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An Event-Driven Approach for Studying Gene Block Evolution in Bacteria [article]

David C Ream, Asma R Bankapur, Iddo Friedberg
2015 arXiv   pre-print
As for genome C, c was deleted, so C(a, b) are neighboring.  ...  For the scenario described, we can say that there was a gene split event between A and B, and a gene deletion event between C and any of the other genomes for the gene block A(a, b, c).  ... 
arXiv:1501.00302v2 fatcat:77ya53djzfcvbl3qclqeggwp2y

An event-driven approach for studying gene block evolution in bacteria

David C. Ream, Asma R. Bankapur, Iddo Friedberg
2015 Computer applications in the biosciences : CABIOS  
As for genome C, c was deleted, so Cða; bÞ are neighboring.  ...  The boxes outline (top to bottom): a-, -, b-, and c-proteobacteria.  ... 
doi:10.1093/bioinformatics/btv128 pmid:25717195 pmcid:PMC4481853 fatcat:ygphaizjvvepdkhpj2xuarq3ym

Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes

David C. Ream, Samuel T. Murakami, Emily E. Schmidt, Guo-Hua Huang, Chun Liang, Iddo Friedberg, Xiao-Wen Cheng
2013 Virus Research  
Although the average A/T content of baculoviruses is 58.67%, the A/T MNR frequency is significantly higher than that of the G/C MNRs.  ...  is higher than the G/C MNRs (Gragg et al., 2002; Subramanian et al., 2003; Zhang et al., 2001) .  ...  (C) Relationship between baculovirus genome A/T contents and A7/T7 percentage. No correlation was found.  ... 
doi:10.1016/j.virusres.2013.10.005 pmid:24140718 fatcat:7mafijc4fjgd5j4whvplxuwdsa

Diversity and Expression of RubisCO Genes in a Perennially Ice-Covered Antarctic Lake during the Polar Night Transition

Weidong Kong, David C. Ream, John C. Priscu, Rachael M. Morgan-Kiss
2012 Applied and Environmental Microbiology  
PCR was performed in triplicate, using 25 cycles of 94°C for 1 min, 52°C for 20 s, and 72°C for 30 s.  ...  Amplification conditions were 5 min at 95°C followed by 35 cycles of 1 min at 94°C, 20 s at 52°C, and 30 s at 72°C, and fluorescence intensity was acquired at 83°C (above the melting point of primer dimers  ... 
doi:10.1128/aem.00029-12 pmid:22492447 pmcid:PMC3370527 fatcat:gy4dzivxqfbsbddu3swwidif2i

Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate

Brock A. Arivett, Steven E. Fiester, David C. Ream, Daniela Centrón, Maria S. Ramírez, Marcelo E. Tolmasky, Luis A. Actis
2015 Genome Announcements  
Citation Arivett BA, Fiester SE, Ream DC, Centrón D, Ramírez MS, Tolmasky ME, Actis LA. 2015. Draft genome of the multidrug-resistant Acinetobacter baumannii strain A155 clinical isolate.  ...  Briefly, the A155 isolate was routinely stored at Ϫ80°C in 10% glycerol, passaged to overnight LB cultures grown with agitation at 37°C, and total DNA was isolated using the DNeasy blood and tissue kit  ... 
doi:10.1128/genomea.00212-15 pmid:25814610 pmcid:PMC4384150 fatcat:zivzduvq35egdk7nea7wumkpdy

Cardiovascular Risk in HIV-Infected and Uninfected Postmenopausal Minority Women: Use of the Framingham Risk Score

Yamnia I. Cortés, Nancy Reame, Cosmina Zeana, Haomiao Jia, David C. Ferris, Elizabeth Shane, Michael T. Yin
2017 Journal of Women's Health  
., Hepatitis C infection, dyslipidemia, and diabetes), alcohol consumption, and injection drug use. 22, 25 Information on HIV-1 RNA levels, current and nadir CD4, ART use (ever), ART regimen at time  ...  IQR]) 23.7 [15.2, 33.7] 22.0 [13.7, 31.1] 0.52 Chronic conditions and medications, n (%) Alcohol (>1 drink/day) 10 (16.9) 8 (16.0) 0.89 Injection drug use 8 (13.6) 4 (8.0) 0.54 Hepatitis C  ... 
doi:10.1089/jwh.2015.5736 pmid:27611626 pmcid:PMC5361765 fatcat:srbcxzmuvfeupf5pnickxfnrh4

Draft Genome Sequences of Klebsiella pneumoniae Clinical Type Strain ATCC 13883 and Three Multidrug-Resistant Clinical Isolates

Brock A. Arivett, David C. Ream, Steven E. Fiester, Katrin Mende, Clinton K. Murray, Mitchell G. Thompson, Shrinidhi Kanduru, Amy M. Summers, Amanda L. Roth, Daniel V. Zurawski, Luis A. Actis
2015 Genome Announcements  
The strains were routinely stored at -80°C in 10% glycerol. DNA was isolated from overnight LB cultures grown with agitation at 37°C using the DNeasy blood and tissue kit (Qiagen, Valencia, CA).  ... 
doi:10.1128/genomea.01385-14 pmid:25593250 pmcid:PMC4299892 fatcat:nqujmitu7rcqbksufjn727pxz4

SIRT1-NOX4 signaling axis regulates cancer cachexia

Aneesha Dasgupta, Surendra K Shukla, Enza Vernucci, Ryan J King, Jaime Abrego, Scott E Mulder, Nicholas J Mullen, Gavin Graves, Kyla Buettner, Ravi Thakur, Divya Murthy, Kuldeep S Attri (+18 others)
2020 Journal of Experimental Medicine  
Reames, M. Teoh-Fitzgerald, R. Oberley-Deegan, F. Yu, K.A. Klute, M.A. Hollingsworth, M.C. Zimmerman, K. Mehla, J. Sadoshima, D.A. Tuveson, and P.K. Singh contributed reagents or analytic tools; A.  ...  (C and D) Postnecropsy tumor weight (C) and gastrocnemius muscle weight (D) for S2-013-implanted mice with and without GKT treatment.  ... 
doi:10.1084/jem.20190745 pmid:32441762 pmcid:PMC7336299 fatcat:aierkxuahra4rdcu4jygpv36fu

Ambulatory Rhythm Monitoring to Detect Late High-Grade Atrioventricular Block Following Transcatheter Aortic Valve Replacement

Karen Ream, Amneet Sandhu, Javier Valle, Rachel Weber, Alexander Kaizer, Dominik M. Wiktor, Ryan T. Borne, Alexis Z. Tumolo, Megan Kunkel, Matthew M. Zipse, Joseph Schuller, Christine Tompkins (+9 others)
2019 Journal of the American College of Cardiology  
Ream et al.  ...  However, RBBB and LBBB patients were combined in their analyses, CONCLUSIONS M A Y 2 8 , 2 0 1 9 : 2 5 3 8 -4 7 J A C C V O L . 7 3 , N O . 2 0 , 2 0 1 9 M A Y 2 8 , 2 0 1 9 : 2 5  ... 
doi:10.1016/j.jacc.2019.02.068 pmid:31118148 fatcat:bi2urun745fm7hmxzw5davuuya

Gaps and opportunities in refractory status epilepticus research in children: A multi-center approach by the Pediatric Status Epilepticus Research Group (pSERG)

Iván Sánchez Fernández, Nicholas S. Abend, Satish Agadi, Sookee An, Ravindra Arya, Jessica L. Carpenter, Kevin E. Chapman, William D. Gaillard, Tracy A. Glauser, David B. Goldstein, Joshua L. Goldstein, Howard P. Goodkin (+10 others)
2014 Seizure  
Status epilepticus (SE) is a life-threatening condition that can be refractory to initial treatment. Randomized controlled studies to guide treatment choices, especially beyond first-line drugs, are not available. This report summarizes the evidence that guides the management of refractory convulsive SE (RCSE) in children, defines gaps in our clinical knowledge and describes the development and works of the 'pediatric Status Epilepticus Research Group' (pSERG). A literature review was performed
more » ... to evaluate current gaps in the pediatric SE and RCSE literature. In person and online meetings helped to develop and expand the pSERG network. The care of pediatric RCSE is largely based on extrapolations of limited evidence derived from adult literature and supplemented with case reports and case series in children. No comparative effectiveness trials have been performed in the pediatric population. Gaps in knowledge include risk factors for SE, biomarkers of SE and RCSE, second- and third-line treatment options, and long-term outcome. The care of children with RCSE is based on limited evidence. In order to address these knowledge gaps, the multicenter pSERG was established to facilitate prospective collection, analysis, and sharing of de-identified data and biological specimens from children with RCSE. These data will allow identification of treatment strategies associated with better outcomes and delineate evidence-based interventions to improve the care of children with SE.
doi:10.1016/j.seizure.2013.10.004 pmid:24183923 pmcid:PMC6387832 fatcat:tz4e5sy6x5bunmtl27qauhkj2u

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg, Christine A. Orengo
2013 PLoS Computational Biology  
These two terms are also closely associated, in RNAi whole-genome gene knockdowns in C. elegans, D. melanogaster and one in C. albicans.  ...  These studies mostly use the same RNAi libraries, and target the whole C. elegans genome using common data resources. Hence the large redundancy observed for C. elegans in Table 2 .  ... 
doi:10.1371/journal.pcbi.1003063 pmid:23737737 pmcid:PMC3667760 fatcat:dyez23i4n5hxjbh3lctoen3uvi

Page 427 of The Journal of Arthroplasty Vol. 22, Issue 3 [page]

2007 The Journal of Arthroplasty  
Muller C, Frigg R, Pfister U. diameter and reamed design on the increase of Effect of flexible drive pressure in the medullary cavity during reaming. Injury 1993;24:40.  ...  Mousavi M, David R, Ehteshami J, et al. Pressure changes during reaming with different parameters and reamer designs. Clin Orthop Relat Res 2000; ) 373:295. Study of Femoral Dobrjanski D.  ... 

Page 974 of The Solicitors' Journal Vol. 23, Issue [page]

1879 The Solicitors' Journal  
Helen’s, C.; and of Messrs. HARVEY & DAVIDS, Auctioneers and Surveyors, 117, Bishopsgate-street, Corshill, E.C. PRELIMINARY.  ...  ., and 8s. per ream, Lanae Buiuz Norte, 36, 6d., 4s. 6d., and 6s. 6d. per ream.  ... 

Page 924 of The Solicitors' Journal Vol. 21, Issue [page]

1877 The Solicitors' Journal  
C. Guthrie, Esq. Louis Huth, Esq. Henry J. B. Kendall, Esq. Charles Ly «ll, Esq. Capt. R. W. Pelly, R.N. David Powell, Esq. P. F. Robertson, Esq. Robert Ryrie, Esq. David P. Sellar, Esq. Col.  ...  ., and 18s 6d, per ream. Cream-Laip Nore, 3s., 4s,, and 5s. per ream. Large Caram-iarp Norte, 4s. 6d., 63. 6d., and 8s. per ream, LaBee BivE Norte, 3s. 6d., 4s. 6d., and 6s. 6d. per ream.  ... 

Page 684 of The Solicitors' Journal Vol. 21, Issue [page]

1877 The Solicitors' Journal  
C. Guthrie, Esq. Lonis Harn, Esq. Henre J. B. Kendall, Esq. Charles Ly li, Esq. Orpt. R. W. Pelly, R.N. David Powell, Esq. P. F. Robertson, Esq. Robert Ryrie, Esq. David P, sellar, Esq.  ...  ,and 9s. 9d. per ream. P Brier Parer, 15s. 6d., 17s. 6d., and 23s. 6d. per ream. Footscar Paper, 10s. 6d., 14s. 6d., and 188 6d, per ream. Cream-taip Norse, 3s., 4s,, and 5s. per ream.  ... 
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