hoffman, KD, Homeier, A, Hoshina, K, Hubert, D, and Huelsnitz, W

Subjects
Nuclear & Particles Physics, Quantum Physics, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Atomic, Molecular, Nuclear, Particle and Plasma Physics
Abstract

We present the search for Cherenkov signatures from relativistic magnetic monopoles in data taken with the AMANDA-II detector, a neutrino telescope deployed in the Antarctic ice cap at the Geographic South Pole. The non-observation of a monopole signal in data collected during the year 2000 improves present experimental limits on the flux of relativistic magnetic monopoles: Our flux limit varies between 3.8 × 10-17 cm-2 s-1 sr-1 (for monopoles moving at the vacuum speed of light) and 8.8 × 10-16 cm-2 s-1 sr-1 (for monopoles moving at a speed β=v/c=0.76, just above the Cherenkov threshold in ice). These limits apply to monopoles that are energetic enough to penetrate the Earth and enter the detector from below the horizon. The limit obtained for monopoles reaching the detector from above the horizon is less stringent by roughly an order of magnitude, due to the much larger background from down-going atmospheric muons. This looser limit is however valid for a larger class of magnetic monopoles, since the monopoles are not required to pass through the Earth. © 2010 The Author(s).

Published
2010

178. Limits to Quantum Gravity Effects from Observations of TeV Flares in Active Galaxies

Author

Biller, S. D., Breslin, A. C., Buckley, J., Catanese, M., Carson, M., Carter-Lewis, D. A., Cawley, M. F., Fegan, D. J., Finley, J., Gaidos, J. A., Hillas, A. M., Krennrich, F., Lamb, R. C., Lessard, R., Masterson, C., McEnery, J. E., McKernan, B., Moriarty, P., Quinn, J., Rose, H. J., Samuelson, F., Sembroski, G., Skelton, P., and Weekes, T. C.

Subjects
General Relativity and Quantum Cosmology, Astrophysics, High Energy Physics - Phenomenology, High Energy Physics - Theory
Abstract

We have used data from the TeV gamma-ray flare associated with the active galaxy Markarian 421 observed on 15 May 1996 to place bounds on the possible energy-dependence of the speed of light in the context of an effective quantum gravitational energy scale. The possibility of an observable time dispersion in high energy radiation has recently received attention in the literature, with some suggestions that the relevant energy scale could be less than the Planck mass and perhaps as low as 10^16 GeV. The limits derived here indicate this energy scale to be in excess of 4x10^16 GeV at the 95% confidence level. To the best of our knowledge, this constitutes the first convincing limit on such phenomena in this energy regime., Comment: 6 pages, including 2 figures

Published
1998
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185. PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models.

Author

Poretsky, Elly, Andorf, Carson M., and Sen, Taner Z.

Subjects
LANGUAGE models, PROTEIN models, PHOSPHORYLATION, POST-translational modification, CELL communication
Abstract

Protein phosphorylation is a dynamic and reversible post‐translational modification that regulates a variety of essential biological processes. The regulatory role of phosphorylation in cellular signaling pathways, protein–protein interactions, and enzymatic activities has motivated extensive research efforts to understand its functional implications. Experimental protein phosphorylation data in plants remains limited to a few species, necessitating a scalable and accurate prediction method. Here, we present PhosBoost, a machine‐learning approach that leverages protein language models and gradient‐boosting trees to predict protein phosphorylation from experimentally derived data. Trained on data obtained from a comprehensive plant phosphorylation database, qPTMplants, we compared the performance of PhosBoost to existing protein phosphorylation prediction methods, PhosphoLingo and DeepPhos. For serine and threonine prediction, PhosBoost achieved higher recall than PhosphoLingo and DeepPhos (.78,.56, and.14, respectively) while maintaining a competitive area under the precision‐recall curve (.54,.56, and.42, respectively). PhosphoLingo and DeepPhos failed to predict any tyrosine phosphorylation sites, while PhosBoost achieved a recall score of.6. Despite the precision‐recall tradeoff, PhosBoost offers improved performance when recall is prioritized while consistently providing more confident probability scores. A sequence‐based pairwise alignment step improved prediction results for all classifiers by effectively increasing the number of inferred positive phosphosites. We provide evidence to show that PhosBoost models are transferable across species and scalable for genome‐wide protein phosphorylation predictions. PhosBoost is freely and publicly available on GitHub. [ABSTRACT FROM AUTHOR]

Published
2023
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188. Photoreceptor disc incisures form as an adaptive mechanism ensuring the completion of disc enclosure

Author

Tylor R. Lewis, Sebastien Phan, Carson M. Castillo, Keun-Young Kim, Kelsey Coppenrath, William Thomas, Ying Hao, Nikolai P. Skiba, Marko E. Horb, Mark H. Ellisman, and Vadim Y. Arshavsky

Abstract

The first steps of vision take place within a stack of tightly packed disc-shaped membranes, or “discs”, located in the outer segment compartment of photoreceptor cells. In rod photoreceptors, discs are enclosed inside the outer segment and contain deep indentations in their rims called “incisures”. The presence of incisures has been documented in a variety of species, yet their role remains elusive. In this study, we combined traditional electron microscopy with three-dimensional electron tomography to demonstrate that incisures are formed only after discs become completely enclosed. We also observed that, at the earliest stage of their formation, discs are not round as typically depicted but rather are highly irregular in shape and resemble expanding lamellipodia. Using genetically manipulated mice and frogs and measuring outer segment protein abundances by quantitative mass spectrometry, we further found that incisure size is determined by the molar ratio between peripherin-2, a disc rim protein critical for the process of disc enclosure, and rhodopsin, the major structural component of disc membranes. While a high perpherin-2 to rhodopsin ratio causes an increase in incisure size and structural complexity, a low ratio precludes incisure formation. Based on these data, we propose a model whereby normal rods express a modest excess of peripherin-2 over the amount required for complete disc enclosure in order to ensure that this important step of disc formation is accomplished. Once the disc is enclosed, the excess peripherin-2 incorporates into the rim to form an incisure.

Published
2023

190. The maize W22 genome provides a foundation for functional genomics and transposon biology

Author

Springer, Nathan M., Anderson, Sarah N., Andorf, Carson M., Ahern, Kevin R., Bai, Fang, Barad, Omer, Barbazuk, W. Brad, Bass, Hank W., Baruch, Kobi, Ben-Zvi, Gil, Buckler, Edward S., Bukowski, Robert, Campbell, Michael S., Cannon, Ethalinda K. S., Chomet, Paul, Dawe, R. Kelly, Davenport, Ruth, Dooner, Hugo K., Du, Limei He, Du, Chunguang, Easterling, Katherine A., Gault, Christine, Guan, Jiahn-Chou, Hunter, Charles T., Jander, Georg, Jiao, Yinping, Koch, Karen E., Kol, Guy, Köllner, Tobias G., Kudo, Toru, Li, Qing, Lu, Fei, Mayfield-Jones, Dustin, Mei, Wenbin, McCarty, Donald R., Noshay, Jaclyn M., Portwood, II, John L., Ronen, Gil, Settles, A. Mark, Shem-Tov, Doron, Shi, Jinghua, Soifer, Ilya, Stein, Joshua C., Stitzer, Michelle C., Suzuki, Masaharu, Vera, Daniel L., Vollbrecht, Erik, Vrebalov, Julia T., Ware, Doreen, Wei, Sharon, Wimalanathan, Kokulapalan, Woodhouse, Margaret R., Xiong, Wenwei, and Brutnell, Thomas P.

Published
2018
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191. Combat-Related Invasive Fungal Wound Infections

Author

Rodriguez, (Ret.) Carlos J, Ganesan, Anuradha, Shaikh, Faraz, Carson, M Leigh, Bradley, William, Warkentien, Tyler E, and Tribble, David R

Subjects
Military Personnel, Afghan Campaign 2001, Blast Injuries, Wound Infection, Public Health, Environmental and Occupational Health, Humans, Supplement Article, General Medicine, Communicable Diseases, Invasive Fungal Infections, Retrospective Studies
Abstract

Introduction During Operation Enduring Freedom in Afghanistan, an outbreak of combat-related invasive fungal wound infections (IFIs) emerged among casualties with dismounted blast trauma and became a priority issue for the Military Health System. Methods In 2011, the Trauma Infectious Disease Outcomes Study (TIDOS) team led the Department of Defense IFI outbreak investigation to describe characteristics of IFIs among combat casualties and provide recommendations related to management of the disease. To support the outbreak investigation, existing IFI definitions and classifications utilized for immunocompromised patients were modified for use in epidemiologic research in a trauma population. Following the conclusion of the outbreak investigation, multiple retrospective analyses using a population of 77 IFI patients (injured during June 2009 to August 2011) were conducted to evaluate IFI epidemiology, wound microbiology, and diagnostics to support refinement of Joint Trauma System (JTS) clinical practice guidelines. Following cessation of combat operations in Afghanistan, the TIDOS database was comprehensively reviewed to identify patients with laboratory evidence of a fungal infection and refine the IFI classification scheme to incorporate timing of laboratory fungal evidence and include categories that denote a high or low level of suspicion for IFI. The refined IFI classification scheme was utilized in a large-scale epidemiologic assessment of casualties injured over a 5.5-year period. Results Among 720 combat casualties admitted to participating hospitals (2009-2014) who had histopathology and/or wound cultures collected, 94 (13%) met criteria for an IFI and 61 (8%) were classified as high suspicion of IFI. Risk factors for development of combat-related IFIs include sustaining a dismounted blast injury, experiencing a traumatic transfemoral amputation, and requiring resuscitation with large-volume (>20 units) blood transfusions. Moreover, TIDOS analyses demonstrated the adverse impact of IFIs on wound healing, particularly with order Mucorales. A polymerase chain reaction (PCR)-based assay to identify filamentous fungi and support earlier IFI diagnosis was also assessed using archived formalin-fixed, paraffin-embedded tissue specimens. Although the PCR-based assay had high specificity (99%), there was low sensitivity (63%); however, sensitivity improved to 83% in tissues collected from sites with angioinvasion. Data obtained from the initial IFI outbreak investigation (37 IFI patients) and subsequent TIDOS analyses (77 IFI patients) supported development and refinement of a JTS clinical practice guideline for the management of IFIs in war wounds. Furthermore, a local clinical practice guideline to screen for early tissue-based evidence of IFIs among blast casualties at the Landstuhl Regional Medical Center was critically evaluated through a TIDOS investigation, providing additional clinical practice support. Through a collaboration with the Uniformed Services University Surgical Critical Care Initiative, findings from TIDOS analyses were used to support development of a clinical decision support tool to facilitate early risk stratification. Conclusions Combat-related IFIs are a highly morbid complication following severe blast trauma and remain a threat for future modern warfare. Our findings have supported JTS clinical recommendations, refined IFI classification, and confirmed the utility of PCR-based assays as a complement to histopathology and/or culture to promote early diagnosis. Analyses underway or planned will add to the knowledge base of IFI epidemiology, diagnostics, prevention, and management.

Published
2022

199. MaizeDIG: Maize Database of Images and Genomes

Author

Kyoung Tak Cho, John L. Portwood, Jack M. Gardiner, Lisa C. Harper, Carolyn J. Lawrence-Dill, Iddo Friedberg, and Carson M. Andorf

Subjects
MaizeDIG, BioDIG, phenotype, genes, QTL, gene model, Plant culture, SB1-1110
Abstract

Background: An organism can be described by its observable features (phenotypes) and the genes and genomic information (genotypes) that cause these phenotypes. For many decades, researchers have tried to find relationships between genotypes and phenotypes, and great strides have been made. However, improved methods and tools for discovering and visualizing these phenotypic relationships are still needed. The maize genetics and genomics database (MaizeGDB, www.maizegdb.org) provides an array of useful resources for diverse data types including thousands of images related to mutant phenotypes in Zea mays ssp. mays (maize). To integrate mutant phenotype images with genomics information, we implemented and enhanced the web-based software package BioDIG (Biological Database of Images and Genomes).Findings: We developed a genotype-phenotype database for maize called MaizeDIG. MaizeDIG has several enhancements over the original BioDIG package. MaizeDIG, which supports multiple reference genome assemblies, is seamlessly integrated with genome browsers to accommodate custom tracks showing tagged mutant phenotypes images in their genomic context and allows for custom tagging of images to highlight the phenotype. This is accomplished through an updated interface allowing users to create image-to-gene links and is accessible via the image search tool.Conclusions: We have created a user-friendly and extensible web-based resource called MaizeDIG. MaizeDIG is preloaded with 2,396 images that are available on genome browsers for 10 different maize reference genomes. Approximately 90 images of classically defined maize genes have been manually annotated. MaizeDIG is available at http://maizedig.maizegdb.org/. The code is free and open source and can be found at https://github.com/Maize-Genetics-and-Genomics-Database/maizedig.

Published
2019
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