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3. A retrospective cohort study of bacterial native vertebral osteomyelitis and its management in the UK

Author

Bousfield, R, Ramsay, I, Warne, B, Kotecha, D, Mitchell, T, Sandoe, J, Moore, E, Nickerson, E, Kirby, A, Enoch, D, and the NITCAR Collaborative

Abstract

Background: Bacterial native vertebral osteomyelitis (NVO) can present diagnostic and therapeutic challenges leading to high levels of morbidity and mortality. To inform strategies aimed at improving outcomes in these patients, data are needed on the current aetiology, diagnostic interventions, management and risk factors for treatment failure. Methods: This was a retrospective, multicentre, observational cohort study of adult patients with bacterial NVO across the UK between 1st January 2015 and 31st December 2016. Infectious Disease Society of America (IDSA) guideline standards were selected and used to audit practice relating to the management of these patients. Results: A total of 286 patients were included from 40 hospitals. An organism was identified in 61% of cases by blood culture or biopsy. Of these, 51% were due to Staphylococcus aureus and 12% were due to Gram-negative bacteria. When performed, biopsy obtained a microbiological diagnosis in 50% of cases. Nearly 10% of patients required admission to an Intensive Care Unit, 20% were re-admitted to hospital, 56% experienced complications and 6% died within 90 days. Higher Charlson comorbidity index (CCI) was significantly associated with treatment failure at one month (p = 0.004). Conclusions: This study identified opportunities to improve UK practice in the investigation and management of bacterial NVO. The range of organisms isolated supports the use of diagnostic biopsy where blood cultures are non-diagnostic, to guide antimicrobial therapy and strive to avoid treatment failure or complications. This study shows a clear need for antibiotic guidelines to reflect the current aetiology of NVO and authors support the creation of a formal registry.

Published
2021

4. Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p-derived miRNA hairpin loop sequences

Author

Pugh, T J, Yu, W, Yang, J, Field, A L, Ambrogio, L, Carter, S L, Cibulskis, K, Giannikopoulos, P, Kiezun, A, Kim, J, McKenna, A, Nickerson, E, Getz, G, Hoffher, S, Messinger, Y H, Dehner, L P, Roberts, C WM, Rodriguez-Galindo, C, Williams, G M, Rossi, C T, Meyerson, M, and Hill, D A

Published
2014
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11. Panton-Valentine leucocidin positive CC121 strain methicillin-sensitive Staphylococcus aureus is associated with pyomyositis in Cambodian children

Author

Young, B, Soeng, S, Sar, P, Kumar, V, Sar, V, Hor, S, Bousfield, R, Emary, K, Nickerson, E, Stoesser, N, Parry, C, Day, N, Wilson, D, and Moore, C

Abstract

Background: Pyomyositis is primarily a disease primarily of children in tropical regions. 90% of cases are caused by Staphylococcus aureus. Only small case series have been reported, and the bacterial genetic factors underlying this disease are incompletely understood. We present a genome wide association study of S. aureus isolated from pyomyositis and asymptomatic carriage from the same human paediatric population. Material/methods: Bacterial isolates were identified from 102 children, attending Angkor Hospital for Children in Siem Reap, Cambodia over a six-year period 2007-12, who had a clinical diagnosis of pyomyositis and S. aureus cultured from the abscess samples. 418 S. aureus nasal carriers were identified from two studies of S. aureus carriage in the same population in 2008 (n=222) and 2012 (n=196). A single isolate was cultured from each clinical sample and underwent whole-genome sequencing on the Illumina HiSeq platform, yielding 520 high quality sequences. Single nucleotide polymorphisms (SNPs) were identified after mapping reads against a reference genome (MRSA252) and de novo assembly was performed using Velvet. We tested for loci associated with pyomyositis by performing association testing for all SNPs and short sequences (kmers) using Gemma, which controls for bacterial population structure. We examined strains associated with pyomyositis using Bugwas, which identifies bacterial lineages and tests them for association with phenotype. Multi-locus sequence type was determined in silico using blast. Results: The phylogeny of S. aureus isolated from asymptomatic carriage and pyomyositis shows that 87/102 (85%) of pyomyositis isolates are found within a single clade (Figure) (p=1.6x10-30). These isolates belong to Clonal Complex (CC) 121. In contrast, carriage isolates include a global diversity of global lineages, including CC121, as well as CC1, CC5, CC15, CC45. Strikingly, 41 carriage isolates form a sub-clade within CC121 and no cases of pyomyositis are observed in this sub-clade. This lineage is strongly associated with carriage rather than pyomyositis (p=4x10-14). Both CC121 lineages were found as asymptomatic carriers in 2008 and 2012. In addition to lineage effects, we find a strong association between the presence of Panton-Valentine leucocidin (PVL) and pyomyositis, even after controlling for population structure (p=5x10-20). Kmers mapping to PVL were found in 99/102 (97%) of pyomyositis isolates, compared with 84/418 (20%) of carriage isolates. PVL is a known S. aureus virulence factor, and is often carried by CC121, but is absent from the protective carriage sub-clade. PVL was not limited to CC121 isolates in this study, but is found in multiple lineages (Figure). Conclusions: We have discovered strong evidence for bacterial genetic determinants for this relatively neglected, serious bacterial disease using a non-selective method with no prior assumptions. We find both lineage and gene specific effects, with an overwhelming association between PVL and pyomyositis in Cambodian children.

Published
2017

18. CPHLN recommendations for the laboratory detection of Shiga toxin-producing (O157 and non-O157).

Author

Chui, L., Christianson, S., Alexander, D. C., Arseneau, V., Bekal, S., Berenger, B., Chen, Y., Davidson, R., Farrell, D. J., German, G. J., Gilbert, L., Hoang, L. M. N., Johnson, R. P., MacKeen, A., Maki, A., Nadon, C., Nickerson, E., Peralta, A., Arneson, S. M. Radons, and Yu, Y.

Subjects
ESCHERICHIA coli, PUBLIC health, ENZYME-linked immunosorbent assay, FOOD safety, MEDICAL care
Abstract

Shiga toxin-producing Escherichia coli (STEC) are important enteric pathogens responsible for sporadic cases and outbreaks of gastroenteritis. E.coli O157:H7/NM (STEC O157) are the most commonly known STEC serotypes but it is now increasingly apparent that non-O157 STEC serotypes have been underreported in the past because they were not part of routine screening in many front-line laboratories. The Canadian Public Health Laboratory Network (CPHLN) has identified the need for improved detection and surveillance of non-O157 STEC and has developed the following recommendations to assist in the decision-making process for clinical and reference microbiology laboratories. These recommendations should be followed to the best of a laboratory's abilities based on the availability of technology and resources. The CPHLN recommends that when screening for the agents of bacterial gastroenteritis from a stool sample, front-line laboratories use either a chromogenic agar culture or a culture-independent diagnostic test (CIDT). CIDT options include nucleic acid amplification tests (NAATs) to detect Shiga toxin genes or enzyme immunoassays (EIAs) to detect Shiga toxins. If either CIDT method is positive for possible STEC, laboratories must have a mechanism to culture and isolate STEC in order to support both provincial and national surveillance as well as outbreak investigations and response. These CPHLN recommendations should result in improved detection of STEC in patients presenting with diarrhea, especially when due to the non-O157 serotypes. These measures should enhance the overall quality of healthcare and food safety, and provide better protection of the public via improved surveillance and outbreak detection and response. [ABSTRACT FROM AUTHOR]

Published
2018
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19. CPHLN recommendations for the laboratory detection of Shiga toxin-producing Escherichia coli (O157 and non-O157).

Author

Chui, L., Christianson, S., Alexander, D. C., Arseneau, V., Bekal, S., Berenger, B., Chen, Y., Davidson, R., Farrell, D. J., German, G. J., Gilbert, L., Hoang, L. M. N., Johnson, R. P., MacKeen, A., Maki, A., Nadon, C., Nickerson, E., Peralta, A., Arneson, S. M. Radons, and Yu, Y.

Subjects
GASTROENTERITIS, ESCHERICHIA coli, FOOD pathogens, NUCLEIC acid analysis, NUCLEIC acids, NUCLEIC acid amplification techniques
Abstract

Shiga toxin-producing Escherichia coli (STEC) are important enteric pathogens responsible for sporadic cases and outbreaks of gastroenteritis. E.coli O157:H7/NM (STEC O157) are the most commonly known STEC serotypes but it is now increasingly apparent that non-O157 STEC serotypes have been underreported in the past because they were not part of routine screening in many front-line laboratories. The Canadian Public Health Laboratory Network (CPHLN) has identified the need for improved detection and surveillance of non-O157 STEC and has developed the following recommendations to assist in the decision-making process for clinical and reference microbiology laboratories. These recommendations should be followed to the best of a laboratory's abilities based on the availability of technology and resources. The CPHLN recommends that when screening for the agents of bacterial gastroenteritis from a stool sample, front-line laboratories use either a chromogenic agar culture or a culture-independent diagnostic test (CIDT). CIDT options include nucleic acid amplification tests (NAATs) to detect Shiga toxin genes or enzyme immunoassays (EIAs) to detect Shiga toxins. If either CIDT method is positive for possible STEC, laboratories must have a mechanism to culture and isolate STEC in order to support both provincial and national surveillance as well as outbreak investigations and response. These CPHLN recommendations should result in improved detection of STEC in patients presenting with diarrhea, especially when due to the non-O157 serotypes. These measures should enhance the overall quality of healthcare and food safety, and provide better protection of the public via improved surveillance and outbreak detection and response. [ABSTRACT FROM AUTHOR]

Published
2018
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23. OMICS AND PROGNSTIC MARKERS

Author

Adachi, K., primary, Sasaki, H., additional, Nagahisa, S., additional, Yoshida, K., additional, Hattori, N., additional, Nishiyama, Y., additional, Kawase, T., additional, Hasegawa, M., additional, Abe, M., additional, Hirose, Y., additional, Alentorn, A., additional, Marie, Y., additional, Poggioli, S., additional, Alshehhi, H., additional, Boisselier, B., additional, Carpentier, C., additional, Mokhtari, K., additional, Capelle, L., additional, Figarella-Branger, D., additional, Hoang-Xuan, K., additional, Sanson, M., additional, Delattre, J.-Y., additional, Idbaih, A., additional, Yust-Katz, S., additional, Anderson, M., additional, Olar, A., additional, Eterovic, A., additional, Ezzeddine, N., additional, Chen, K., additional, Zhao, H., additional, Fuller, G., additional, Aldape, K., additional, de Groot, J., additional, Andor, N., additional, Harness, J., additional, Lopez, S. G., additional, Fung, T. L., additional, Mewes, H. W., additional, Petritsch, C., additional, Arivazhagan, A., additional, Somasundaram, K., additional, Thennarasu, K., additional, Pandey, P., additional, Anandh, B., additional, Santosh, V., additional, Chandramouli, B., additional, Hegde, A., additional, Kondaiah, P., additional, Rao, M., additional, Bell, R., additional, Kang, R., additional, Hong, C., additional, Song, J., additional, Costello, J., additional, Nagarajan, R., additional, Zhang, B., additional, Diaz, A., additional, Wang, T., additional, Bie, L., additional, Li, Y., additional, Liu, H., additional, Luyo, W. F. C., additional, Carnero, M. H., additional, Iruegas, M. E. P., additional, Morell, A. R., additional, Figueiras, M. C., additional, Lopez, R. L., additional, Valverde, C. F., additional, Chan, A. K.-Y., additional, Pang, J. C.-S., additional, Chung, N. Y.-F., additional, Li, K. K.-W., additional, Poon, W. S., additional, Chan, D. T.-M., additional, Wang, Y., additional, Ng, H.-a. K., additional, Chaumeil, M., additional, Larson, P., additional, Yoshihara, H., additional, Vigneron, D., additional, Nelson, S., additional, Pieper, R., additional, Phillips, J., additional, Ronen, S., additional, Clark, V., additional, Omay, Z. E., additional, Serin, A., additional, Gunel, J., additional, Omay, B., additional, Grady, C., additional, Youngblood, M., additional, Bilguvar, K., additional, Baehring, J., additional, Piepmeier, J., additional, Gutin, P., additional, Vortmeyer, A., additional, Brennan, C., additional, Pamir, M. N., additional, Kilic, T., additional, Krischek, B., additional, Simon, M., additional, Yasuno, K., additional, Gunel, M., additional, Cohen, A. L., additional, Sato, M., additional, Aldape, K. D., additional, Mason, C., additional, Diefes, K., additional, Heathcock, L., additional, Abegglen, L., additional, Shrieve, D., additional, Couldwell, W., additional, Schiffman, J. D., additional, Colman, H., additional, D'Alessandris, Q. G., additional, Cenci, T., additional, Martini, M., additional, Ricci-Vitiani, L., additional, De Maria, R., additional, Larocca, L. M., additional, Pallini, R., additional, Theeler, B., additional, Lang, F., additional, Rao, G., additional, Gilbert, M., additional, Sulman, E., additional, Luthra, R., additional, Eterovic, K., additional, Routbort, M., additional, Verhaak, R., additional, Mills, G., additional, Mendelsohn, J., additional, Meric-Bernstam, F., additional, Yung, A., additional, MacArthur, K., additional, Hahn, S., additional, Kao, G., additional, Lustig, R., additional, Alonso-Basanta, M., additional, Chandrasekaran, S., additional, Wileyto, E. P., additional, Reyes, E., additional, Dorsey, J., additional, Fujii, K., additional, Kurozumi, K., additional, Ichikawa, T., additional, Onishi, M., additional, Ishida, J., additional, Shimazu, Y., additional, Kaur, B., additional, Chiocca, E. A., additional, Date, I., additional, Geisenberger, C., additional, Mock, A., additional, Warta, R., additional, Schwager, C., additional, Hartmann, C., additional, von Deimling, A., additional, Abdollahi, A., additional, Herold-Mende, C., additional, Gevaert, O., additional, Achrol, A., additional, Gholamin, S., additional, Mitra, S., additional, Westbroek, E., additional, Loya, J., additional, Mitchell, L., additional, Chang, S., additional, Steinberg, G., additional, Plevritis, S., additional, Cheshier, S., additional, Xu, J., additional, Napel, S., additional, Zaharchuk, G., additional, Harsh, G., additional, Gutman, D., additional, Holder, C., additional, Colen, R., additional, Dunn, W., additional, Jain, R., additional, Cooper, L., additional, Hwang, S., additional, Flanders, A., additional, Brat, D., additional, Hayes, J., additional, Droop, A., additional, Thygesen, H., additional, Boissinot, M., additional, Westhead, D., additional, Short, S., additional, Lawler, S., additional, Bady, P., additional, Kurscheid, S., additional, Delorenzi, M., additional, Hegi, M. E., additional, Crosby, C., additional, Faulkner, C., additional, Smye-Rumsby, T., additional, Kurian, K., additional, Williams, M., additional, Hopkins, K., additional, Palmer, A., additional, Williams, H., additional, Wragg, C., additional, Haynes, H. R., additional, Kurian, K. M., additional, White, P., additional, Oka, T., additional, Jalbert, L., additional, Elkhaled, A., additional, Jensen, R., additional, Salzman, K., additional, Schabel, M., additional, Gillespie, D., additional, Mumert, M., additional, Johnson, B., additional, Mazor, T., additional, Barnes, M., additional, Yamamoto, S., additional, Ueda, H., additional, Tatsuno, K., additional, Aihara, K., additional, Bollen, A., additional, Hirst, M., additional, Marra, M., additional, Mukasa, A., additional, Saito, N., additional, Aburatani, H., additional, Berger, M., additional, Taylor, B., additional, Popov, S., additional, Mackay, A., additional, Ingram, W., additional, Burford, A., additional, Jury, A., additional, Vinci, M., additional, Jones, C., additional, Jones, D. T. W., additional, Hovestadt, V., additional, Picelli, S., additional, Wang, W., additional, Northcott, P. A., additional, Kool, M., additional, Reifenberger, G., additional, Pietsch, T., additional, Sultan, M., additional, Lehrach, H., additional, Yaspo, M.-L., additional, Borkhardt, A., additional, Landgraf, P., additional, Eils, R., additional, Korshunov, A., additional, Zapatka, M., additional, Radlwimmer, B., additional, Pfister, S. M., additional, Lichter, P., additional, Joy, A., additional, Smirnov, I., additional, Reiser, M., additional, Shapiro, W., additional, Kim, S., additional, Feuerstein, B., additional, Jungk, C., additional, Friauf, S., additional, Unterberg, A., additional, Juratli, T. A., additional, McElroy, J., additional, Meng, W., additional, Huebner, A., additional, Geiger, K. D., additional, Krex, D., additional, Schackert, G., additional, Chakravarti, A., additional, Lautenschlaeger, T., additional, Kim, B. Y., additional, Jiang, W., additional, Beiko, J., additional, Prabhu, S., additional, DeMonte, F., additional, Sawaya, R., additional, Cahill, D., additional, McCutcheon, I., additional, Lau, C., additional, Wang, L., additional, Terashima, K., additional, Yamaguchi, S., additional, Burstein, M., additional, Sun, J., additional, Suzuki, T., additional, Nishikawa, R., additional, Nakamura, H., additional, Natsume, A., additional, Terasaka, S., additional, Ng, H.-K., additional, Muzny, D., additional, Gibbs, R., additional, Wheeler, D., additional, Zhang, X.-q., additional, Sun, S., additional, Lam, K.-f., additional, Kiang, K. M. Y., additional, Pu, J. K. S., additional, Ho, A. S. W., additional, Leung, G. K. K., additional, Loebel, F., additional, Curry, W. T., additional, Barker, F. G., additional, Lelic, N., additional, Chi, A. S., additional, Cahill, D. P., additional, Lu, D., additional, Yin, J., additional, Teo, C., additional, McDonald, K., additional, Madhankumar, A., additional, Weston, C., additional, Slagle-Webb, B., additional, Sheehan, J., additional, Patel, A., additional, Glantz, M., additional, Connor, J., additional, Maire, C., additional, Francis, J., additional, Zhang, C.-Z., additional, Jung, J., additional, Manzo, V., additional, Adalsteinsson, V., additional, Homer, H., additional, Blumenstiel, B., additional, Pedamallu, C. S., additional, Nickerson, E., additional, Ligon, A., additional, Love, C., additional, Meyerson, M., additional, Ligon, K., additional, Jalbert, L. E., additional, Nelson, S. J., additional, Bollen, A. W., additional, Smirnov, I. V., additional, Song, J. S., additional, Olshen, A. B., additional, Berger, M. S., additional, Chang, S. M., additional, Taylor, B. S., additional, Costello, J. F., additional, Mehta, S., additional, Armstrong, B., additional, Peng, S., additional, Bapat, A., additional, Berens, M., additional, Melendez, B., additional, Mollejo, M., additional, Mur, P., additional, Hernandez-Iglesias, T., additional, Fiano, C., additional, Ruiz, J., additional, Rey, J. A., additional, Stadler, V., additional, Schulte, A., additional, Lamszus, K., additional, Schichor, C., additional, Westphal, M., additional, Tonn, J.-C., additional, Morozova, O., additional, Katzman, S., additional, Grifford, M., additional, Salama, S., additional, Haussler, D., additional, Olshen, A., additional, Fouse, S., additional, Nakamizo, S., additional, Sasayama, T., additional, Tanaka, H., additional, Tanaka, K., additional, Mizukawa, K., additional, Yoshida, M., additional, Kohmura, E., additional, Northcott, P., additional, Jones, D., additional, Pfister, S., additional, Otani, R., additional, Takayanagi, S., additional, Saito, K., additional, Tanaka, S., additional, Shin, M., additional, Ozawa, T., additional, Riester, M., additional, Cheng, Y.-K., additional, Huse, J., additional, Helmy, K., additional, Charles, N., additional, Squatrito, M., additional, Michor, F., additional, Holland, E., additional, Perrech, M., additional, Dreher, L., additional, Rohn, G., additional, Goldbrunner, R., additional, Timmer, M., additional, Pollo, B., additional, Palumbo, V., additional, Calatozzolo, C., additional, Patane, M., additional, Nunziata, R., additional, Farinotti, M., additional, Silvani, A., additional, Lodrini, S., additional, Finocchiaro, G., additional, Lopez, E., additional, Rioscovian, A., additional, Ruiz, R., additional, Siordia, G., additional, de Leon, A. P., additional, Rostomily, C., additional, Rostomily, R., additional, Silbergeld, D., additional, Kolstoe, D., additional, Chamberlain, M., additional, Silber, J., additional, Roth, P., additional, Keller, A., additional, Hoheisel, J., additional, Codo, P., additional, Bauer, A., additional, Backes, C., additional, Leidinger, P., additional, Meese, E., additional, Thiel, E., additional, Korfel, A., additional, Weller, M., additional, Nagae, G., additional, Nagane, M., additional, Sanborn, J. Z., additional, Mikkelsen, T., additional, Jhanwar, S., additional, Chin, L., additional, Nishihara, M., additional, Schliesser, M., additional, Grimm, C., additional, Weiss, E., additional, Claus, R., additional, Weichenhan, D., additional, Weiler, M., additional, Hielscher, T., additional, Sahm, F., additional, Wiestler, B., additional, Klein, A.-C., additional, Blaes, J., additional, Plass, C., additional, Wick, W., additional, Stragliotto, G., additional, Rahbar, A., additional, Soderberg-Naucler, C., additional, Won, M., additional, Ezhilarasan, R., additional, Sun, P., additional, Blumenthal, D., additional, Vogelbaum, M., additional, Jenkins, R., additional, Jeraj, R., additional, Brown, P., additional, Jaeckle, K., additional, Schiff, D., additional, Dignam, J., additional, Atkins, J., additional, Brachman, D., additional, Werner-Wasik, M., additional, Mehta, M., additional, Shen, J., additional, Luan, J., additional, Yu, A., additional, Matsutani, M., additional, Liang, Y., additional, Man, T.-K., additional, Trister, A., additional, Tokita, M., additional, Mikheeva, S., additional, Mikheev, A., additional, Friend, S., additional, van den Bent, M., additional, Erdem, L., additional, Gorlia, T., additional, Taphoorn, M., additional, Kros, J., additional, Wesseling, P., additional, Dubbink, H., additional, Ibdaih, A., additional, French, P., additional, van Thuijl, H., additional, Heimans, J., additional, Ylstra, B., additional, Reijneveld, J., additional, Prabowo, A., additional, Scheinin, I., additional, van Essen, H., additional, Spliet, W., additional, Ferrier, C., additional, van Rijen, P., additional, Veersema, T., additional, Thom, M., additional, Meeteren, A. S.-v., additional, Aronica, E., additional, Kim, H., additional, Zheng, S., additional, Brat, D. J., additional, Virk, S., additional, Amini, S., additional, Sougnez, C., additional, Barnholtz-Sloan, J., additional, Verhaak, R. G. W., additional, Watts, C., additional, Sottoriva, A., additional, Spiteri, I., additional, Piccirillo, S., additional, Touloumis, A., additional, Collins, P., additional, Marioni, J., additional, Curtis, C., additional, Tavare, S., additional, Tews, B., additional, Yeung, T. P. C., additional, Al-Khazraji, B., additional, Morrison, L., additional, Hoffman, L., additional, Jackson, D., additional, Lee, T.-Y., additional, Yartsev, S., additional, Bauman, G., additional, Fu, J., additional, Vegesna, R., additional, Mao, Y., additional, Heathcock, L. E., additional, Torres-Garcia, W., additional, Wang, S., additional, McKenna, A., additional, Brennan, C. W., additional, Yung, W. K. A., additional, Weinstein, J. N., additional, Sulman, E. P., additional, and Koul, D., additional

Published
2013
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24. Deletions of the elastin gene at 7q11.23 occur in approximately 90% of patients with Williams syndrome

Author

Nickerson, E, Greenberg, F, Keating, M T, McCaskill, C, and Shaffer, L G

Subjects
Male, macromolecular substances, Aortic Valve Stenosis, Polymerase Chain Reaction, Elastin, Face, Intellectual Disability, Karyotyping, Humans, Abnormalities, Multiple, Female, Chromosomes, Human, Pair 7, Gene Deletion, Growth Disorders, In Situ Hybridization, Fluorescence, Research Article
Abstract

To investigate the frequency of deletions of the elastin gene in patients with Williams syndrome (WS), we screened 44 patients by both FISH and PCR amplification of a dinucleotide repeat polymorphism. FISH was performed using cosmids containing either the 5' or the 3' end of the elastin gene. PCR analysis was performed on the patients and their parents with a (CA)n repeat polymorphism found in intron 17 of the elastin locus. Of the 44 patients screened, 91% were shown to be deleted by FISH. Using the DNA polymorphism, both maternally (39%) and paternally (61%) derived deletions were found. Four patients were not deleted for elastin but have clinical features of WS. Since deletions of elastin cannot account for several features found in WS, these patients will be valuable in further delineation of the critical region responsible for the WS phenotype. Although PCR can be useful for determining the parental origin of the deletion, our results demonstrate that FISH analysis of the elastin locus provides a more rapid and informative test to confirm a clinical diagnosis of WS. The presence of two copies of the elastin locus in a patient does not, however, rule out WS as a diagnosis.

Published
1995

26. Erratum: Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing

Author

Thomas, R K, Nickerson, E, Simons, J F, Janne, P A, Tengs, T, Yuza, Y, Garraway, L A, LaFramboise, T, Lee, J C, Shah, K, O'Neill, K, Sasaki, H, Lindeman, N, Wong, K-K, Borras, A M, Gutmann, E J, Dragnev, K H, DeBiasi, R, Chen, T-H, Glatt, K A, Greulich, H, Desany, B, Lubeski, C K, Brockman, W, Alvarez, P, Hutchison, S K, Leamon, J H, Ronan, M T, Turenchalk, G S, Egholm, M, Sellers, W R, Rothberg, J M, and Meyerson, M

Abstract

Author(s): R K Thomas; E Nickerson; J F Simons; P A Janne; T Tengs; Y Yuza; L A Garraway; T LaFramboise; J C Lee; K Shah; K O'Neill; H Sasaki; [...]

Published
2006
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27. Detection of Oncogenic Mutations in the EGFR Gene in Lung Adenocarcinoma with Differential Sensitivity to EGFR Tyrosine Kinase Inhibitors

Author

THOMAS, R.K., primary, GREULICH, H., additional, YUZA, Y., additional, LEE, J.C., additional, TENGS, T., additional, FENG, W., additional, CHEN, T.-H., additional, NICKERSON, E., additional, SIMONS, J., additional, EGHOLM, M., additional, ROTHBERG, J.M., additional, SELLERS, W.R., additional, and MEYERSON, M.L., additional

Published
2005
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28. Pollutant transport in coastal areas with and without background wind

Author

Universitat Rovira i Virgili, Camps J; Massons J; Soler M; Nickerson E, Universitat Rovira i Virgili, and Camps J; Massons J; Soler M; Nickerson E

Abstract

A three-dimensional meteorological model and a Lagrangian particle dispersion model are used to study the effects of a uniform large-scale wind on the dispersion of a non-reactive pollutant in a coastal region with complex terrain. Simulations are carried out both with and without a background wind. A comparison between model results and measured data (wind and pollutant concentrations) indicates that the coupled model system provides a useful mechanism for analyzing pollutant dispersion in coastal regions.

Published
1997

31. Parker and Davis Jim Crow quickstep (1904)

Author

Nickerson, E. G., Nickerson, E. G., Nickerson, E. G., and Nickerson, E. G.

Abstract

A song in support of Henry Gassaway Davis and Alton B. Parker in the 1904 presidential election and arranged by Rudolf Thaler.

Published
1904

35. An Upper Bound on the Stress in Plane Couette Flow

Author

Nickerson, E. C.

Abstract

An absolute upper bound on the momentum number in turbulent plane Couette flow is obtained proportional to the two-thirds power of the Reynolds number. The derivation is based upon the energy integral and the specification of an internally consistent constraint on the fluctuating velocity field. A boundary layer approximation for the mean velocity profile is also obtained and the results are found to be consistent with the two-thirds power law.

Published
1973
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37. Un schéma de paramétrisation de la fusion des particules de glace

Author

Richard, E., Nickerson, E. C., Rosset, R., NOAA Forecast Systems Laboratory, National Oceanic and Atmospheric Administration (NOAA), Laboratoire de Météorologie Physique (LaMP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and MOITRIER, Catherine

Subjects
[PHYS.PHYS.PHYS-AO-PH]Physics [physics]/Physics [physics]/Atmospheric and Oceanic Physics [physics.ao-ph], [PHYS.PHYS.PHYS-AO-PH] Physics [physics]/Physics [physics]/Atmospheric and Oceanic Physics [physics.ao-ph], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
1982

38. Advanced Decoy Technology Program ADTECH IV. Appendix I, Part I. Program Description--Optimum Decoy Design Program.

Author

AVCO GOVERNMENT PRODUCTS GROUP WILMINGTON MA AVCO MISSILE SYSTEMS DIV, MacFarlane, R. A., Nickerson, E. R., AVCO GOVERNMENT PRODUCTS GROUP WILMINGTON MA AVCO MISSILE SYSTEMS DIV, MacFarlane, R. A., and Nickerson, E. R.

Abstract

This technical report describes analyses and techniques used in the design and evaluation of advanced decoy concepts. The work described addresses both the design of specific penetration aid elements and the formulation of techniques for their evaluation. The three major technical areas covered in this report are: Investigation of a penetration aid technique that degrades the measurement capability of the radar sensor, The design of a computer program to solve the decoy design problem with flexibility in the selection of optimization criteria and constraints, and Studies of the use of certain discrimination techniques for a hard point defense system. This appendix to this report contains detailed description of the optimum decoy design program. (Author), See also Appendix 1, Part 2, AD-853 820.

Published
1969

39. Numerical Simulation of Wind, Temperature, Shear Stress and Turbulent Energy over Nonhomogeneous Terrain.

Author

COLORADO STATE UNIV FORT COLLINS FLUID DYNAMICS AND DIFFUSION LAB, Huang,Chin-hua, Nickerson,E. C., COLORADO STATE UNIV FORT COLLINS FLUID DYNAMICS AND DIFFUSION LAB, Huang,Chin-hua, and Nickerson,E. C.

Abstract

Airflow in the atmospheric surface layer over nonhomogeneous surfaces with discontinuities in surface roughness and temperature is investigated by numerical techniques. A computational scheme is developed for solving the steady state two-dimensional boundary layer equations. Several theorems of convergence are proved. A successful numerical test, which has been compared to the exact solution, is achieved. Some iterative schemes, which have already enjoyed considerable success without theoretical support are here shown to be convergent. The variations in pressure and buoyancy force associated with changes in surface roughness have been neglected by previous investigators whose work is included in the present study. The numerical results of velocity and shear stress are compared with wind tunnel and field data. The roughness and temperature discontinuities are shown to have an effect on the upstream as well as the downstream flow conditions. (Author)

Published
1972

40. Response of a Turbulent Boundary Layer to Lateral Roughness Discontinuities.

Author

COLORADO STATE UNIV FORT COLLINS FLUID DYNAMICS AND DIFFUSION LAB, Wang,Hua, Nickerson,E. C., COLORADO STATE UNIV FORT COLLINS FLUID DYNAMICS AND DIFFUSION LAB, Wang,Hua, and Nickerson,E. C.

Abstract

The structure of the turbulent boundary layer on a flat plate consisting of alternate, longitudinal strips of smooth and rough (Sand paper, Grit 4) surfaces parallel to the direction of the flow has been investigated. Measurements of mean velocity, wall shear stress, turbulent intensities, turbulent shear stresses and energy spectra of the streamwise turbulent velocity were obtained. (Author)

Published
1972

41. Wind Tunnel Study of the Dugway Proving Ground Tower Grid.

Author

COLORADO STATE UNIV FORT COLLINS FLUID MECHANICS PROGRAM, Anyiwo,J., Nickerson,E. C., COLORADO STATE UNIV FORT COLLINS FLUID MECHANICS PROGRAM, Anyiwo,J., and Nickerson,E. C.

Abstract

A wind tunnel study has been carried out in order to simulate mean flow conditions and turbulence characteristics in the vicinity of the Tower Grid at Dugway Proving Ground. Significant modifications of the upstream flow conditions were found to occur primarily in the region between the Grid Center and the Downstream meteorological tower where the turbulence increased and local accelerations of the flow occurred. (Author)

Published
1970

42. AIR FLOW OVER ROUGHNESS DISCONTINUITY.

Author

COLORADO STATE UNIV FORT COLLINS FLUID DYNAMICS AND DIFFUSION LAB, Yeh,Fei-Fan, Nickerson,E. C., COLORADO STATE UNIV FORT COLLINS FLUID DYNAMICS AND DIFFUSION LAB, Yeh,Fei-Fan, and Nickerson,E. C.

Abstract

Measurements of mean velocity, mean-square turbulent velocity, turbulent shear stress, one-dimensional spectrum, and mass concentration distributions following a step increase in surface roughness of a wind-tunnel boundary-layer flow are presented. The mean velocity distributions agree well with Nickerson's numerical calculations for a small roughness change. The mixing-length distribution in the 'transitory' region is not experimentally consistent with that established for fully-developed turbulent boundary layer. Turbulent intensity and shear stress are generated progressively towards the upper layer as one moves downstream from the roughness discontinuity. The high frequency end of the spectra in the 'transitory' region can be exactly represented by the high frequency shape of the undisturbed turbulent boundary layer. Self-preserving mass concentration profiles are in general possible for both the vertical and horizontal distributions. The adjustment of the mean motion to the roughness change is more rapid than that of the turbulence. (Author)

Published
1970

43. WIND TUNNEL STUDIES AND SIMULATIONS OF TURBULENT SHEAR FLOWS RELATED TO ATMOSPHERIC SCIENCE AND ASSOCIATED TECHNOLOGIES.

Author

COLORADO STATE UNIV FORT COLLINS FLUID DYNAMICS AND DIFFUSION LAB, Cermak,J. E., Garrison,J. A., Meroney,R. N., Nickerson,E. C., Plate,E. J., COLORADO STATE UNIV FORT COLLINS FLUID DYNAMICS AND DIFFUSION LAB, Cermak,J. E., Garrison,J. A., Meroney,R. N., Nickerson,E. C., and Plate,E. J.

Abstract

A summary of accomplishments is given of both an experimental and analytical nature in the following specific studies: (1) Airflow in simulated temperate and tropical forest canopy. (2) Methods of modeling diffusion tests ahead of time to design most efficient and economical field experiments. (3) Use of controlled models of field tests to extend empirical data on CB transport and diffusion. (4) Extend wind tunnel investigation to thermally stratified boundary layers and broader ranges of surface roughness. (5) Investigation of longitudinal dispersion through both shear flow and turbulence. (6) Extend the Lagrangian similarity hypothesis considering a more realistic probability function. (7) Model Dugway Proving Ground and study mean wind patterns near the ground when flow aloft is oriented SW-SE. (Author)

Published
1969

47. Phenotypic spectrum and prevalence of INPP5E mutations in Joubert Syndrome and related disorders

Author

Lorena, Travaglini, Francesco, Brancati, Jennifer, Silhavy, Miriam, Iannicelli, Elizabeth, Nickerson, Nadia, Elkhartoufi, Eric, Scott, Emily, Spencer, Stacey, Gabriel, Sophie, Thomas, Bruria, Ben Zeev, Enrico, Bertini, Eugen, Boltshauser, Malika, Chaouch, Maria, Roberta Cilio, Mirjam, M. de Jong, Hulya, Kayserili, Gonul, Ogur, Andrea, Poretti, Sabrina, Signorini, Graziella, Uziel, Maha, S. Zaki, Ali Pacha, L, Zankl, A, Leventer, R, Grattan Smith, P, Janecke, A, Koch, J, Freilinger, M, D'Hooghe, M, Sznajer, Y, Vilain, C, Van Coster, R, Demerleir, L, Dias, K, Moco, C, Moreira, A, Ae Kim, C, Maegawa, G, Dakovic, I, Loncarevic, D, Mejaski Bosnjak, V, Petkovic, D, Abdel Salam GM, Abdel Aleem, A, Marti, I, Pinard, Jm, Quijano Roy, S, Sigaudy, S, de Lonlay, P, Romano, S, Verloes, A, Touraine, R, Koenig, M, Dollfus, H, Flori, E, Fradin, M, Lagier Tourenne, C, Messer, J, Collignon, P, Penzien, Jm, Bussmann, C, Merkenschlager, A, Philippi, H, Kurlemann, G, Grundmann, K, Dacou Voutetakis, C, Kitsiou Tzeli, S, Pons, R, Jerney, J, Halldorsson, S, Johannsdottir, J, Ludvigsson, P, Phadke, Sr, Girisha, Km, Doshi, H, Udani, V, Kaul, M, Stuart, B, Magee, A, Spiegel, R, Shalev, S, Mandel, H, Lev, D, Michelson, M, Idit, M, Ben Zeev, B, Gershoni Baruch, R, Ficcadenti, A, Fischetto, R, Gentile, M, Della Monica, M, Pezzani, M, Graziano, C, Seri, M, Benedicenti, F, Stanzial, F, Borgatti, R, Romaniello, R, Accorsi, P, Battaglia, S, Fazzi, E, Giordano, L, Pinelli, L, Boccone, L, Barone, R, Sorge, G, Briatore, E, Bigoni, S, Ferlini, A, Donati, Ma, Biancheri, R, Caridi, G, Divizia, Mt, Faravelli, F, Ghiggeri, G, Mirabelli, M, Pessagno, A, Rossi, A, Uliana, V, Amorini, M, Briguglio, M, Briuglia, S, Salpietro, Cd, Tortorella, G, Adami, A, Bonati, Mt, Castorina, P, D'Arrigo, S, Lalatta, F, Marra, G, Moroni, I, Pantaleoni, C, Riva, D, Scelsa, B, Spaccini, L, Del Giudice, E, Ludwig, K, Permunian, A, Suppiej, A, Macaluso, C, Pichiecchio, A, Battini, R, Di Giacomo, M, Priolo, M, Timpani, P, Pagani, G, Di Sabato ML, Emma, F, Leuzzi, V, Mancini, F, Majore, S, Micalizzi, A, Parisi, P, Romani, M, Stringini, G, Zanni, G, Ulgheri, L, Pollazzon, M, Renieri, Alessandra, Belligni, E, Grosso, E, Pieri, I, Silengo, M, Devescovi, R, Greco, D, Romano, C, Cazzagon, M, Simonati, A, Al Tawari AA, Bastaki, L, Mégarbané, A, Sabolic Avramovska, V, Said, E, Stromme, P, Koul, R, Rajab, A, Azam, M, Barbot, C, Salih, Ma, Tabarki, B, Jocic Jakubi, B, Martorell Sampol, L, Rodriguez, B, Pascual Castroviejo, I, Gener, B, Puschmann, A, Starck, L, Capone, A, Lemke, J, Fluss, J, Niedrist, D, Hennekam, Rc, Wolf, N, Gouider Khouja, N, Kraoua, I, Ceylaner, S, Teber, S, Akgul, M, Anlar, B, Comu, S, Kayserili, H, Yüksel, A, Akcakus, M, Caglayan, Ao, Aldemir, O, Al Gazali, L, Sztriha, L, Nicholl, D, Woods, Cg, Bennett, C, Hurst, J, Sheridan, E, Barnicoat, A, Hemingway, C, Lees, M, Wakeling, E, Blair, E, Bernes, S, Sanchez, H, Clark, Ae, Demarco, E, Donahue, C, Sherr, E, Hahn, J, Sanger, Td, Gallager, Te, Daugherty, C, Krishnamoorthy, Ks, Sarco, D, Walsh, Ca, Mckanna, T, Milisa, J, Chung, Wk, De Vivo DC, Raynes, H, Schubert, R, Seward, A, Brooks, Dg, Goldstein, A, Caldwell, J, Finsecke, E, Maria, Bl, Holden, K, Cruse, Rp, Karaca, E, Swoboda, Kj, Viskochil, D, Dobyns, Wb, Colin, Johnson, Tania, Attié Bitach, Joseph, G. Gleeson, Enza, Maria Valente, ANS - Amsterdam Neuroscience, APH - Amsterdam Public Health, Human Genetics, Paediatrics, OMÜ, University of Zurich, Valente, Enza Maria, Fluss, Joel Victor, Travaglini, L, Brancati, F, Silhavy, J, Iannicelli, M, Nickerson, E, Elkhartoufi, N, Scott, E, Spencer, E, Gabriel, S, Thomas, S, Ben Zeev, B, Bertini, E, Boltshauser, E, Chaouch, M, Cilio, Mr, de Jong, Mm, Kayserili, H, Ogur, G, Poretti, A, Signorini, S, Uziel, G, Zaki, M, Johnson, C, Atti? Bitach, T, Gleeson, Jg, Valente, Em, International JSRD Study, Group, and DEL GIUDICE, Ennio

Subjects
Male, Ciliata -- Anatomy, Proband, 10039 Institute of Medical Genetics, Meckel syndrome, RPGRIP1L, Syndromes, INPP5E, MODIFIER, Phosphoric Monoester Hydrolases/genetics, Ciliopathies, Polycystic Kidney Diseases/diagnosis/genetics, CILIUM, 0302 clinical medicine, Gene Frequency, Cerebellum, Prenatal Diagnosis, RETINAL DEGENERATION, Prevalence, MECKEL, ciliopathies, Joubert syndrome and related disorders, Eye Abnormalities, Child, Genetics (clinical), Encephalocele, Joubert syndrome, Genetics, Polycystic Kidney Diseases, 0303 health sciences, ddc:618, Cerebellar Diseases/diagnosis/genetics, Kidney Diseases, Cystic, Pedigree, 3. Good health, Phenotype, Child, Preschool, Medical genetics, Female, Retinitis Pigmentosa, FORM, Ciliary Motility Disorders, Heterozygote, medicine.medical_specialty, 2716 Genetics (clinical), Adolescent, Molecular Sequence Data, Encephalocele/diagnosis/genetics, AHI1, 610 Medicine & health, Biology, Retina, Article, Ciliopathies, INPP5E, Joubert syndrome and related disorders, Meckel syndrome, NO, Ciliary Motility Disorders/diagnosis/genetics, 03 medical and health sciences, 1311 Genetics, Cerebellar Diseases, REVEALS, medicine, Humans, Abnormalities, Multiple, Amino Acid Sequence, Kidney Diseases, Cystic/diagnosis/genetics, abnormalities, multiple, adolescent, amino acid sequence, cerebellar diseases, cerebellum, child, preschool, ciliary motility disorders, encephalocele, eye abnormalities, female, heterozygote, humans, infant, kidney diseases, cystic, male, molecular sequence data, pedigree, phosphoric monoester hydrolases, polycystic kidney diseases, prenatal diagnosis, prevalence, retina, gene frequency, mutation, phenotype, 030304 developmental biology, Eye Abnormalities/diagnosis/genetics, COACH SYNDROME, Retina/abnormalities, Genetic heterogeneity, Respiration disorders -- Therapy, Infant, medicine.disease, Phosphoric Monoester Hydrolases, INPP5E mutation, 10036 Medical Clinic, Mutation, 030217 neurology & neurosurgery
Abstract

Joubert syndrome and related disorders (JSRD) are clinically and genetically heterogeneous ciliopathies sharing a peculiar midbrain–hindbrain malformation known as the ‘molar tooth sign’. To date, 19 causative genes have been identified, all coding for proteins of the primary cilium. There is clinical and genetic overlap with other ciliopathies, in particular with Meckel syndrome (MKS), that is allelic to JSRD at nine distinct loci. We previously identified the INPP5E gene as causative of JSRD in seven families linked to the JBTS1 locus, yet the phenotypic spectrum and prevalence of INPP5E mutations in JSRD and MKS remain largely unknown. To address this issue, we performed INPP5E mutation analysis in 483 probands, including 408 JSRD patients representative of all clinical subgroups and 75 MKS fetuses. We identified 12 different mutations in 17 probands from 11 JSRD families, with an overall 2.7% mutation frequency among JSRD. The most common clinical presentation among mutated families (7/11, 64%) was Joubert syndrome with ocular involvement (either progressive retinopathy and/or colobomas), while the remaining cases had pure JS. Kidney, liver and skeletal involvement were not observed. None of the MKS foetuses carried INPP5E mutations, indicating that the two ciliopathies are not allelic at this locus., peer-reviewed

Published
2013

50. Head computed tomography in suspected physical abuse: time to rethink?

Author

Glenn K, Nickerson E, Bennett CV, Naughton A, Cowley LE, Morris E, Murtagh U, Kontos K, and Kemp AM

Subjects
Humans, Infant, Retrospective Studies, Male, Female, Child, Preschool, Practice Guidelines as Topic, Skull Fractures diagnostic imaging, Infant, Newborn, Physical Abuse statistics & numerical data, Tomography, X-Ray Computed methods, Tomography, X-Ray Computed statistics & numerical data, Child Abuse diagnosis, Child Abuse statistics & numerical data, Craniocerebral Trauma diagnostic imaging
Abstract

Background: National guidance recommends CT-head for all children <1 year old with suspected physical abuse, and to be considered for those <2 years old to exclude abusive head trauma., Objectives: To investigate whether this guidance is followed, and the associations between clinical presentation and CT findings, to determine whether guidance could be refined., Materials and Methods: A retrospective case note review of all children <2 years old who underwent medical assessment for suspected abuse (2009-2017). Outcome measures were frequency of CT-head, and diagnostic yield of intracranial injury, skull fracture or both., Results: CT-head was undertaken in 60.3% (152/252) of children <12 months old and 7.8% (13/167) of those aged 12-24 months. The diagnostic yield in children who had a CT-head was 27.1% in children <6 months old, 14.3% in those 6-12 months old (p=0.07) and 42.6% (6/13) in those 12-24 months old. For those with head swelling or neurological impairment, it was 84.2% (32/38). In children <12 months old without these clinical features, the estimated prevalence of occult head injury was 6.1% (7/115). The strongest predictors of an abnormal CT-head were swelling to the head (OR 46.7), neurological impairment (OR 20.6) and a low haemoglobin (OR 11.8)., Conclusion: All children <2 years of age with suspected physical abuse and neurological impairment or head swelling should undergo CT-head. Where the technical skills and the requisite expertise to interpret MRI exist, an MRI scan may be the optimal first-line neuroimaging investigation in infants who are neurologically stable with injuries unrelated to the head to minimise cranial radiation exposure., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. No commercial re-use. See rights and permissions. Published by BMJ.)

Published
2021
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