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The energy-spectrum of bicompatible sequences [article]

Fenix W. Huang and Christopher L. Barrett and Christian M. Reidys
2019 arXiv   pre-print
Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequences that satisfy the base pairing constraints of a given RNA structure play an important role in the context of neutral networks and inverse folding. Sequences satisfying the constraints of two structures simultaneously are called bicompatible and phenotypic change, induced by erroneously replicating populations of RNA sequences,
more » ... s closely connected to bicompatibility. Furthermore, bicompatible sequences are relevant for riboswitch sequences, beacons of evolution, realizing two distinct phenotypes. Results: We present a full loop energy model Boltzmann sampler of bicompatible sequences for pairs of structures. The novel dynamic programming algorithm is based on a topological framework encapsulating the relations between loops. We utilize our sequence sampler to study the energy spectra and density of bicompatible sequences, the rankings of the structures and key properties for evolutionary transitions. Conclusion: Our analysis of riboswitch sequences shows that key properties of bicompatible sequences depend on the particular pair of structures. While there always exist bicompatible sequences for random structure pairs, they are less suited to facilitate transitions. We show that native riboswitch sequences exhibit a distinct signature with regards to the ranking of their two phenotypes relative to the minimum free energy, suggesting a new criterion for identifying native sequences and sequences subjected to evolutionary pressure.
arXiv:1910.00190v1 fatcat:huhbkackpzhd7eiwf4pccqamw4

Liver injury, hypoalbuminaemia and severe SARS-CoV-2 infection

Clare Elizabeth Foley, Christopher Mulvey, Maria Boylan, Niamh Reidy, Paul Reidy, David Moynan, Amy Worrall, Ger Curley, Karen Boland, Eoghan de Barra, John D Ryan
2021 Gut  
Contributors CEF collected and analysed the data. CM and KB carried out the statistics on the data. MB, NR, PR and AW collected the data. GC, EdB and JR supervised the project.
doi:10.1136/gutjnl-2021-324570 pmid:34083385 fatcat:s54xcrpeivg7tlmp37yocqcztu

Sequence-structure relations of biopolymers [article]

Christopher Barrett, Fenix W. Huang, Christian M. Reidys
2016 arXiv   pre-print
., 2008) and in (Reidys et al., 2011) a polynomial time, loop-based folding algorithm of topological RNA structures was given.  ...  Recent results (Huang and Reidys, 2016 ) associate a topological RNA structure with a certain, arc-labeled secondary structure, called λ-structure.  ... 
arXiv:1511.03141v2 fatcat:oh4onyucs5b4xl45ysmoyj2hve

Genetic robustness of let-7 miRNA sequence-structure pairs [article]

Qijun He, Fenix W. Huang, Christopher Barrett, Christian M. Reidys
2018 arXiv   pre-print
Genetic robustness, the preservation of evolved phenotypes against genotypic mutations, is one of the central concepts in evolution. In recent years a large body of work has focused on the origins, mechanisms, and consequences of robustness in a wide range of biological systems. In particular, research on ncRNAs studied the ability of sequences to maintain folded structures against single-point mutations. In these studies, the structure is merely a reference. However, recent work revealed
more » ... ce that structure itself contributes to the genetic robustness of ncRNAs. We follow this line of thought and consider sequence-structure pairs as the unit of evolution and introduce the spectrum of inverse folding rates (IFR-spectrum) as a measurement of genetic robustness. Our analysis of the miRNA let-7 family captures key features of structure-modulated evolution and facilitates the study of robustness against multiple-point mutations.
arXiv:1801.05056v1 fatcat:6bbcgfggd5dcvbmoaqhk6em7fy

An efficient dual sampling algorithm with Hamming distance filtration [article]

Fenix W. Huang, Qijun He, Christopher Barrett, Christian M. Reidys
2017 arXiv   pre-print
Neutral networks have been studied theoretically via random graph theory (Reidys, 1997) , in the context of the molecular quasispecies and by exhaustive enumeration (Grüner et al., 1996; Göbel, 2000  ... 
arXiv:1711.10549v1 fatcat:3tb7v25acfbrxo7rmdtnuhk2ty

The energy-spectrum of bicompatible sequences

Fenix W. Huang, Christopher L. Barrett, Christian M. Reidys
2021 Algorithms for Molecular Biology  
Background Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences, which satisfy the base-pairing constraints of a given RNA structure, play an important role in the context of neutral evolution. Sequences that are simultaneously compatible with two given structures (bicompatible sequences), are beacons in phenotypic transitions, induced by erroneously replicating populations of RNA sequences.
more » ... A riboswitches, which are capable of expressing two distinct secondary structures without changing the underlying sequence, are one example of bicompatible sequences in living organisms. Results We present a full loop energy model Boltzmann sampler of bicompatible sequences for pairs of structures. The sequence sampler employs a dynamic programming routine whose time complexity is polynomial when assuming the maximum number of exposed vertices, $$\kappa $$ κ , is a constant. The parameter $$\kappa $$ κ depends on the two structures and can be very large. We introduce a novel topological framework encapsulating the relations between loops that sheds light on the understanding of $$\kappa $$ κ . Based on this framework, we give an algorithm to sample sequences with minimum $$\kappa $$ κ on a particular topologically classified case as well as giving hints to the solution in the other cases. As a result, we utilize our sequence sampler to study some established riboswitches. Conclusion Our analysis of riboswitch sequences shows that a pair of structures needs to satisfy key properties in order to facilitate phenotypic transitions and that pairs of random structures are unlikely to do so. Our analysis observes a distinct signature of riboswitch sequences, suggesting a new criterion for identifying native sequences and sequences subjected to evolutionary pressure. Our free software is available at: https://github.com/FenixHuang667/Bifold.
doi:10.1186/s13015-021-00187-4 pmid:34074304 pmcid:PMC8167974 fatcat:3a3kf5xjkbagpovlsvfse57rum

RNA secondary structures having a compatible sequence of certain nucleotide ratios [article]

Christopher L. Barrett and Thomas J. X. Li and Christian M. Reidys
2016 arXiv   pre-print
An RNA sequence is compatible with a structure S, if and only if for any S-arc (i, j), the pair (x i , x j ) forms a base pair (Reidys et al., 1997) .  ... 
arXiv:1603.03653v1 fatcat:rqkxkruicjefjpcxsflyg5cflu

Use of mental simulations to change theory of planned behaviour variables

Christopher J. Armitage, John G. Reidy
2008 British Journal of Health Psychology  
ARMITAGE, Christopher J. and REIDY, John G. (2008). Use of mental simulations to change theory of planned behaviour variables. Abstract Published version Objectives.  ... 
doi:10.1348/135910707x227088 pmid:17650364 fatcat:6opi6iyutbhevegcmm4ojltqdm

Residential Water Demand Management: Lessons from Aurora, Colorado1

Douglas S. Kenney, Christopher Goemans, Roberta Klein, Jessica Lowrey, Kevin Reidy
2008 Journal of the American Water Resources Association  
The calculated coefficient for the Water Smart Reader, wsr, is also highly significant (+0.16), KENNEY, GOEMANS, KLEIN, LOWREY, AND REIDY JAWRA 202 although the positive sign of the result was initially  ...  houseowned i þ / 4 newhome i þ / 5 oldhome i þ / 6 numbedrooms i þ e it 0 B B B B B B B B B B B B B B B B @ 1 C C C C C C C C C C C C C C C C A e it ¼ g i þ l it ð1Þ KENNEY, GOEMANS, KLEIN, LOWREY, AND REIDY  ... 
doi:10.1111/j.1752-1688.2007.00147.x fatcat:5lipapchnrbudn6nkgu5b3igqm

Genetic robustness of let-7 miRNA sequence-structure pairs

Qijun He, Fenix Wenda Huang, Christopher Barrett, Christian Reidys
2019 RNA: A publication of the RNA Society  
The presence of neutral networks (Grüner et al. 1996a,b; Reidys et al. 1997 ) of RNA secondary structures shows that there are complementary sequences that fold into the same structure.  ...  The mutational robustness against multiplepoint mutations facilitates the existence of a broad and highly connected region in the neutral network around the native sequence (Reidys et al. 1997) .  ... 
doi:10.1261/rna.065763.118 pmid:31548338 pmcid:PMC6859847 fatcat:ppqb3iqbbveora2j5tkhkxpbk4

Evidence that process simulations reduce anxiety in patients receiving dental treatment: randomized exploratory trial

Christopher J. Armitage, John G. Reidy
2012 Anxiety, Stress, & Coping  
Armitage and Reidy, 2008; Pham & Taylor, 1999) . Given that self-efficacy both manages anxiety in dental contexts (e.g.  ...  Armitage & Reidy, 2008; Pham & Taylor, 1999) . The implication is that process simulations might work in a variety of contexts for a variety of purposes.  ... 
doi:10.1080/10615806.2011.604727 pmid:21851147 fatcat:6bdjzb2dy5gt5cmtypuow4lp54

Protein Supplementation Does Not Affect Myogenic Adaptations to Resistance Training

PAUL T. REIDY, CHRISTOPHER S. FRY, SHERRY IGBINIGIE, RACHEL R. DEER, KRISTOFER JENNINGS, MARK B. COPE, RATNA MUKHERJEA, ELENA VOLPI, BLAKE B. RASMUSSEN
2017 Medicine & Science in Sports & Exercise  
It has been proposed that protein supplementation during resistance exercise training enhances muscle hypertrophy. The degree of hypertrophy during training is controlled in part through the activation of satellite cells and myonuclear accretion. Purpose: This study aimed to determine the efficacy of protein supplementation (and the type of protein) during traditional resistance training on myofiber cross-sectional area, satellite cell content, and myonuclear addition. Methods: Healthy young
more » ... participated in supervised whole-body progressive resistance training 3 dIwk j1 for 12 wk. Participants were randomized to one of three groups ingesting a daily 22-g macronutrient dose of soy-dairy protein blend (PB, n = 22), whey protein isolate (WP, n = 15), or an isocaloric maltodextrin placebo (MDP, n = 17). Lean mass, vastus lateralis myofiber-type-specific cross-sectional area, satellite cell content, and myonuclear addition were assessed before and after resistance training. Results: PB and the pooled protein treatments (PB + WP = PRO) exhibited a greater whole-body lean mass %change compared with MDP (P = 0.057 for PB) and (P = 0.050 for PRO), respectively. All treatments demonstrated similar leg muscle hypertrophy and vastus lateralis myofiber-type-specific cross-sectional area (P G 0.05). Increases in myosin heavy chain I and II myofiber satellite cell content and myonuclei content were also detected after exercise training (P G 0.05). Conclusion: Protein supplementation during resistance training has a modest effect on whole-body lean mass as compared with exercise training without protein supplementation, and there was no effect on any outcome between protein supplement types (blend vs whey). However, protein supplementation did not enhance resistance exercise-induced increases in myofiber hypertrophy, satellite cell content, or myonuclear addition in young healthy men. We propose that as long as protein intake is adequate during muscle overload, the adaptations in muscle growth and function will not be influenced by protein supplementation.
doi:10.1249/mss.0000000000001224 pmid:28346813 pmcid:PMC5433887 fatcat:kispzj4ft5ceznevxvhxsxhidi

Postexercise essential amino acid supplementation amplifies skeletal muscle satellite cell proliferation in older men 24 hours postexercise

Paul T. Reidy, Christopher S. Fry, Jared M. Dickinson, Micah J. Drummond, Blake B. Rasmussen
2017 Physiological Reports  
Reidy et al.Muscle Satellite Cell, Exercise and EAA Ingestion in Aging Muscle Satellite Cell, Exercise and EAA Ingestion in Aging P. T. Reidy et al.  ... 
doi:10.14814/phy2.13269 pmid:28596299 pmcid:PMC5471431 fatcat:6znha3xbozgm3hmqgk54ihiwhm

Post-absorptive muscle protein turnover affects resistance training hypertrophy

Paul T. Reidy, Michael S. Borack, Melissa M. Markofski, Jared M. Dickinson, Christopher S. Fry, Rachel R. Deer, Elena Volpi, Blake B. Rasmussen
2017 European Journal of Applied Physiology  
Reidy et al. Page 25 Author Manuscript Author Manuscript Author Manuscript Author Manuscript Fig. 5. Reidy et al.  ...  Muscle water content was determined, as previously described (Reidy et al. 2014b ).  ... 
doi:10.1007/s00421-017-3566-4 pmid:28280974 pmcid:PMC5389914 fatcat:k6m4tls53rgwzm4ab2rwg5dvta

Evaluation of SMP Shared Memory Machines for Use with In-Memory and OpenMP Big Data Applications

Andrew J. Younge, Christopher Reidy, Robert Henschel, Geoffrey C. Fox
2016 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)  
While distributed memory systems have shaped the field of distributed systems for decades, the demand for many-core shared memory resources is increasing. Symmetric Multiprocessor Systems (SMPs) have become increasingly important recently among a wide array of disciplines, ranging from Bioinformatics to astrophysics, and beyond. With the increase in big data computing, the size and scope of traditional commodity server systems is often outpaced. While some big data applications can be mapped to
more » ... distributed memory systems found through many cluster and cloud technologies today, this effort represents a large barrier of entry that some projects cannot cross. Shared memory SMP systems look to effectively and efficiently fill this niche within distributed systems by providing high throughput and performance with minimized development effort, as the computing environment often represents what many researchers are already familiar with. In this paper we look at the use of two common shared memory systems, the ScaleMP vSMP virtualized SMP deployment at Indiana University, and the SGI UV architecture deployed at University of Arizona. While both systems are notably different in their design, their potential impact on computing are remarkably similar. As such, we look to compare each system first under a set of OpenMP threaded benchmarks via the SPEC group, and follow up with our experience using each machine for Trinity de-novo assembly. We find both SMP systems are well suited to support various big data applications, with the newer vSMP deployment often slightly faster, however certain caveats and performance considerations are necessary when considering such SMP systems.
doi:10.1109/ipdpsw.2016.133 dblp:conf/ipps/YoungeRHF16 fatcat:czrbuv6etrhodakrpjwbrgqzva
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