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The Astonishing General: The Life and Legacy of Sir Isaac Brock by Wesley B. Turner

John R. Grodzinski
2012 Ontario History  
Clements Library, University of Michigan I n his 1999 study British Generals of the War of 1812, historian Wesley Turner explored the reasons why Major-General Isaac Brock, who held responsibility for  ...  Turner explains that in preparing this biography he has "something different to say" (p. 9) about this subject.  ... 
doi:10.7202/1065399ar fatcat:ssl4cz5tfbcfbctgbkfxycye5i

Hereditary Prostate Cancer [chapter]

Aubrey R. Turner, William B. Isaacs, Jianfeng Xu
2003 Prostate Cancer  
However, as mentioned above, an examination of a large number of prostate cancer families for other cancers by Isaacs et al.  ...  Work from a large number of laboratories has identified a number of commonly occurring alterations in prostate cancer DNA (reviewed in Isaacs and Bova [38] ).  ... 
doi:10.1016/b978-012286981-5/50018-5 fatcat:kec3f2jw2rhctgnh74rdu7auji

Integrating long-range connectivity information into de Bruijn graphs [article]

Isaac Turner, Kiran V. Garimella, Zamin Iqbal, Gil McVean
2017 bioRxiv   pre-print
Motivation: The de Bruijn graph is a simple and efficient data structure that is used in many areas of sequence analysis including genome assembly, read error correction and variant calling. The data structure has a single parameter k, is straightforward to implement and is tractable for large genomes with high sequencing depth. It also enables representation of multiple samples simultaneously to facilitate comparison. However, unlike the string graph, a de Bruijn graph does not retain long
more » ... e information that is inherent in the read data. For this reason, applications that rely on de Bruijn graphs can produce sub-optimal results given their input. Results: We present a novel assembly graph data structure: the Linked de Bruijn Graph (LdBG). Constructed by adding annotations on top of a de Bruijn graph, it stores long range connectivity information through the graph. We show that with error-free data it is possible to losslessly store and recover sequence from a Linked de Bruijn graph. With assembly simulations we demonstrate that the LdBG data structure outperforms both the de Bruijn graph and the String Graph Assembler (SGA). Finally we apply the LdBG to Klebsiella pneumoniae short read data to make large (12 kbp) variant calls, which we validate using PacBio sequencing data, and to characterise the genomic context of drug-resistance genes. Availability: Linked de Bruijn Graphs and associated algorithms are implemented as part of McCortex, available under the MIT license at https://github.com/mcveanlab/mccortex.
doi:10.1101/147777 fatcat:pd5gmzelkfbu5oiqdd4upkftve

Associations between hOGG1 sequence variants and prostate cancer susceptibility

Jianfeng Xu, Siqun L Zheng, Aubrey Turner, Sarah D Isaacs, Kathy E Wiley, Gregory A Hawkins, Bao-li Chang, Eugene R Bleecker, Patrick C Walsh, Deborah A Meyers, William B Isaacs
2002 Cancer Research  
8-Hydroxyguanine is a mutagenic base lesion produced by reactive oxygen species. The hOGG1 gene encodes a DNA glycosylase/AP lyase that can suppress the mutagenic effects of 8-hydroxyguanine by catalyzing its removal from oxidized DNA. A population-based (245 cases and 222 controls) and family-based (159 hereditary prostate cancer families) association study was performed to test the hypothesis that sequence variants of hOGG1 increase susceptibility to prostate cancer. We found that the
more » ... frequency of two sequence variants (11657A/G and Ser326Cys) was significantly different between cases and controls. The association with 11657A/G is confirmed and strengthened by our family-based association study. These results suggest that sequence variants in this gene are associated with prostate cancer risk, presumably through defective DNA repair function of hOGG1.
pmid:11956079 fatcat:kj3kl7grebderbchhcwx46tkjy

High Frequency and Prevalence of Community-Based Asymptomatic SARS-CoV-2 Infection [article]

Lao Allan-Blitz, Isaac Turner, Fred Hertlein, Jeffrey D. Klausner
2020 medRxiv   pre-print
Approximately 20-40% of SARS-CoV-2 infection is asymptomatic; however, data are limited on drivers of such infection. Among over 730,000 SARS-CoV-2 test results in Los Angeles between August-October, 2020, we found heterogenous frequencies of asymptomatic infection among various sup-populations. Further research is needed to delineate drivers of asymptomatic SARS-CoV-2 infection.
doi:10.1101/2020.12.09.20246249 fatcat:c4xgdf325bc7fmpmpmqmh3wdzu

Integrating long-range connectivity information into de Bruijn graphs

Isaac Turner, Kiran V Garimella, Zamin Iqbal, Gil McVean, Bonnie Berger
2018 Bioinformatics  
Motivation: The de Bruijn graph is a simple and efficient data structure that is used in many areas of sequence analysis including genome assembly, read error correction and variant calling. The data structure has a single parameter k, is straightforward to implement and is tractable for large genomes with high sequencing depth. It also enables representation of multiple samples simultaneously to facilitate comparison. However, unlike the string graph, a de Bruijn graph does not retain long
more » ... e information that is inherent in the read data. For this reason, applications that rely on de Bruijn graphs can produce sub-optimal results given their input. Results: We present a novel assembly graph data structure: the Linked de Bruijn Graph (LdBG). Constructed by adding annotations on top of a de Bruijn graph, it stores long range connectivity information through the graph. We show that with error-free data it is possible to losslessly store and recover sequence from a Linked de Bruijn graph. With assembly simulations we demonstrate that the LdBG data structure outperforms both the de Bruijn graph and the String Graph Assembler (SGA). Finally we apply the LdBG to Klebsiella pneumoniae short read data to make large (12 kbp) variant calls, which we validate using PacBio sequencing data, and to characterise the genomic context of drug-resistance genes. Availability: Linked de Bruijn Graphs and associated algorithms are implemented as part of McCortex, available under the MIT license at https://github.com/mcveanlab/
doi:10.1093/bioinformatics/bty157 pmid:29554215 pmcid:PMC6061703 fatcat:7ksbpf6i7nfofajzazgezy5ohe

The neprilysin (NEP) family of zinc metalloendopeptidases: Genomics and function

Anthony J. Turner, R. Elwyn Isaac, David Coates
2001 Bioessays  
The tortuous route to the subsequent isolation and cloning of the physiologically relevant ECE is reviewed in Turner and Murphy.  ...  Turner, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. E-mail: a.j.turner@leeds.ac.uk 1 2  ... 
doi:10.1002/1521-1878(200103)23:3<261::aid-bies1036>3.0.co;2-k pmid:11223883 fatcat:bck633tppbfwhc2r27n5u4k2hu

Biomarkers and Stimulation Algorithms for Adaptive Brain Stimulation

Kimberly B. Hoang, Isaac R. Cassar, Warren M. Grill, Dennis A. Turner
2017 Frontiers in Neuroscience  
., 2006; Patil and Turner, 2008) . The update time for BMI systems is typically on the order of ∼20 Hz (i.e., ∼50 ms for updating the next prediction) (Hanson et al., 2012) .  ... 
doi:10.3389/fnins.2017.00564 pmid:29066947 pmcid:PMC5641319 fatcat:5xzkghr3cngodkfthmrj4lphka

A Polymorphism in theCDKN1BGene Is Associated with Increased Risk of Hereditary Prostate Cancer

Bao-li Chang, Siqun L Zheng, Sarah D. Isaacs, Kathy E. Wiley, Aubrey Turner, Ge Li, Patrick C. Walsh, Deborah A. Meyers, William B. Isaacs, Jianfeng Xu
2004 Cancer Research  
The loss of cell cycle control is believed to be an important mechanism in the promotion of carcinogenesis. CDKN1B (p27) belongs to the Cip/Kip family and functions as an important cell cycle gatekeeper. Several lines of evidence from clinical studies and laboratory experiments demonstrate that CDKN1B is an important tumor suppressor gene in prostate cancer etiology. In addition, a case-control study has shown that the 326T/G (V109G) polymorphism in CDKN1B is associated with advanced prostate
more » ... ncer. In light of the evidence for linkage between the chromosomal location of the CDKN1B gene (12p13) and prostate cancer susceptibility in several hereditary prostate cancer (HPC) populations, we hypothesized that sequence variants of CDKN1B play a role in HPC. To test this hypothesis, we first resequenced this gene in 96 HPC probands to identify germ-line mutations and sequence variants. We then genotyped the identified sequence variants among all family members of 188 HPC families and tested for their cosegregation with prostate cancer. In total, 10 sequence variants were identified, including three nonsynonymous changes. A family-based test, which is free from the effects of population stratification, revealed a significant association between single nucleotide polymorphism (SNP) -79C/T and prostate cancer (with a nominal P of 0.0005). The C allele of -79C/T was overtransmitted from parents to their affected offspring. Evidence for this association was primarily contributed by affected offspring whose age at diagnosis was <65 years. Together with the previous association study in a sporadic prostate cancer population, our new findings additionally suggest that germ-line variants of this gene play a role in prostate cancer susceptibility.
doi:10.1158/0008-5472.can-03-2340 pmid:15026335 fatcat:hbfn4kzcg5gbbdi3arh2rvblay

Stable recombination hotspots in birds [article]

Sonal Singhal, Ellen Leffler, Keerthi Sannareddy, Isaac Turner, Oliver Venn, Daniel Hooper, Alva Strand, Qiye Li, Brian Raney, Christopher Balakrishnan, Simon Griffith, Gil McVean (+1 others)
2015 biorxiv/medrxiv   pre-print
Although the DNA-binding protein PRDM9 plays a critical role in the specification of meiotic recombination hotspots in mice and apes, it appears to be absent from many vertebrate species, including birds. To learn about the determinants of fine-scale recombination rates and their evolution in natural populations lacking PRDM9, we inferred fine-scale recombination maps from population resequencing data for two bird species, the zebra finchTaeniopygia guttata, and the long-tailed finch,Poephila
more » ... uticauda, whose divergence is on par with that between human and chimpanzee. We find that both bird species have hotspots, and these are enriched near CpG islands and transcription start sites. In sharp contrast to what is seen in mice and apes, the hotspots are largely shared between the two species, with indirect evidence of conservation extending across bird species tens of millions of years diverged. These observations link the evolution of hotspots to their genetic architecture, suggesting that in the absence of PRDM9 binding specificity, accessibility of the genome to the cellular recombination machinery, particularly around functional genomic elements, both enables increased recombination and constrains its evolution.
doi:10.1101/023101 fatcat:zpn7musj6jghxkt3h3wpar5b2u

Molecular residual disease and adjuvant trials design in solid tumors

Maria Coakley, Isaac Garcia-Murillas, Nicholas C. Turner
2019 Clinical Cancer Research  
Turner reports receiving commercial research grants from AstraZeneca, Bio-Rad, Pfizer, Roche/Genentech, Clovis, and Guardant Health, and is a consultant/advisory board member for AstraZeneca, Bristol-Myers  ... 
doi:10.1158/1078-0432.ccr-19-0152 pmid:31088829 fatcat:6hqpcq7hx5hmvj5h3j26pvhxva

Determination of HER2 Amplification Status on Tumour DNA by Digital PCR

Isaac Garcia-Murillas, Maryou Lambros, Nicholas C. Turner, Baochuan Lin
2013 PLoS ONE  
Citation: Garcia-Murillas I, Lambros M, Turner NC (2013) Determination of HER2 Amplification Status on Tumour DNA by Digital PCR. PLoS ONE 8(12): e83409.  ... 
doi:10.1371/journal.pone.0083409 pmid:24386193 pmcid:PMC3873285 fatcat:c7paaz5wjvgi7hayrgygtoffz4

Polymorphisms in the CYP1B1 gene are associated with increased risk of prostate cancer

B L Chang, S L Zheng, S D Isaacs, A Turner, G A Hawkins, K E Wiley, E R Bleecker, P C Walsh, D A Meyers, W B Isaacs, J Xu
2003 British Journal of Cancer  
doi:10.1038/sj.bjc.6601288 pmid:14562027 pmcid:PMC2394327 fatcat:6rdvovqduvc3dowrnuqvhlmrxy

Managing the pediatric patient with celiac disease: a multidisciplinary approach

Daniela Migliarese Isaac, Jessica Wu, Diana Mager, Justine Turner
2016 Journal of Multidisciplinary Healthcare  
celiac disease CD patients may face the additional management complexity of being affected by associated health conditions, such as type 1 diabetes mellitus, autoimmune hypothyroidism, Down syndrome, and Turner  ...  45% to 60%, many of which are likely overestimates. 3, [7] [8] [9] [10] Adolescents have been identified as a subgroup with a particularly high rate of noncompliance. 11 Dovepress Dovepress 530 Isaac  ... 
doi:10.2147/jmdh.s95323 pmid:27785047 pmcid:PMC5067051 fatcat:nwvl5rtxwza35analv4rsm5mna

Chylothorax and Chylopericardium: A Complication of Long-Term Central Venous Catheter Use

James Livesay, Isaac Biney, J. Francis Turner
2019 Case Reports in Pulmonology  
The development of chylothorax and chylopericardium is an uncommon complication of the long-term use of central venous catheters. We describe a unique case of an end stage renal disease patient on hemodialysis with a left jugular tunneled catheter who developed superior vena cava syndrome. Our patient presented with both a large pleural and pericardial effusion that despite drainage continued to reaccumulate. Further imaging with CT scan of the thorax revealed stenosis of the superior vena cava
more » ... leading to recurrent chylothorax and chylopericardium.
doi:10.1155/2019/4908259 pmid:31380138 pmcid:PMC6657625 fatcat:4dqfgi3wrjcbfkgiekorwdxo6e
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