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2. Design and Performance of an Interferometric Trigger Array for Radio Detection of High-Energy Neutrinos

Author

Allison, P., Archambault, S., Bard, R., Beatty, J. J., Beheler-Amass, M., Besson, D. Z., Beydler, M., Bogdan, M., Chen, C. -C., Chen, C. -H., Chen, P., Clark, B. A., Clough, A., Connolly, A., Cremonesi, L., Davies, J., Deaconu, C., DuVernois, M. A., Friedman, E., Hanson, J., Hanson, K., Haugen, J., Hoffman, K. D., Hokanson-Fasig, B., Hong, E., Hsu, S. -Y., Hu, L., Huang, J. -J., Huang, M. -H., Hughes, K., Ishihara, A., Karle, A., Kelley, J. L., Khandelwal, R., Kim, M., Kravchenko, I., Kruse, J., Kurusu, K., Landsman, H., Latif, U. A., Laundrie, A., Li, C. -J., Liu, T. C., Lu, M. -Y., Ludwig, A., Mase, K., Meures, T., Nam, J., Nichol, R. J., Nir, G., Oberla, E., OMurchadha, A., Pan, Y., Pfendner, C., Ransom, M., Ratzla, K., Roth, J., Sandstrom, P., Seckel, D., Shiao, Y. -S., Shultz, A., Smith, D., Song, M., Sullivan, M., Touart, J., Vieregg, A. G., Wang, M. -Z., Wang, S. -H., Wei, K., Wissel, S. A., Yoshida, S., and Young, R.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Instrumentation and Detectors
Abstract

Ultra-high energy neutrinos are detectable through impulsive radio signals generated through interactions in dense media, such as ice. Subsurface in-ice radio arrays are a promising way to advance the observation and measurement of astrophysical high-energy neutrinos with energies above those discovered by the IceCube detector ($\geq$1 PeV) as well as cosmogenic neutrinos created in the GZK process ($\geq$100 PeV). Here we describe the $\textit{NuPhase}$ detector, which is a compact receiving array of low-gain antennas deployed 185 m deep in glacial ice near the South Pole. Signals from the antennas are digitized and coherently summed into multiple beams to form a low-threshold interferometric phased array trigger for radio impulses. The NuPhase detector was installed at an Askaryan Radio Array (ARA) station during the 2017/18 Austral summer season. $\textit{In situ}$ measurements with an impulsive, point-source calibration instrument show a 50% trigger efficiency on impulses with voltage signal-to-noise ratios (SNR) of $\le$2.0, a factor of $\sim$1.8 improvement in SNR over the standard ARA combinatoric trigger. Hardware-level simulations, validated with $\textit{in situ}$ measurements, predict a trigger threshold of an SNR as low as 1.6 for neutrino interactions that are in the far field of the array. With the already-achieved NuPhase trigger performance included in ARASim, a detector simulation for the ARA experiment, we find the trigger-level effective detector volume is increased by a factor of 1.8 at neutrino energies between 10 and 100 PeV compared to the currently used ARA combinatoric trigger. We also discuss an achievable near term path toward lowering the trigger threshold further to an SNR of 1.0, which would increase the effective single-station volume by more than a factor of 3 in the same range of neutrino energies., Comment: 19 pages, 19 figures, submitted to Nuclear Instruments and Methods in Physics Research A

Published
2018
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3. Development Toward a Ground-Based Interferometric Phased Array for Radio Detection of High Energy Neutrinos

Author

Avva, J., Bechtol, K., Chesebro, T., Cremonisi, L., Deaconu, C., Gupta, A., Ludwig, A., Messino, W., Miki, C., Nichol, R., Oberla, E., Ransom, M., Romero-Wolf, A., Saltzberg, D., Schlupf, C., Shipp, N., Varner, G., Vieregg, A. G., and Wissel, S. A.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - High Energy Astrophysical Phenomena
Abstract

The in-ice radio interferometric phased array technique for detection of high energy neutrinos looks for Askaryan emission from neutrinos interacting in large volumes of glacial ice, and is being developed as a way to achieve a low energy threshold and a large effective volume at high energies. The technique is based on coherently summing the impulsive Askaryan signal from multiple antennas, which increases the signal-to-noise ratio for weak signals. We report here on measurements and a simulation of thermal noise correlations between nearby antennas, beamforming of impulsive signals, and a measurement of the expected improvement in trigger efficiency through the phased array technique. We also discuss the noise environment observed with an analog phased array at Summit Station, Greenland, a possible site for an interferometric phased array for radio detection of high energy neutrinos., Comment: 13 Pages, 14 Figures

Published
2016
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17. Design and performance of an interferometric trigger array for radio detection of high-energy neutrinos

Author

Allison, P., primary, Archambault, S., additional, Bard, R., additional, Beatty, J.J., additional, Beheler-Amass, M., additional, Besson, D.Z., additional, Beydler, M., additional, Bogdan, M., additional, Chen, C.-C., additional, Chen, C.-H., additional, Chen, P., additional, Clark, B.A., additional, Clough, A., additional, Connolly, A., additional, Cremonesi, L., additional, Davies, J., additional, Deaconu, C., additional, DuVernois, M.A., additional, Friedman, E., additional, Hanson, J., additional, Hanson, K., additional, Haugen, J., additional, Hoffman, K.D., additional, Hokanson-Fasig, B., additional, Hong, E., additional, Hsu, S.-Y., additional, Hu, L., additional, Huang, J.-J., additional, Huang, M.-H., additional, Hughes, K., additional, Ishihara, A., additional, Karle, A., additional, Kelley, J.L., additional, Khandelwal, R., additional, Kim, M., additional, Kravchenko, I., additional, Kruse, J., additional, Kurusu, K., additional, Landsman, H., additional, Latif, U.A., additional, Laundrie, A., additional, Li, C.-J., additional, Liu, T.C., additional, Lu, M.-Y., additional, Ludwig, A., additional, Mase, K., additional, Meures, T., additional, Nam, J., additional, Nichol, R.J., additional, Nir, G., additional, Oberla, E., additional, ÓMurchadha, A., additional, Pan, Y., additional, Pfendner, C., additional, Ransom, M., additional, Ratzlaff, K., additional, Roth, J., additional, Sandstrom, P., additional, Seckel, D., additional, Shiao, Y.-S., additional, Shultz, A., additional, Smith, D., additional, Song, M., additional, Sullivan, M., additional, Touart, J., additional, Vieregg, A.G., additional, Wang, M.-Z., additional, Wang, S.-H., additional, Wei, K., additional, Wissel, S.A., additional, Yoshida, S., additional, and Young, R., additional

Published
2019
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18. Urinary tract infections in very low birthweight infants: A two-center analysis of microbiology, imaging and heart rate characteristics.

Author

Aviles-Otero, N., Ransom, M., Weitkamp, J., Charlton, J.R., Sullivan, B.A., Kaufman, D.A., and Fairchild, K.D.

Subjects
*URINARY tract infections, *CARDIAC imaging, *HEART beat, *CLINICAL trials monitoring, *INFANTS, *BIRTH weight
Abstract

BACKGROUND: Increased understanding of characteristics of urinary tract infection (UTI) among very low birthweight infants (VLBW) might lead to improvement in detection and treatment. Continuous monitoring for abnormal heart rate characteristics (HRC) could provide early warning of UTIs. OBJECTIVE: Describe the characteristics of UTI, including HRC, in VLBW infants. METHODS: We reviewed records of VLBW infants admitted from 2005–2010 at two academic centers participating in a randomized clinical trial of HRC monitoring. Results of all urine cultures, renal ultrasounds (RUS), and voiding cystourethrograms (VCUG) were assessed. Change in the HRC index was analyzed before and after UTI. RESULTS: Of 823 VLBW infants (27.7±2.9 weeks GA, 53% male), 378 had > / = 1 urine culture obtained. A UTI (≥10,000 CFU and >five days of antibiotics) was diagnosed in 80 infants, (10% prevalence, mean GA 25.8±2.0 weeks, 76% male). Prophylactic antibiotics were administered to 29 (36%) infants after UTI, of whom four (14%) had another UTI. Recurrent UTI also occurred in 7/51 (14%) of infants not on uroprophylaxis after their first UTI. RUS was performed after UTI in 78%, and hydronephrosis and other major anomalies were found in 19%. A VCUG was performed in 48% of infants and 18% demonstrated vesicoureteral reflux (VUR). The mean HRC rose and fell significantly in the two days before and after diagnosis of UTI. CONCLUSIONS: UTI was diagnosed in 10% of VLBW infants, and the HRC index increased prior to diagnosis, suggesting that continuous HRC monitoring in the NICU might allow earlier diagnosis and treatment of UTI. [ABSTRACT FROM AUTHOR]

Published
2021
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19. Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants

Author

Juran BD, Hirschfield GM, Invernizzi P, Atkinson EJ, Li Y, Xie G, Kosoy R, Ransom M, Sun Y, Bianchi I, Schlicht EM, Lleo A, Coltescu C, Bernuzzi F, Podda M, Lammert C, Shigeta R, Chan LL, Balschun T, Marconi M, Cusi D, Heathcote EJ, Mason AL, Myers RP, Milkiewicz P, Odin JA, Luketic VA, Bacon BR, Bodenheimer HC Jr, Liakina V, Vincent C, Levy C, Franke A, Gregersen PK, Bossa F, Gershwin ME, deAndrade M, Amos CI, Italian PBC Genetics Study Group, Lazaridis KN, Seldin MF, Siminovitch KA, Almasio PL, Alvaro D, Andriulli A, Barlassina C, Battezzati PM, Benedetti A, Bragazzi M, Brunetto M, Bruno S, Caliari L, Casella G, Civardi F, Coco B, Colli A, Colombo M, Colombo S, Cursaro C, Crocè LS, Crosignani A, Donato F, Fabris L, Ferrari C, Floreani A, Fontana R, Galli A, Grattagliano I, Lazzari R, Macaluso F, Malinverno F, Marra F, Marzioni M, Mascia E, Mattalia A, Montanari R, Morini L, Morisco F, Niro GA, Picciotto A, Portincasa P, Prati D, Rosina F, Rossi S, Selmi C, Spinzi G, Strazzabosco M, Tarallo S, Tiribelli C, Toniutto P, Vinci M, Zuin M., ANDREONE, PIETRO, MURATORI, LUIGI, MURATORI, PAOLO, Juran BD, Hirschfield GM, Invernizzi P, Atkinson EJ, Li Y, Xie G, Kosoy R, Ransom M, Sun Y, Bianchi I, Schlicht EM, Lleo A, Coltescu C, Bernuzzi F, Podda M, Lammert C, Shigeta R, Chan LL, Balschun T, Marconi M, Cusi D, Heathcote EJ, Mason AL, Myers RP, Milkiewicz P, Odin JA, Luketic VA, Bacon BR, Bodenheimer HC Jr, Liakina V, Vincent C, Levy C, Franke A, Gregersen PK, Bossa F, Gershwin ME, deAndrade M, Amos CI, Italian PBC Genetics Study Group, Lazaridis KN, Seldin MF, Siminovitch KA, Almasio PL, Alvaro D, Andreone P, Andriulli A, Barlassina C, Battezzati PM, Benedetti A, Bragazzi M, Brunetto M, Bruno S, Caliari L, Casella G, Civardi F, Coco B, Colli A, Colombo M, Colombo S, Cursaro C, Crocè LS, Crosignani A, Donato F, Fabris L, Ferrari C, Floreani A, Fontana R, Galli A, Grattagliano I, Lazzari R, Macaluso F, Malinverno F, Marra F, Marzioni M, Mascia E, Mattalia A, Montanari R, Morini L, Morisco F, Muratori L, Muratori P, Niro GA, Picciotto A, Portincasa P, Prati D, Rosina F, Rossi S, Selmi C, Spinzi G, Strazzabosco M, Tarallo S, Tiribelli C, Toniutto P, Vinci M, Zuin M., Juran, Bd, Hirschfield, Gm, Invernizzi, P, Atkinson, Ej, Li, Y, Xie, G, Kosoy, R, Ransom, M, Sun, Y, Bianchi, I, Schlicht, Em, Lleo, A, Coltescu, C, Bernuzzi, F, Podda, M, Lammert, C, Shigeta, R, Chan, Ll, Balschun, T, Marconi, M, Cusi, D, Heathcote, Ej, Mason, Al, Myers, Rp, Milkiewicz, P, Odin, Ja, Luketic, Va, Bacon, Br, Bodenheimer HC, Jr, Liakina, V, Vincent, C, Levy, C, Franke, A, Gregersen, Pk, Bossa, F, Gershwin, Me, Deandrade, M, Amos, Ci, Lazaridis, Kn, Seldin, Mf, Siminovitch, Ka, Morisco, Filomena, Italian PBC Genetics Study, Group, Juran, B, Hirschfield, G, Atkinson, E, Schlicht, E, Chan, L, Heathcote, E, Mason, A, Myers, R, Odin, J, Luketic, V, Bacon, B, Bodenheimer, H, Gregersen, P, Gershwin, M, Amos, C, Italian PBC Genetics Study, G, Lazaridis, K, Seldin, M, Siminovitch, K, Almasio, P, Alvaro, D, Andreone, P, Andriulli, A, Barlassina, C, Battezzati, P, Benedetti, A, Bragazzi, M, Brunetto, M, Bruno, S, Caliari, L, Casella, G, Civardi, F, Coco, B, Colli, A, Colombo, M, Colombo, S, Cursaro, C, Crocè, L, Crosignani, A, Donato, F, Fabris, L, Ferrari, C, Floreani, A, Fontana, R, Galli, A, Grattagliano, I, Lazzari, R, Macaluso, F, Malinverno, F, Marra, F, Marzioni, M, Mascia, E, Mattalia, A, Montanari, R, Morini, L, Morisco, F, Muratori, L, Muratori, P, Niro, G, Picciotto, A, Portincasa, P, Prati, D, Rosina, F, Rossi, S, Selmi, C, Spinzi, G, Strazzabosco, M, Tarallo, S, Tiribelli, C, Toniutto, P, Vinci, M, Zuin, M, Almasio, Pl, Battezzati, Pm, Croce', Saveria, Niro, Ga, Tiribelli, Claudio, and Zuin, M.

Subjects
MULTILOCUS GENOTYPE DATA, PRIMARY BILIARY CIRRHOSIS, PBC, 0302 clinical medicine, Gene Frequency, MED/12 - GASTROENTEROLOGIA, HLA Antigens, REGULATORY T-CELLS, RHEUMATOID-ARTHRITIS, VITAMIN-D, Genetics (clinical), Oligonucleotide Array Sequence Analysis, Genetics, CLASSICAL HLA ALLELES, 0303 health sciences, Liver Cirrhosis, Biliary, PBC, HLA alleles, Association Studies Articles, CELIAC-DISEASE, General Medicine, GENOME-WIDE ASSOCIATION, SUSCEPTIBILITY LOCI, GENETIC RISK, 3. Good health, Chromosomes, Human, Pair 1, SINGLE NUCLEOTIDE POLYMORPHISMS, 030211 gastroenterology & hepatology, Chromosomes, Human, Pair 7, GENETIC ANALYSES, Genotype, Single-nucleotide polymorphism, Locus (genetics), Human leukocyte antigen, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Humans, SNP, Genetic Predisposition to Disease, Allele, Molecular Biology, Allele frequency, Alleles, 030304 developmental biology, Chromosomes, Human, Pair 13, Haplotype, Epistasis, Genetic, Genetic Loci, Case-Control Studies, Imputation (genetics)
Abstract

To further characterize the genetic basis of primary biliary cirrhosis (PBC), we genotyped 2426 PBC patients and 5731 unaffected controls from three independent cohorts using a single nucleotide polymorphism (SNP) array (Immunochip) enriched for autoimmune disease risk loci. Meta-analysis of the genotype data sets identified a novel disease-associated locus near the TNFSF11 gene at 13q14, provided evidence for association at six additional immune-related loci not previously implicated in PBC and confirmed associations at 19 of 22 established risk loci. Results of conditional analyses also provided evidence for multiple independent association signals at four risk loci, with haplotype analyses suggesting independent SNP effects at the 2q32 and 16p13 loci, but complex haplotype driven effects at the 3q25 and 6p21 loci. By imputing classical HLA alleles from this data set, four class II alleles independently contributing to the association signal from this region were identified. Imputation of genotypes at the non-HLA loci also provided additional associations, but none with stronger effects than the genotyped variants. An epistatic interaction between the IL12RB2 risk locus at 1p31and the IRF5 risk locus at 7q32 was also identified and suggests a complementary effect of these loci in predisposing to disease. These data expand the repertoire of genes with potential roles in PBC pathogenesis that need to be explored by follow-up biological studies.

Published
2012

20. Classical HLA-DRB1 and DPB1 alleles account for HLA associations with primary biliary cirrhosis

Author

Italian PBC Genetics Study Group, Seldin, Mf, Gershwin, Me, Podda, M, de Bakker PI, Cusi, D, Siminovitch, Ka, Gregersen, Pk, Amos, Ci, Bossa, F, Franke, A, Shigeta, R, Lleo, A, Kosoy, R, Raychaudhuri, S, Ransom, M, Invernizzi, P, Almasio, Pl, Alvaro, D, Andreone, P, Andriulli, A, Barlassina, C, Benedetti, A, Bernuzzi, F, Bianchi, I, Bragazzi, Mc, Brunetto, M, Bruno, S, Caliari, L, Casella, G, Civardi, F, Coco, B, Colli, A, Colombo, M, Colombo, S, Cursaro, C, Croce, Ls, Crosignani, A, Donato, F, Fabris, L, Ferrari, C, Floreani, A, Galli, A, Grattagliano, I, Lazzari, R, Macaluso, F, Marra, F, Marzioni, M, Mattalia, A, Montanari, R, Morini, L, Morisco, F, Moroni, L, Muratori, L, Muratori, P, Niro, G, Picciotto, A, Portincasa, P, Prati, D, Prisco, C, Rosina, F, Rossi, S, Selmi, C, Spinzi, G, Strazzabosco, M, Tarallo, S, Tiribelli, C, Toniutto, P, Vinci, M, Zuin, M., Invernizzi P, Ransom M, Raychaudhuri S, Kosoy R, Lleo A, Shigeta R, Franke A, Bossa F, Amos CI, Gregersen PK, Siminovitch KA, Cusi D, de Bakker PI, Podda M, Gershwin ME, Seldin MFAlmasio PL, Alvaro D, Andreone P, Andriulli A, Barlassina C, Benedetti A, Bernuzzi F, Bianchi I, Bragazzi MC, Brunetto M, Bruno S, Caliari L, Casella G, Civardi F, Coco B, Colli A, Colombo M, Colombo S, Cursaro C, Croce LS, Crosignani A, Donato F, Fabris L, Ferrari C, Floreani A, Galli A, Grattagliano I, Lazzari R, Macaluso F, Marra F, Marzioni M, Mattalia A, Montanari R, Morini L, Morisco F, Moroni L, Muratori L, Muratori P, Niro G, Picciotto A, Portincasa P, Prati D, Prisco C, Rosina F, Rossi S, Selmi C, Spinzi G, Strazzabosco M, Tarallo S, Tiribelli C, Toniutto P, Vinci M, Zuin M., Invernizzi, P., Ransom, M., Raychaudhuri, S., Kosoy, R., Lleo, A., Shigeta, R., Franke, A, Bossa, F., Amos, Ci, Gregersen, Pk, Siminovitch, Ka, Cusi, D., de Bakker, Pi, Podda, M, Gershwin, Me, Seldin, Mf, The Italian PBC Genetics Study, Group, Croce', Saveria, Tiribelli, Claudio, Invernizzi, P, Ransom, M, Raychaudhuri, S, Kosoy, R, Lleo, A, Shigeta, R, Bossa, F, Cusi, D, Morisco, Filomena, Italian PBC Genetics Study, Group, Amos, C, Gregersen, P, Siminovitch, K, de Bakker, P, Gershwin, M, Seldin, M, Almasio, P, Alvaro, D, Andreone, P, Andriulli, A, Barlassina, C, Benedetti, A, Bernuzzi, F, Bianchi, I, Bragazzi, M, Brunetto, M, Bruno, S, Caliari, L, Casella, G, Civardi, F, Coco, B, Colli, A, Colombo, M, Colombo, S, Cursaro, C, Croce, L, Crosignani, A, Donato, F, Fabris, L, Ferrari, C, Floreani, A, Galli, A, Grattagliano, I, Lazzari, R, Macaluso, F, Marra, F, Marzioni, M, Mattalia, A, Montanari, R, Morini, L, Morisco, F, Moroni, L, Muratori, L, Muratori, P, Niro, G, Picciotto, A, Portincasa, P, Prati, D, Prisco, C, Rosina, F, Rossi, S, Selmi, C, Spinzi, G, Strazzabosco, M, Tarallo, S, Tiribelli, C, Toniutto, P, Vinci, M, and Zuin, M

Subjects
AUTOIMMUNITY, PRIMARY BILIARY CIRRHOSIS, genetic risk, imputation, 0302 clinical medicine, Primary biliary cirrhosis, Gene Frequency, MED/12 - GASTROENTEROLOGIA, immune system diseases, Risk Factors, Genetic risk, skin and connective tissue diseases, HLA-DRB1, Genetics (clinical), HLA-DP beta-Chains, Oligonucleotide Array Sequence Analysis, Genetics, 0303 health sciences, Liver Cirrhosis, Biliary, antigen binding pocket, Italy, HLA-DRB1 Chain, 030211 gastroenterology & hepatology, Case-Control Studie, antigen-binding pocket, Human, musculoskeletal diseases, risk allele, European Continental Ancestry Group, Immunology, Autoimmune Diseases, autoimmune disease, Biology, Polymorphism, Single Nucleotide, White People, Article, 03 medical and health sciences, medicine, Humans, Genetic Predisposition to Disease, Allele, 030304 developmental biology, Autoimmune disease, Oligonucleotide Array Sequence Analysi, Risk Factor, HLA polymorfism, PBC, HLA-DRB1, HLA-DPB1, Hla association, medicine.disease, HLA-DP beta-Chain, Case-Control Studies, Risk allele, Imputation (genetics), Genome-Wide Association Study, HLA-DRB1 Chains
Abstract

Susceptibility to primary biliary cirrhosis (PBC) is strongly associated with human leukocyte antigen (HLA)-region polymorphisms. To determine if associations can be explained by classical HLA determinants, we studied Italian, 676 cases and 1440 controls, genotyped with dense single-nucleotide polymorphisms (SNPs) for which classical HLA alleles and amino acids were imputed. Although previous genome-wide association studies and our results show stronger SNP associations near DQB1, we demonstrate that the HLA signals can be attributed to classical DRB1 and DPB1 genes. Strong support for the predominant role of DRB1 is provided by our conditional analyses. We also demonstrate an independent association of DPB1. Specific HLA-DRB1 genes (*08, *11 and *14) account for most of the DRB1 association signal. Consistent with previous studies, DRB1*08 (P=1.59 × 10(-11)) was the strongest predisposing allele, whereas DRB1*11 (P=1.42 × 10(-10)) was protective. Additionally, DRB1*14 and the DPB1 association (DPB1*03:01; P=9.18 × 10(-7)) were predisposing risk alleles. No signal was observed in the HLA class 1 or class 3 regions. These findings better define the association of PBC with HLA and specifically support the role of classical HLA-DRB1 and DPB1 genes and alleles in susceptibility to PBC.Genes and Immunity advance online publication, 10 May 2012; doi:10.1038/gene.2012.17.

Published
2012

25. Land-Use Management Using a Soil Survey Geographic Database for Finney County, Kansas

Author

Wu, J., Ransom, M. D., Kluitenberg, G. J., Nellis, M. D., and Seyler, H. L.

Subjects
Land use -- Management, Soils -- Environmental aspects, Soil moisture -- Environmental aspects, Earth sciences
Abstract

The determination of best management practices for land resources is often complicated by the lack of a means for evaluation and lack of quality data. Soil surveys are an important source of data that can be used to improve farm and ranch planning and environmental protection. In this study, we examined the use of a soil survey geographic (SSURGO) database within a geographic information system (GIS) coupled with remote sensing data for land-use management in Finney County, Kansas. The objectives were (i) to identify land-use change; (ii) to evaluate the influence of soil, groundwater, and physiography on land use; and (iii) to assess land-use potential and present management alternatives. Land-use/land-cover (LULC) maps for 1987,1989, and 1992 were derived from Landsat Thematic Mapper data. These LULC layers were manipulated with layers: organic matter content, thickness, and texture of the surface soil horizon; land capability class; aquifer thickness (AT); and physiography. The acreage of fallow land decreased and the acreage of grassland increased from 1987 to 1992 because of an increase in the acreage of land used in the Conservation Reserve Program (CRP). Broad cropping patterns (irrigated vs. nonirrigated) did not change significantly between 1987 and 1992 and were related to AT. Some currently cropped areas had high erosion potential, whereas some grasslands had relatively low erosion hazards. These grasslands could be used as alternatives for cropping. The study demonstrates the potential of using SSURGO within a GIS coupled with remote sensing information in planning and management for natural resources.

Published
2001

26. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits

Author

Diogo, D., Bastarache, L., Liao, K.P., Graham, R.R., Fulton, R.S., Greenberg, J.D., Eyre, S., Bowes, J., Cui, J., Lee, A., Pappas, D.A., Kremer, H., Barton, A., Coenen, M.J.H., Franke, B., Kiemeney, L.A.L.M., Mariette, X., Richard-Miceli, C., Canhao, H., Fonseca, J.E., Vries, N. de, Tak, P.P., Crusius, J.B.A., Nurmohamed, M.T., Kurreeman, F., Mikuls, T.R., Okada, Y., Stahl, E.A., Larson, D.E., Deluca, T.L., O'Laughlin, M., Fronick, C.C., Fulton, L.L., Kosoy, R., Ransom, M., Bhangale, T.R., Ortmann, W., Cagan, A., Gainer, V., Karlson, E.W., Kohane, I., Murphy, S.N., Martin, J., Zhernakova, A., Klareskog, L., Padyukov, L., Worthington, J., Mardis, E.R., Seldin, M.F., Gregersen, P.K., Behrens, T., Raychaudhuri, S., Denny, J.C., Plenge, R.M., Diogo, D., Bastarache, L., Liao, K.P., Graham, R.R., Fulton, R.S., Greenberg, J.D., Eyre, S., Bowes, J., Cui, J., Lee, A., Pappas, D.A., Kremer, H., Barton, A., Coenen, M.J.H., Franke, B., Kiemeney, L.A.L.M., Mariette, X., Richard-Miceli, C., Canhao, H., Fonseca, J.E., Vries, N. de, Tak, P.P., Crusius, J.B.A., Nurmohamed, M.T., Kurreeman, F., Mikuls, T.R., Okada, Y., Stahl, E.A., Larson, D.E., Deluca, T.L., O'Laughlin, M., Fronick, C.C., Fulton, L.L., Kosoy, R., Ransom, M., Bhangale, T.R., Ortmann, W., Cagan, A., Gainer, V., Karlson, E.W., Kohane, I., Murphy, S.N., Martin, J., Zhernakova, A., Klareskog, L., Padyukov, L., Worthington, J., Mardis, E.R., Seldin, M.F., Gregersen, P.K., Behrens, T., Raychaudhuri, S., Denny, J.C., and Plenge, R.M.

Abstract

Contains fulltext : 154077.pdf (publisher's version ) (Open Access), Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3 x 10(-21)), A928V (rs35018800, OR = 0.53, P = 1.2 x 10(-9)), and I684S (rs12720356, OR = 0.86, P = 4.6 x 10(-7)). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6 x 10(-18)), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P(omnibus) = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.

Published
2015

28. A Rapier and its Scabbard from West Row, Suffolk

Author

Coles, John M, Trump, B A V A V, and Ransom, M E

Abstract

Proceedings of the Cambridge Antiquarian Society, 60, 1-6, TL 663754. The earliest known scabbard remains of the British MBA appear on a rapier of Lisburn type recently found during ploughing. The low-set rivets of the rapier place it in a localised sub-group, probably of 11th cent BC. The scabbard was of flat hazel laths held together by strips of sheet bronze or copper and glued rather than pinned. The hilt has not survived, and the lack of hiltmark suggests the weapon was lost or buried in its scabbard while still quite new.

Published
2008
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29. Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants.

Author

Juran, B, Hirschfield, G, Invernizzi, P, Atkinson, E, Li, Y, Xie, G, Kosoy, R, Ransom, M, Sun, Y, Bianchi, I, Schlicht, E, Lleo, A, Coltescu, C, Bernuzzi, F, Podda, M, Lammert, C, Shigeta, R, Chan, L, Balschun, T, Marconi, M, Cusi, D, Heathcote, E, Mason, A, Myers, R, Milkiewicz, P, Odin, J, Luketic, V, Bacon, B, Bodenheimer, H, Liakina, V, Vincent, C, Levy, C, Franke, A, Gregersen, P, Bossa, F, Gershwin, M, Deandrade, M, Amos, C, Italian PBC Genetics Study, G, Lazaridis, K, Seldin, M, Siminovitch, K, Almasio, P, Alvaro, D, Andreone, P, Andriulli, A, Barlassina, C, Battezzati, P, Benedetti, A, Bragazzi, M, Brunetto, M, Bruno, S, Caliari, L, Casella, G, Civardi, F, Coco, B, Colli, A, Colombo, M, Colombo, S, Cursaro, C, Crocè, L, Crosignani, A, Donato, F, Fabris, L, Ferrari, C, Floreani, A, Fontana, R, Galli, A, Grattagliano, I, Lazzari, R, Macaluso, F, Malinverno, F, Marra, F, Marzioni, M, Mascia, E, Mattalia, A, Montanari, R, Morini, L, Morisco, F, Muratori, L, Muratori, P, Niro, G, Picciotto, A, Portincasa, P, Prati, D, Rosina, F, Rossi, S, Selmi, C, Spinzi, G, Strazzabosco, M, Tarallo, S, Tiribelli, C, Toniutto, P, Vinci, M, Zuin, M, Juran, BD, Hirschfield, GM, INVERNIZZI, PIETRO, Atkinson, EJ, Schlicht, EM, Bernuzzi, Francesca Veronica, Chan, LL, Heathcote, EJ, Mason, AL, Myers, RP, Odin, JA, Luketic, VA, Bacon, BR, Bodenheimer, HC Jr, Gregersen, PK, Gershwin, ME, deAndrade, M, Amos, CI, Italian PBC Genetics Study Group, Lazaridis, KN, Seldin, MF, Siminovitch, KA, Almasio, PL, Battezzati, PM, Crocè, LS, Niro, GA, STRAZZABOSCO, MARIO, Zuin, M., Juran, B, Hirschfield, G, Invernizzi, P, Atkinson, E, Li, Y, Xie, G, Kosoy, R, Ransom, M, Sun, Y, Bianchi, I, Schlicht, E, Lleo, A, Coltescu, C, Bernuzzi, F, Podda, M, Lammert, C, Shigeta, R, Chan, L, Balschun, T, Marconi, M, Cusi, D, Heathcote, E, Mason, A, Myers, R, Milkiewicz, P, Odin, J, Luketic, V, Bacon, B, Bodenheimer, H, Liakina, V, Vincent, C, Levy, C, Franke, A, Gregersen, P, Bossa, F, Gershwin, M, Deandrade, M, Amos, C, Italian PBC Genetics Study, G, Lazaridis, K, Seldin, M, Siminovitch, K, Almasio, P, Alvaro, D, Andreone, P, Andriulli, A, Barlassina, C, Battezzati, P, Benedetti, A, Bragazzi, M, Brunetto, M, Bruno, S, Caliari, L, Casella, G, Civardi, F, Coco, B, Colli, A, Colombo, M, Colombo, S, Cursaro, C, Crocè, L, Crosignani, A, Donato, F, Fabris, L, Ferrari, C, Floreani, A, Fontana, R, Galli, A, Grattagliano, I, Lazzari, R, Macaluso, F, Malinverno, F, Marra, F, Marzioni, M, Mascia, E, Mattalia, A, Montanari, R, Morini, L, Morisco, F, Muratori, L, Muratori, P, Niro, G, Picciotto, A, Portincasa, P, Prati, D, Rosina, F, Rossi, S, Selmi, C, Spinzi, G, Strazzabosco, M, Tarallo, S, Tiribelli, C, Toniutto, P, Vinci, M, Zuin, M, Juran, BD, Hirschfield, GM, INVERNIZZI, PIETRO, Atkinson, EJ, Schlicht, EM, Bernuzzi, Francesca Veronica, Chan, LL, Heathcote, EJ, Mason, AL, Myers, RP, Odin, JA, Luketic, VA, Bacon, BR, Bodenheimer, HC Jr, Gregersen, PK, Gershwin, ME, deAndrade, M, Amos, CI, Italian PBC Genetics Study Group, Lazaridis, KN, Seldin, MF, Siminovitch, KA, Almasio, PL, Battezzati, PM, Crocè, LS, Niro, GA, STRAZZABOSCO, MARIO, and Zuin, M.

Abstract

To further characterize the genetic basis of primary biliary cirrhosis (PBC), we genotyped 2426 PBC patients and 5731 unaffected controls from three independent cohorts using a single nucleotide polymorphism (SNP) array (Immunochip) enriched for autoimmune disease risk loci. Meta-analysis of the genotype data sets identified a novel disease-associated locus near the TNFSF11 gene at 13q14, provided evidence for association at six additional immune-related loci not previously implicated in PBC and confirmed associations at 19 of 22 established risk loci. Results of conditional analyses also provided evidence for multiple independent association signals at four risk loci, with haplotype analyses suggesting independent SNP effects at the 2q32 and 16p13 loci, but complex haplotype driven effects at the 3q25 and 6p21 loci. By imputing classical HLA alleles from this data set, four class II alleles independently contributing to the association signal from this region were identified. Imputation of genotypes at the non-HLA loci also provided additional associations, but none with stronger effects than the genotyped variants. An epistatic interaction between the IL12RB2 risk locus at 1p31and the IRF5 risk locus at 7q32 was also identified and suggests a complementary effect of these loci in predisposing to disease. These data expand the repertoire of genes with potential roles in PBC pathogenesis that need to be explored by follow-up biological studies.

Published
2012

30. Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis

Author

Liu, X, Invernizzi, P, Lu, Y, Kosoy, R, Bianchi, I, Podda, M, Xu, C, Xie, G, Macciardi, F, Selmi, C, Lupoli, S, Shigeta, R, Ransom, M, Lleo, A, Lee, A, Mason, A, Myers, R, Peltekian, K, Ghent, C, Bernuzzi, F, Zuin, M, Rosina, F, Borghesio, E, Floreani, A, Lazzari, R, Niro, G, Andriulli, A, Muratori, L, Muratori, P, Almasio, P, Andreone, P, Margotti, M, Brunetto, M, Coco, B, Alvaro, D, Bragazzi, M, Marra, F, Pisano, A, Rigamonti, C, Colombo, M, Marzioni, M, Benedetti, A, Fabris, L, Strazzabosco, M, Portincasa, P, Palmieri, V, Tiribelli, C, Croce, L, Bruno, S, Rossi, S, Vinci, M, Prisco, C, Mattalia, A, Toniutto, P, Picciotto, A, Galli, A, Ferrari, C, Colombo, S, Casella, G, Morini, L, Caporaso, N, Colli, A, Spinzi, G, Montanari, R, Gregersen, P, Heathcote, E, Hirschfield, G, Siminovitch, K, Amos, C, Gershwin, M, Seldin, M, INVERNIZZI, PIETRO, Lee, AT, Mason, AL, Myers, RP, Peltekian, KM, Ghent, CN, Bernuzzi, Francesca Veronica, Almasio, PL, Bragazzi, MC, STRAZZABOSCO, MARIO, Palmieri, VO, Gregersen, PK, Heathcote, EJ, Hirschfield, GM, Siminovitch, KA, Amos, CI, Gershwin, ME, Seldin, MF, Liu, X, Invernizzi, P, Lu, Y, Kosoy, R, Bianchi, I, Podda, M, Xu, C, Xie, G, Macciardi, F, Selmi, C, Lupoli, S, Shigeta, R, Ransom, M, Lleo, A, Lee, A, Mason, A, Myers, R, Peltekian, K, Ghent, C, Bernuzzi, F, Zuin, M, Rosina, F, Borghesio, E, Floreani, A, Lazzari, R, Niro, G, Andriulli, A, Muratori, L, Muratori, P, Almasio, P, Andreone, P, Margotti, M, Brunetto, M, Coco, B, Alvaro, D, Bragazzi, M, Marra, F, Pisano, A, Rigamonti, C, Colombo, M, Marzioni, M, Benedetti, A, Fabris, L, Strazzabosco, M, Portincasa, P, Palmieri, V, Tiribelli, C, Croce, L, Bruno, S, Rossi, S, Vinci, M, Prisco, C, Mattalia, A, Toniutto, P, Picciotto, A, Galli, A, Ferrari, C, Colombo, S, Casella, G, Morini, L, Caporaso, N, Colli, A, Spinzi, G, Montanari, R, Gregersen, P, Heathcote, E, Hirschfield, G, Siminovitch, K, Amos, C, Gershwin, M, Seldin, M, INVERNIZZI, PIETRO, Lee, AT, Mason, AL, Myers, RP, Peltekian, KM, Ghent, CN, Bernuzzi, Francesca Veronica, Almasio, PL, Bragazzi, MC, STRAZZABOSCO, MARIO, Palmieri, VO, Gregersen, PK, Heathcote, EJ, Hirschfield, GM, Siminovitch, KA, Amos, CI, Gershwin, ME, and Seldin, MF

Abstract

A genome-wide association screen for primary biliary cirrhosis risk alleles was performed in an Italian cohort. The results from the Italian cohort replicated IL12A and IL12RB associations, and a combined meta-analysis using a Canadian dataset identified newly associated loci at SPIB (P = 7.9 × 10−11, odds ratio (OR) = 1.46), IRF5-TNPO3 (P = 2.8 × 10−10, OR = 1.63) and 17q12-21 (P = 1.7 × 10−10, OR = 1.38).

Published
2010

31. Amerindian ancestry in Argentina is associated with increased risk for systemic lupus erythematosus

Author

Seldin, M. F., Qi, L., Scherbarth, H. R., Tian, C., Ransom, M., Silva, G., Belmont, J. W., Gamron, S., Allievi, A., Palatnik, S. A., Saurit, V., Paira, S., Graf, C., Guillerón, C., Catoggio, L. J., Prigione, C., Berbotto, G. A., García, M. A., Perandones, C. E., Truedsson, L., Abderrahim, H., Battagliotti, C. G., Pons-Estel, B. A., Alarcon-Riquelme, Marta E., Seldin, M. F., Qi, L., Scherbarth, H. R., Tian, C., Ransom, M., Silva, G., Belmont, J. W., Gamron, S., Allievi, A., Palatnik, S. A., Saurit, V., Paira, S., Graf, C., Guillerón, C., Catoggio, L. J., Prigione, C., Berbotto, G. A., García, M. A., Perandones, C. E., Truedsson, L., Abderrahim, H., Battagliotti, C. G., Pons-Estel, B. A., and Alarcon-Riquelme, Marta E.

Abstract

Previous studies have demonstrated that in admixed populations, West African ancestry is associated with an increased prevalence of systemic lupus erythematosus (SLE). In the current study, the effect of Amerindian ancestry in SLE was examined in an admixed population in Argentina. The Argentine population is predominantly European with approximately 20% Amerindian admixture, and a very small (<2%) contribution from West Africa. The results indicate that Amerindian admixture in this population is associated with a substantial increase in SLE susceptibility risk (Odds Ratio=7.94, P=0.00006). This difference was not due to known demographic factors, including site of collection, age and gender. In addition, there were trends towards significance for Amerindian ancestry influencing renal disease, age of onset and anti-SSA antibodies. These studies suggest that populations with Amerindian admixture, like those with West African admixture, should be considered in future studies to identify additional allelic variants that predispose to SLE.

Published
2008
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32. 1400 DISCOVERY OF A DIRECT ASSOCIATION BETWEEN PRIMARY BILIARY CIRRHOSIS AND LOW BONE MASS: IDENTIFICATION OF TNFSF11/RANKL AS A RISK LOCUS FOR PATIENTS WITH PBC

Author

Hirschfield, G.M., primary, Juran, B.D., additional, Invernizzi, P., additional, Atkinson, E.J., additional, Li, Y., additional, Xie, G., additional, Kosoy, R., additional, Ransom, M., additional, Sun, Y., additional, Bianchi, I., additional, Schlicht, E.M., additional, Lleo, A., additional, Coltescu, C., additional, Bernuzzi, F., additional, Lammert, C., additional, Shigetta, R., additional, Chan, L.L., additional, Balschun, T., additional, Marconi, M., additional, Cusi, D., additional, Mason, A.L., additional, Myers, R.P., additional, Milkiewicz, P., additional, Odin, J.A., additional, Luketic, V.A., additional, Bacon, B., additional, Bodenheimer, H., additional, Liakina, V., additional, Vincent, C., additional, Levy, C., additional, Franke, A., additional, Gregerson, P.K., additional, Annese, V., additional, Gershwin, M.E., additional, de Andrade, M., additional, Amos, C.I., additional, Lazaridis, K.N., additional, Seldin, M.F., additional, and Siminovitch, K.A., additional

Published
2012
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33. LADTs: what are the characteristics?

Author

Ransom, M. Niel

Subjects
Packet switching -- Design and construction, Data communications -- Design and construction, Business, Telecommunications industry
Published
1984

42. USING LAW AND POLICY TO ADDRESS CHEMICAL EXPOSURES: EXAMINING FEDERAL AND STATE APPROACHES.

Author

SHIBLEY, G., FARQUHAR, D., RANSOM, M., and CAUCCI, L.

Subjects
HEALTH policy, TOXIC substance exposure, UNITED States. Pure Food & Drug Act of 1906, HAZARDS, FEDERAL Insecticide, Fungicide & Rodenticide Act (U.S.), GOVERNMENT policy, PREVENTION, LAW
Abstract

The article focuses on federal and state policy approaches for addressing chemical exposures in the U.S with reference to laws relevant to consumer and household exposures. Topics discussed include state efforts to restrict or regulate harmful chemical exposures, the U.S Pure Food & Drug Act of 1906 as well as the Insecticide, Fungicide, and Rodenticide Act and the attempts made by the U.S Department of Health and Human Services in protection of human health from environmental hazards.

Published
2014

50. Identification of hormonal parameters for successful systemic single-dose methotrexate therapy in ectopic pregnancy.

Author

Corsan, Gregory H., Karacan, Meric, Qasim, Suna, Bohrer, Michael K., Ransom, Mark X., Kemmann, Ekkehard, Corsan, G H, Karacan, M, Qasim, S, Bohrer, M K, Ransom, M X, and Kemmann, E

Abstract

Single-dose methotrexate is an alternative to surgery in treating ectopic pregnancy. Because success rates vary, we sought to identify factors which predict treatment outcome. A total of 44 women with ectopic gestation were treated. The non-laparoscopic diagnosis of ectopic pregnancy was made following history, physical examination, ultrasound, endometrial biopsy and the measurement of serial beta-human chorionic gonadotrophin (HCG) and progesterone concentrations. Methotrexate (50 mg/m2 i.m.) was administered, with a second dose given 1 week later in patients with plateauing or rising beta-HCG concentrations. Of 44 patients, 23 (52.3%) were successfully treated with one dose. An additional 10 women (22.7%) were also successfully managed but required a second dose, giving an overall success rate of 75.0%. In all, 11 women (25.0%) required surgery, four of whom experienced tubal rupture. Receiver operator curves were constructed to optimally select pretreatment beta-HCG and progesterone cut-off concentrations for successful treatment. Using beta-HCG < 1500 IU/l or progesterone < 7.0 ng/ml (22.3 nmol/l) as a cut-off concentration produced a diagnostic test with a sensitivity of 87.5%, a specificity of 90.0%, a positive predictive value of 96.6% and a negative predictive value of 69.2%. Conversely, this model predicts that patients with serum beta-HCG concentrations > or = 1500 IU/l and progesterone concentrations > or = 7.0 ng/ml are at far greater risk of failing single-dose methotrexate therapy. [ABSTRACT FROM AUTHOR]

Published
1995

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