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Predicting Periodicity with Temporal Difference Learning [article]

Kristopher De Asis, Brendan Bennett, Richard S. Sutton
2018 arXiv   pre-print
Temporal difference (TD) learning is an important approach in reinforcement learning, as it combines ideas from dynamic programming and Monte Carlo methods in a way that allows for online and incremental model-free learning. A key idea of TD learning is that it is learning predictive knowledge about the environment in the form of value functions, from which it can derive its behavior to address long-term sequential decision making problems. The agent's horizon of interest, that is, how
more » ... or long-term a TD learning agent predicts into the future, is adjusted through a discount rate parameter. In this paper, we introduce an alternative view on the discount rate, with insight from digital signal processing, to include complex-valued discounting. Our results show that setting the discount rate to appropriately chosen complex numbers allows for online and incremental estimation of the Discrete Fourier Transform (DFT) of a signal of interest with TD learning. We thereby extend the types of knowledge representable by value functions, which we show are particularly useful for identifying periodic effects in the reward sequence.
arXiv:1809.07435v1 fatcat:uvmltmayynfd3puqbnwoiqz43e

Mutagenesis of p22phoxHistidine 94

Karla J. Biberstine-Kinkade, Lixin Yu, Natalie Stull, Brendan LeRoy, Shelley Bennett, Andrew Cross, Mary C. Dinauer
2002 Journal of Biological Chemistry  
The NADPH oxidase is a multicomponent enzyme that transfers electrons from NADPH to O 2 to generate superoxide (O 2 . ), the precursor of microbicidal oxygen species that play an important role in host defense. Flavocytochrome b 558 , a heterodimeric oxidoreductase comprised of gp91 phox and p22 phox subunits, contains two nonidentical, bis-histidine-ligated heme groups imbedded within the membrane. Four histidine residues that appear to serve as noncovalent axial heme ligands reside within the
more » ... hydrophobic N terminus of gp91 phox , but the role of p22 phox in heme binding is unclear. We compared biochemical and functional features of wild type flavocytochrome b 558 with those in cells co-expressing gp91 phox with p22 phox harboring amino acid substitutions at histidine 94, the only invariant histidine residue within the p22 phox subunit. Substitution with leucine, tyrosine, or methionine did not affect heterodimer formation or flavocytochrome b 558 function. The heme spectrum in purified preparations of flavocytochrome b 558 containing the p22 phox derivative was unaffected. In contrast, substitution of histidine 94 with arginine appeared to disrupt the intrinsic stability of p22 phox and, secondarily, the stability of mature gp91 phox and abrogated O 2 . production. These findings demonstrate that His 94 p22 phox is not required for heme binding or function of flavocytochrome b 558 in the NADPH oxidase. 1 The abbreviations used are: CGD, chronic granulomatous disease; mAb, monoclonal antibody; INT, iodonitrotetrazolium; CHO, Chinese hamster ovary; RT, reverse transcription; HPRT, hypoxanthine phosphoribosyltransferase.
doi:10.1074/jbc.m203993200 pmid:12042318 fatcat:ci4v2dvoonfuxjnssxaigjoomy

Back to Square One: Superhuman Performance in Chutes and Ladders Through Deep Neural Networks and Tree Search [article]

Dylan Ashley, Anssi Kanervisto, Brendan Bennett
2021 arXiv   pre-print
We present AlphaChute: a state-of-the-art algorithm that achieves superhuman performance in the ancient game of Chutes and Ladders. We prove that our algorithm converges to the Nash equilibrium in constant time, and therefore is -- to the best of our knowledge -- the first such formal solution to this game. Surprisingly, despite all this, our implementation of AlphaChute remains relatively straightforward due to domain-specific adaptations. We provide the source code for AlphaChute here in our Appendix.
arXiv:2104.00698v1 fatcat:kolmfhs7hbbpbdikjfao4k4eym

Eradication of Helicobacter pylori for non-ulcer dyspepsia

Paul Moayyedi, Shelly Soo, Jonathan J Deeks, Brendan Delaney, Adam Harris, Michael Innes, R Oakes, Sue Wilson, A Roalfe, Cathy Bennett, David Forman
2011 The Cochrane library  
P O T E N T I A L C O N F L I C T O F I N T E R E S T Paul Moayyedi, David Forman and Brendan Delaney have received honoraria for talks from pharmaceutical companies making proton pump inhibitors.  ... 
doi:10.1002/14651858.cd002096.pub5 pmid:21328254 fatcat:5dl2sl6fbfb43duureu3ibvimi

Why Australia needs a Medical Research Future Fund

Anthony L Cunningham, Teresa Anderson, Christine C Bennett, Brendan S Crabb, Gareth Goodier, Douglas Hilton, Elizabeth Koff, Joe Trapani
2015 Medical Journal of Australia  
doi:10.5694/mja14.01618 pmid:25669464 fatcat:st5lmkgwxrd3bcqxcdtgqf7ipi

Emergence of the E484K Mutation in SARS-CoV-2 Lineage B.1.1.220 in Upstate New York [article]

Emil Lesho, Brendan Corey, Francois Lebreton, Ana Ong, Brett Swierczewski, Jason Bennett, Edward Walsh, Patrick McGann
2021 medRxiv   pre-print
Some authors (Bennett, Mc Gann, Toole, Á et al. Pangolin: lineage assignment in an emerging pandemic as an , N.G., et al. Estimated transmissibility and impact of SARS-England. Science (2021).  ... 
doi:10.1101/2021.03.11.21253231 fatcat:xi3zpzfvzvdqxhsl4wkj22s5i4

Anatomy of an Extensively Drug Resistant Klebsiella pneumoniae Outbreak in Tuscany, Italy [article]

Melissa J Martin, Brendan W Corey, Filomena Sannio, Lindsey R Hall, Ulrike MacDonald, Brendan T Jones, Emma G Mills, Jason Stam, Rosslyn Maybank, Yoon Kwak, Katharina Schaufler, Karsten Becker (+10 others)
2021 bioRxiv   pre-print
A protracted outbreak of New Delhi metallo–β–lactamase (NDM)–producing carbapenem–resistant Klebsiella pneumoniae, started in Tuscany, Italy, in November 2018 and has continued in 2020 and through 2021. To understand the regional emergence and transmission dynamics over time, we collected and sequenced the genomes of 117 extensively drug–resistant, NDM–producing K. pneumoniae isolates cultured over a 20–month period from 76 patients at several health care facilities in South–East Tuscany. All
more » ... olates belonged to high–risk clone ST–147 and were typically non–susceptible to all first line antibiotics. Albeit sporadic, resistances to colistin, tigecycline and fosfomycin were also observed as a result of repeated, independent mutations. Genomic analysis revealed that ST–147 isolates circulating in Tuscany were monophyletic, highly genetically related (including a network of 42 patients from the same hospital and sharing nearly identical isolates) and shared a recent ancestor with isolates collected from the Middle East. While the blaNDM–1 gene was carried by an IncFIB–type plasmid, our investigations revealed that the ST–147 lineage from Italy also acquired a hybrid IncH–type plasmid carrying the 16S methyltransferase armA gene as well as key virulence biomarkers often found in hypervirulent isolates. This plasmid shared extensive homologies with mosaic plasmids circulating globally including from ST–11 and ST–307 convergent lineages. Phenotypically, the carriage of this hybrid plasmid resulted in increased siderophore production but did not confer virulence to the level of archetypical, hypervirulent K. pneumoniae in a subcutaneous model of infection with immunocompetent CD1 mice. Our findings highlight the importance of performing genomic surveillance to identify emerging threats.
doi:10.1101/2021.06.02.446696 fatcat:rle7j6lzfbd7pksg5ejl5dhmkq

Patient outcomes in nonagenarians undergoing elective and emergency general surgical procedures: The West Suffolk hospital experience

Brendan Bates, Philip Bennett, Craig Vickery
2012 International Journal of Surgery  
doi:10.1016/j.ijsu.2012.06.233 fatcat:wqnqtppklnbghhwzyeeuaudsxm

Opportunistic Emulation of Computationally Expensive Simulations via Deep Learning [article]

Conrad Sanderson, Dan Pagendam, Brendan Power, Frederick Bennett, Ross Darnell
2021 arXiv   pre-print
Computationally Expensive Simulations via Deep Learning Conrad Sanderson †‡ , Dan Pagendam † , Brendan  ...  Power 4 , Frederick Bennett , Ross Darnell † † Data61  ... 
arXiv:2108.11057v3 fatcat:w2mngjkjpbcnfawy3344oddpvu

Chemical switching behaviour of tricarbonylrhenium(i) complexes of a new redox active 'Pincer' ligand

Sarath Wanniarachchi, Brendan J. Liddle, John Toussaint, Sergey V. Lindeman, Brian Bennett, James R. Gardinier
2010 Dalton Transactions  
General Considerations. The compounds pyrazole, CuI, N,N'-dimethylethylenediamine (DMED), anhydrous K 2 CO 3 powder, Tl(X = PF 6 or OTf) and (NEt 4 )(OH) (1M in MeOH) were purchased from commercial sources and used without further purification while Re(CO) 5 Br, S1 di(2-bromo-4-tolyl)amine, S2 were prepared by literature methods. The solvents used in the preparations were dried by conventional methods and distilled prior to use. Midwest MicroLab, LLC, Indianapolis, Indiana 45250, performed all
more » ... lemental analyses. IR spectra were recorded in the 4000-500 cm -1 region (as KBr pellets or as CH 2 Cl 2 solutions in a cell with KBr windows) on a Nicolet Magna-IR 560 spectrometer. 1 H and 13 C NMR spectra were recorded on a Varian 400 MHz spectrometer. Chemical shifts were referenced to solvent resonances at  H 7.27,  C 77.23 for CDCl 3 ;  H 5.33,  C 54.00 for CDCl 3 ;  H 1.94,  C 118.9 for CD 3 CN and  H 2.05,  C 29.92 for acetone-d 6 . Melting point determinations were made on samples contained in glass capillaries using an Electrothermal 9100 apparatus and are uncorrected. Absorption measurements were recorded on an Agilent 8453 spectrometer. Electrochemical measurements were collected under nitrogen atmosphere at a scan rate of 100 mV/s for samples as 0.1 mM CH 2 Cl 2 solutions with 0.1 M NBu 4 PF 6 as the supporting electrolyte. A three-electrode cell comprised of an Ag/AgCl electrode (separated from the reaction medium with a semipermeable polymer membrane filter), a platinum working electrode, and a glassy carbon counter electrode was used for the voltammetric measurements. With this set up, the ferrocene/ferrocenium couple had an E 1/2 value of +0.53 V consistent with the literature value in this solvent. S3 Mass spectrometric measurements recorded in ESI(+) or ESI(-) mode were obtained on a Micromass Q-TOF spectrometer whereas that performed by using direct-probe analyses were made on a VG 70S instrument. For the ESI(+) experiments, formic acid (approximately 0.1 % v/v) was added
doi:10.1039/c001344g pmid:20449442 fatcat:obmznnkzkvaqhpoucrgdfwfxq4

Single Institutional Experience With Observing 564 Vestibular Schwannomas

Jacob B. Hunter, David O. Francis, Brendan P. O'Connell, Edmond K. Kabagambe, Marc L. Bennett, George B. Wanna, Alejandro Rivas, Reid C. Thompson, David S. Haynes
2016 Otology and Neurotology  
Objective-To characterize the risk and predictors of growth during observation of vestibular schwannomas (VS). Study Design-Retrospective case series. Setting-Single academic, tertiary care center. Patients-564 consecutive VS patients who underwent at least two MRI studies prior to intervention. Intervention(s)-Serial MRI studies Main outcome measure(s)-Tumor growth, defined as a ≥2 mm increase in the maximum tumor diameter between consecutive MRI studies, or between the first and last study.
more » ... sults-A total of 1,296 patients with VS were identified. Of those, 564 patients (median age 59.2 years; 53.5% female) were initially observed and underwent multiple MRI studies (median follow-up 22.9 months, interquartile range [IQR] 11.7 -42.7). The median maximum tumor diameter at presentation was 1.00 cm (IQR 0.6 -1.51 cm). In all, 40.8% of tumors demonstrated growth and 32.1% underwent intervention (21.5% microsurgery, 10.5% radiation) during the surveillance period. Multivariable Cox regression analysis showed that for each tumor, the risk of growth or intervention was significantly increased for larger initial VS diameters (HR=2.22; 95% CI: 1.90 -2.61) and when disequilibrium was a presenting symptom (HR=1.70; 95% CI: 1.30 -2.23). Patient age, gender, aspirin use and presenting symptoms of asymmetric hearing loss, tinnitus, and vertigo, were not associated with tumor growth. Conclusions-To date, this is the largest series of observed VS reported in the literature. Risk of VS growth is significantly increased among patients who present with larger tumors and who have concomitant disequilibrium. IRB-151481 Define Professional Practice Gap & Educational Need-No cohort with this sample size has assessed vestibular schwannoma growth rates in conjunction with this number of variables. Learning Objective-To characterize vestibular schwannoma growth rates and predictors of growth.
doi:10.1097/mao.0000000000001219 pmid:27668793 pmcid:PMC5102804 fatcat:clh53xlfpfhlpj4rldegdigbuy

Directly Estimating the Variance of the λ-Return Using Temporal-Difference Methods [article]

Craig Sherstan, Brendan Bennett, Kenny Young, Dylan R. Ashley, Adam White, Martha White, Richard S. Sutton
2018 arXiv   pre-print
This paper investigates estimating the variance of a temporal-difference learning agent's update target. Most reinforcement learning methods use an estimate of the value function, which captures how good it is for the agent to be in a particular state and is mathematically expressed as the expected sum of discounted future rewards (called the return). These values can be straightforwardly estimated by averaging batches of returns using Monte Carlo methods. However, if we wish to update the
more » ... 's value estimates during learning--before terminal outcomes are observed--we must use a different estimation target called the λ-return, which truncates the return with the agent's own estimate of the value function. Temporal difference learning methods estimate the expected λ-return for each state, allowing these methods to update online and incrementally, and in most cases achieve better generalization error and faster learning than Monte Carlo methods. Naturally one could attempt to estimate higher-order moments of the λ-return. This paper is about estimating the variance of the λ-return. Prior work has shown that given estimates of the variance of the λ-return, learning systems can be constructed to (1) mitigate risk in action selection, and (2) automatically adapt the parameters of the learning process itself to improve performance. Unfortunately, existing methods for estimating the variance of the λ-return are complex and not well understood empirically. We contribute a method for estimating the variance of the λ-return directly using policy evaluation methods from reinforcement learning. Our approach is significantly simpler than prior methods that independently estimate the second moment of the λ-return. Empirically our new approach behaves at least as well as existing approaches, but is generally more robust.
arXiv:1801.08287v2 fatcat:vdygtqgmabb2xp5rxv76e2pjba

Characterisation and cardiac directed differentiation of canine adult cardiac stem cells

Hannah M. Hodgkiss-Geere, David J. Argyle, Brendan M. Corcoran, Bruce Whitelaw, Elspeth Milne, David Bennett, Sally A. Argyle
2012 The Veterinary Journal  
This study describes the isolation and characterisation of adult canine cardiac stem cells, and explores their ability to differentiate into cardiac myocytes. Direct comparisons are also made with available human data. Atrial cardiac explants were taken from dogs post-mortem and cultured to isolate adult stem cells. Cells were able to survive successive passages in serum-free media, were able to form cardiospheres, and under controlled culture conditions were capable of clonal expansion,
more » ... rating their ability for self-renewal. Characterisation of these cells demonstrated the following marker profile: c-kit, GATA 4 and flk-1 positive; cardiac troponin T and NKx2.5 low. Cardiac lineage directed differentiation was performed based on the published literature. Gene expression studies demonstrated that cardiac directed differentiation was partially achieved, with up-regulation of cardiac troponin T and NKx2.5, and down-regulation of c-kit and endothelial lineage markers. However the cells did not express the ryanodine receptor or b 1 -adrenergic receptors and did not contract spontaneously.
doi:10.1016/j.tvjl.2010.12.033 pmid:21330169 fatcat:cvjjor6du5e4vndzqanfh2kknq

Large-Scale Visual Speech Recognition [article]

Brendan Shillingford, Yannis Assael, Matthew W. Hoffman, Thomas Paine, Cían Hughes, Utsav Prabhu, Hank Liao, Hasim Sak, Kanishka Rao, Lorrayne Bennett, Marie Mulville, Ben Coppin, Ben Laurie (+2 others)
2018 arXiv   pre-print
This work presents a scalable solution to open-vocabulary visual speech recognition. To achieve this, we constructed the largest existing visual speech recognition dataset, consisting of pairs of text and video clips of faces speaking (3,886 hours of video). In tandem, we designed and trained an integrated lipreading system, consisting of a video processing pipeline that maps raw video to stable videos of lips and sequences of phonemes, a scalable deep neural network that maps the lip videos to
more » ... sequences of phoneme distributions, and a production-level speech decoder that outputs sequences of words. The proposed system achieves a word error rate (WER) of 40.9% as measured on a held-out set. In comparison, professional lipreaders achieve either 86.4% or 92.9% WER on the same dataset when having access to additional types of contextual information. Our approach significantly improves on other lipreading approaches, including variants of LipNet and of Watch, Attend, and Spell (WAS), which are only capable of 89.8% and 76.8% WER respectively.
arXiv:1807.05162v3 fatcat:yxjktqnisrdnrn7q5wpu3zmts4

Vision and Visual History in Elite/Near-Elite-Level Cricketers and Rugby-League Players

Brendan T. Barrett, Jonathan C. Flavell, Simon J. Bennett, Alice G. Cruickshank, Alex Mankowska, Julie M. Harris, John G. Buckley
2017 Sports Medicine - Open  
which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Abstract Background: The importance of optimal and/or superior vision for participation in high-level sports remains the subject of considerable clinical research interest. Here, we examine the vision and visual history of elite/near-elite cricketers and
more » ... -league players. Methods: Stereoacuity (TNO), colour vision, and distance (with/without pinhole) and near visual acuity (VA) were measured in two cricket squads (elite/international-level, female, n = 16; near-elite, male, n = 23) and one professional rugby-league squad (male, n = 20). Refractive error was determined, and details of any correction worn and visual history were recorded. Results: Overall, 63% had their last eye examination within 2 years. However, some had not had an eye examination for 5 years or had never had one (near-elite cricketers 30%; rugby-league players 15%; elite cricketers 6%). Comparing our results for all participants to published data for young, optimally corrected, non-sporting adults, distance VA was~1 line of letters worse than expected. Adopting α = 0.01, the deficit in distance VA was significant, but only for elite cricketers (p < 0.001) (near-elite cricketers, p = 0. 02; rugby-league players, p = 0.03). Near VA did not differ between subgroups or relative to published norms for young adults (p > 0.02 for all comparisons). On average, near stereoacuity was better than in young adults, but only in elite cricketers (p < 0.001; p = 0.03, near-elite cricketers; p = 0.47, rugby-league players). On-field visual issues were present in 27% of participants and mostly (in 75% of cases) comprised uncorrected ametropia. Some cricketers (near-elite 17.4%; elite 38%) wore refractive correction during play, but no rugby-league player did. Some individuals with prescribed correction choose not to wear it when playing. Conclusions: Aside from near stereoacuity in elite cricketers, the basic visual abilities we measured were not better than equivalent, published data for optimally corrected adults; 20-25% exhibited sub-optimal vision, suggesting that the clearest possible vision might not be critical for participation at the highest levels in the sports of cricket or rugby league. Although vision could be improved in a sizeable proportion of our sample, the impact of correcting these, mostly subtle, refractive anomalies on playing performance is unknown.
doi:10.1186/s40798-017-0106-z pmid:29127516 pmcid:PMC5681452 fatcat:yz3zjvizxrhs3ln6kbsaewl3ru
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